Here you can check which improvements to expect
from a YASARA update.
The list below only contains new features and major bug fixes since the
first publically available release (3.9.1), small
changes are not included. You may have to press the Reload button in your browser.
Version | New feature |
24.10.5 | New highlight: The 'PCA' command performs principal component analysis, the 'PCAPos' command builds structures from current PCA components, for example to create movies of the main movemements. The PCA analysis has become part of the 'md_analyze' macro and includes MP4 movies in the analysis report. Contributed by Kornel Ozvoldik. |
24.9.26 | New feature: YASARA supports residue names that are five characters long, as annnounced by the RCSB in 2023 since all possible three character names have been used. This change requires new versions of *.sce and *.yob files, which cannot be read by older YASARA versions. If you send such files to colleagues, they also need to update YASARA to read them. |
24.9.23 | Improved experiment: 'Docking' now supports covalent docking also with AutoDockGPU. While covalent docking is normally not performance critical, the use of AutoDockGPU provides another opinion, and getting the same best conformation with multiple docking methods increases the reliability. |
24.9.17 | New external development: YASARA macros and shell scripts to split a complex into receptor&ligand, and to definine the binding site for subsequent docking runs at https://github.com/enade-istyastono/binding-site-definition Contributed by Enade P Istyastono. |
24.9.13 | Improved macro: 'md_analyze' can calculate the mean distance matrix, which is needed by some analysis methods like the Shortest Path Maptool (https://spmosuna.com), see the manual at Recipes > Run a molecular dynamics simulation > Analyzing a trajectory > Optionally, the mean distance between atoms... |
24.8.25 | New highlight: The 'md_runsurface' and 'md_runsurfacefast' macros run MD simulations of metal surface adsorption fully automatically. See the manual at Recipes > Run a molecular dynamics simulation > Running a surface simulation the easy way. Contributed by Kornel Ozvoldik. |
24.8.23 | New feature: Adding your own compounds with custom charges to the force fields has become easier: If you load a molecule in a format with charges (e.g. Mol2), the charges are stored as atomic properties, and you can use the improved SavePrep command to save an AMBER Prep topology with these charges as yasara/fof/usertopo_*.fof, all of these user-provided topology files are included automatically during the next force field update. See manual at Recipes > Run a molecular dynamics simulation > Preparing the force field > define force field parameters manually. |
24.8.19 | Improved command: 'Group' now requires group names to be at least six characters long, so that they can be differentiated from the new 5-character PDB residue names |
24.8.12 | Improved experiment: 'Docking' accepts a new 'ClusterMembers' parameter to save more than one member of each cluster to disk, with an additional number at the end of the filename. |
24.8.4 | Improved command: 'SavePDB' saves in PDB format version 3 by default now, since there have been user reports about programs that cannot properly read the older format anymore. |
24.7.20 | Improved command: 'SavePrep' accepts a new 'PropCharges' parameter to save the atomic properties as charges instead of the normal force field charges. This makes is easy to convert a file format with charges (e.g. Mol2) to an AMBER Prep topology for inclusion in the force fields. |
24.7.15 | Improved typing: YASARA now has special support for ferrocene compounds, hydrogen addition, bond typing and MD simulation are supported. |
24.6.15 | Improved command: 'LoadYOb' accepts a new 'Transfer' parameter to automatically place the newly loaded objects on top of the last object. |
24.6.10 | Improved plugins: If the plugin header line 'PLATFORMS' includes the word 'ExternalPython', YASARA will look for an external Python installation to run the plugin, ignoring YASARA's own embedded Python. In case the search fails, you can set the path in yasara.ini with 'PythonPath'. Contributed by Kornel Ozvoldik. |
24.6.5 | Improved command: ColorSurf can return the current default and per-object surface colors, just in case you need to duplicate a surface color. |
24.6.3 | Improved experiment: 'Docking' with AutoDockGPU supports the same metal atom types as the CPU-only AutoDock. Contributed by Kornel Ozvoldik. |
24.5.12 | New feature: The new command line parameter '-dir' allows to specifiy a directory where YASARA writes internal data (e.g. logs, force field caches), improving support for running YASARA without write access in its own directory. |
24.5.10 | Improved macro: 'md_runmembrane' supports a new membrane lipid N-palmitoylsphingomyelin with name 'HWP'. Contributed by Kornel Ozvoldik (Dynamics+). |
24.5.7 | Improved commands: 'WriteReport' and 'SavePlot' support three new plot types 'Rama' (Ramachandran plot), 'Dihedral2D' (scatter plot of two dihedral angles) and 'ScatterSquare' (square scatter plot). Look for 'Ramachandran' in the md_analyze macro for examples. Contributed by Kornel Ozvoldik (Dynamics+). |
24.5.5 | Fixed an issue in the md_analyzebindenergy macro, which always returned binding energies from VINA local docking in kcal/mol, even if kJ/mol was set as YASARA's energy unit. |
24.5.1 | Improved macros: 'md_analyze', 'md_runsteered' and the ligand style plugin 'style.mcr' detect peptide ligands. Contributed by Kornel Ozvoldik. |
24.4.20 | Improved command: 'ShowPlane' accepts a new parameter 'Specular' to disable specular highlights. Contributed by Kornel Ozvoldik. |
24.4.10 | New highlight: Artificial intelligence arrived in YASARA. The homology modeling experiment has been renamed to protein modeling experiment and combines the AI-based folding methods AlphaFold, ESMFold and OmegaFold with classic template-based homology modeling to predict protein structures. Following YASARA standards, your potentially confidential sequences are kept local and not sent to external servers. Visit www.yasara.org/proteinfolding for details. Contributed by Kornel Ozvoldik (Structure). |
24.4.3 | Improved macro: 'md_analyzebindenergy' additionally calculates the binding energy with VINA after performing a local docking in each MD snapshot. To skip this slow step, adapt the 'dockmethod' parameter as needed (Structure). |
24.4.2 | New feature: To make it easier that multiple related structures loaded independently fall on top of each other (e.g. enzyme and ligand), the commands 'LoadPDB', 'LoadCIF' and 'Load*' accept a new 'Transfer' parameter to automatically place the newly loaded object on top of the last object. |
24.3.23 | Improved experiment: 'Docking' accepts the new method 'VINASO', which runs VINA to Score Only. This is normally not needed/recommended, since a minimization should be done before scoring (i.e. VINALS or AutoDockLS) (Structure). |
24.3.18 | New highlight: The 'AlignAtom' command has been re-implemented with many more options and can use gradient-based minimization to perform a flexible structural alignment between two small molecules. It calculates normalized similarity scores to find the most similar compound in a library (Dynamics+). |
24.3.5 | Improved macro: md_analyze can create additional tables with custom data using the 'WriteExtraTable' function. Look at 'H-H pair distances' for an example. |
24.2.22 | New feature: Since the new AI-based folding has specific Python requirements, YASARA for Linux now comes with a minimal embedded Python, just like MacOS and Windows since version 22.7.6. Contributed by Kornel Ozvoldik. |
24.2.14 | Improved command: 'Clean' recognizes amino acids in giant 'residues' (e.g. when building a peptide from a single SMILES string) and places them in separate residues so that visualization and force field parameter assignment handle them like standard amino acids (Dynamics+). |
24.2.5 | New highlight: The FoldMol command runs local installations of the AI-tools ESMFold and OmegaFold to perform ab initio protein structure prediction. About 7 GB disk space are required for the AI infrastructure, and your graphics card should have more than 8 GB memory to accelerate the AI on the GPU (for AMD/nVIDIA in Linux, nVIDIA in Windows, and a slower CPU fallback in all other cases). Click Edit > Build > Molecule and fold with AI. Contributed by Kornel Ozvoldik (Structure). |
24.1.23 | Improved command: 'LoadPDB' with 'Download=AlphaFold' loads models from the AlphaFold database at EBI, using the UniProtID given as filename. You can find the UniProtID by telling the BLAST command to use the AlphaFold sequence database. Click File > Load > PDB file from Internet. Contributed by Kornel Ozvoldik. |
24.1.17 | Improved command: 'SavePDB' accepts a new format 'PDB3NTN' to write a PDB file with No TER Numbers, in case you need a 1:1 correspondance between atom numbers in YASARA and PDB files. |
24.1.1 | Improved plugins: The ColorSelectionWindow accepts a ColorType=Atom to include special colors like 'Element' or 'BFactor'. |
23.12.24 | New highlight: Docking is now GPU-accelerated thanks to AutoDockGPU. Check the manual at 'Recipes > Dock a ligand to a receptor > Useful docking hints' for instructions. Contributed by Kornel Ozvoldik. |
23.12.17 | New insights from YASARA MD simulations of corona virus spike proteins published in Nature: https://www.nature.com/articles/s41586-023-06599-z Contributed by Martin Frank. |
23.12.5 | Improved command: 'CoordSys' accepts a new 'Show' parameter to show arrows that indicate the three main axes of the local coordinate systems in all objects. Click Options > Coordinate system > Show arrows. |
23.11.27 | Fixed problems with finger gestures in MacOS, fullscreen mode in MacOS and Linux. |
23.11.21 | New command: 'CellEdges' returns the three cell edge vectors. With the help of this command, it is now easily possible to build neighboring crystal cells (see example macro at the 'Cell' command). |
23.11.15 | New command: 'Load' loads any file by invoking one of the countless load commands like LoadPDB or LoadSce, depending on the filename extension. |
23.11.9 | New external development: free eBooks with YASARA modeling tutorials in Indonesian language by Enade P. Istyastono available from Google books: "Simulation and validation of molecular docking with YASARA Structure" at https://play.google.com/store/books/details?id=trviEAAAQBAJ and "A cup of coffee and the discovery of diabetes medicine": https://play.google.com/store/books/details?id=rutIEAAAQBAJ |
23.10.25 | New feature: The md_runmembrane macros can build membranes with cardiolipin, just adapt the two percentages after 'CDL' in the line starting with 'memcomplist'. Contributed by Kornel Ozvoldik. |
23.10.18 | Improved macro: md_runmembrane macro supports cholesterol as membrane lipid, |
23.9.28 | New highlight: YASARA has been ported to ARM 64bit CPUs, 340000 lines of highly optimized assembly code are at your service to accelerate all kinds of modeling tasks, e.g. MD simulations, surfaces, fast fourier transforms and molecular graphics. The first supported ARM CPU is Apple Silicon in MacOS, you will now receive universal binaries by default, unless you choose your CPU model. Compared to Rosetta 2, performance can increase by over 50%, e.g. the CPU-only DHFR benchmark result on a MacBook Air M1 (8 cores) from 2020 increases from 75 ns/day to 125 ns/day. Note that Apple now requires the 'YASARA.app/yasara' folder to be moved to 'YASARA.app/Contents/yasara'. Joint project with Kornel Ozvoldik. |
23.9.22 | New download location for PDB files, since the RCSB unfortunately removed the old location on September 22, 2023, instead of simply redirecting it. If your access to updates has expired, visit www.yasara.org/rcsbchange for solutions. |
23.9.15 | New version 1.2.5 of AutoDock VINA is now included in YASARA. |
23.9.5 | Improved virtual screening with AutoDock: YASARA no longer needs to copy the maps to the local working directory, and they are selectively generated as new ligands with new atom types are screened. Fixed an issue if a supplied ligand was outside the coordinate system range of a PDBQT file. |
23.8.23 | Improved command: 'LoadMDCrd' accepts a new 'readCell' parameter to define if the trajectory file contains a cell dimension that should be read or not. |
23.8.16 | Improved experiment: 'Neutralization' considers dative bonds to metal ions to improve the pKa prediction results and avoid incorrect protonation states. It additionally allows to skip the adjustment of protonation states by setting the pH parameter to -1. |
23.8.8 | New macro showing how to loop over a representative subset of the PDB and find all bridged cysteines with a given number of residues in between can be found in the manual at 'Selections > Selection blocks can be combined with explicit operators > The within sequence operator'. |
23.7.23 | Improved command: 'Clean' accepts a new skip flag 'TypeBond' to skip bond typing. |
23.7.16 | Improved selection language: The 'with connection to' operator includes dative bonds in the connection analysis. |
23.7.8 | Improved macro: 'dock_runscreening' includes the SMILES string of every ligand in the log file. |
23.6.28 | Improved command: 'Clean' accepts a new skip flag 'LinkMetal' to skip adjustments to dative bonds with metal ions. |
23.6.14 | Fixed a problem with MD snapshot numbering when reaching 5.3 microseconds (md_run.mcr) or 10.6 microseconds (md_runfast.mcr). |
23.6.12 | Fixed a crash in YASARA View when downloading PDB files from the Internet. |
23.5.19 | New support for the Pico 4 VR headset, but please try it only if you already own it and don't buy it, since it delivers the worst experience of all due to a strong lag of movements. |
23.5.12 | Fixed several problems: A bug in the energy minimization experiment 'introduced' in version 23.4.16 that failed to properly handle rings with stuck molecules (e.g. a lysine side-chain pointing through the middle of a phenylalanine ring). Please update if you own version 23.4.X. The VR projection in the Meta Quest 2 has been corrected, please update to minimize motion sickness. Clicking atoms with parallel projection works again, unsupported VR headsets show controllers, and the VR workstation in Android works again. |
23.5.7 | Improved experiment: 'Neutralization' no longer allows hydrogens in a hydroxyl group to move, since they could be drawn into bumping atoms of opposite charge. Use the minimization experiment to handle them later. |
23.4.25 | New VR headsets supported: The 'Vive Cosmos Elite' and the 'Vive Pro 2' have been tested with YASARA. Both unfortunately work in Windows only, see the updated details in the documentation at 'Decide which headset to buy'. |
23.4.20 | Improved command: 'Distance', 'Angle' and 'Dihedral' work much faster now when the scene contains a large number of atoms, many of which are selected, and then only a few combinations actually chosen with the 'Bound=Yes' flag. |
23.4.16 | New highlight: 25 years after YASARA first supported molecular modeling and interactive MD with a virtual reality headset, VR is back with a vengeance on Linux and Windows for HTC Vive, Vive Pro, Vive Pro Eye, Valve Index and Meta Quest 2. It's not a game, but the professional modeling solution for everyone moaning the disappearance of shutter glasses. Please watch the introductory movie at www.yasara.org/vr and act fast to get your headset before they sell out. Joint project with Kornel Ozvoldik (Model+). |
23.4.12 | New help movie: 'Virtual reality (PC)' demonstrates in eight sections how to set up and use the virtual reality equipment, including the VR controller as a 3D mouse in normal 2D mode, the camera with keyboard and mouse, the tracker to beam your chair into VR and the teleporter for giant scenes. Click Help > Play help movie > 1.6. Virtual reality (PC). Joint project with Kornel Ozvoldik and Elina Krieger (Model+). |
23.4.10 | Fixed a problem with bond typing in porphine rings that yielded a resonance structure with 16 pi electrons and zero charge (oxidized porphine) when a metal was bound (e.g. heme). Now the normal resonance structure with 18 pi electrons is assigned, resulting in charges of -2, 0 or +2 depending on pH and protonation state. If you work with porphyrins, you need to clean the structure or retype the bonds after updating YASARA to get the new charges. |
23.4.7 | New help movie: 'Virtual reality simulations' demonstrates in three sections how to do interactive MD simulations in VR, allowing to pull and push atoms around fluently in simulations with up to a million atoms. If you ever wanted to help an ion pass through an ion channel against the gradient, click Help > Play help movie > 3.7. Virtual reality simulations. Joint project with Kornel Ozvoldik and Elina Krieger (Dynamics+). |
23.4.3 | Improved command: MPEG encoding can be paused and continue with 'SaveMPG pause' and 'SaveMPG continue' (Model+). |
23.3.20 | New feature: The MPEG4 encoder now uses a separate thread to speed up encoding, and when using the Vulkan graphics engine, the encoder is especially fast, allowing to record movies of VR sessions as shown at www.yasara.org/vr (Model+). |
23.3.15 | Improved command: LoadXTC and the md_convert macro will recognize GROMACS trajectories with almost dodecahedral cells as true dodecahedral cells and visualize them accordingly (if the simulation is off). |
23.3.10 | New feature: In order to create a movie of a virtual reality session that shows both the outside view recorded with a camera and the inside view in the headset (e.g. www.yasara.org/vr ) , a custom video cutting program is required to keep both views in sync. This is available as a Yanaconda macro at the 'SaveMPG' command. Contributed by Kornel Ozvoldik (Model+). |
23.3.5 | New command: 'VRPar' sets countless parameters for running YASARA in virtual reality mode. You can even use the controllers as a 3D mouse in normal 2D mode. Click Window > Stereo > Virtual reality parameters. Joint project with Kornel Ozvoldik (Model+). |
23.3.2 | Fixed a problem running OpenBabel, AutoDock and VINA on some Linux virtual machines (segmentation fault unless vsyscall=emulate parameter was provided) |
23.2.25 | Improved command: The general OpenBabel import with 'Load' replaces single quotes in atom names with stars, as known from the original PDB format, since quotes in strings cause a chain of complications. You can undo this change when saving with the 'NameFormat' parameter. |
23.2.23 | New command: 'VRArea' returns the size and location of the VR play area so that you can place objects there. Contributed by Kornel Ozvoldik (Model+). |
23.2.15 | Improved command: 'SaveMPG' accepts two new parameters: 'StartFrame' to start playback at a given frame, and 'FPS' to override the frames per second specified in the movie. Contributed by Kornel Ozvoldik (Model+). |
23.2.9 | Improved command: 'AutoPos' accepts a new 'Shape' parameter to place multiple objects on a sphere or hemisphere. Click Effects > Position > Set for object automatically. Contributed by Kornel Ozvoldik. |
23.1.25 | Improved experiment: 'Minimization' no longer reassigns force field parameters, so you can manually modify the force field parameters (charges, springs..) already before in md_run.mcr, making sure that your modifications are present already during the initial minimization (Dynamics+). |
23.1.21 | Improved graphics engine: When showing gigastructures on GPUs with too little memory, YASARA deletes objects until it fits to show a partial structure instead of bailing out. Resizing the window no longer requires a lengthy rebuilding of instances. |
23.1.18 | Improved command: 'ShowInt' accepts a new 'DelOld' parameter to delete old interaction objects. This makes it easy to step through the interactions of selected units with a single click. See the instructions at the 'ShowInt' command or click 'Show > Per-atom interactions' in any context menu and keep <Tab> pressed to repeat. |
23.1.12 | Fixed a crash when running the old 32bit YASARA in all operating systems. |
23.1.7 | Improved commands: 'LoadTab' and 'SaveTab' now correctly handle Bohr and Angstrom units as well as grid offsets in Gaussian Cube files. |
23.1.1 | Improved commands: 'ListInt' and 'ShowInt' use slightly tuned parameters for hydrophobic interactions. |
22.12.10 | Improved command: 'Align' with method Mustang can now be interrupted in case it takes too long. |
22.12.5 | Improved command: 'LoadWOb' can attach a texture to the mesh, if it has been loaded before (e.g. with LoadPNG or LoadJPG). Contributed by Kornel Ozvoldik (Model+). |
22.11.22 | Fixed a problem in the LoadXTC/LoadMDCrd commands and thus also the md_play macro for XTC and MDCrd trajectories, that caused them to get slower with increasing snapshot number. |
22.11.20 | Improved command: 'Keyboard' accepts a new 'InputScale' parameter to set the size of the virtual keyboard text input area. Click Options > Input devices > Virtual keyboard: Parameters. |
22.11.19 | Fixed a problem with side-chain rotamer prediction of unusual amino acids that could cause a red error message. Please update before building models with unusual amino acids (Structure). |
22.11.1 | Improved macro: 'md_analyze' includes a new plot of interactions made by individual ligand atoms along the trajectory, created with the new 'PlotAtom' function. Contributed by Kornel Ozvoldik (Dynamics+). |
22.10.30 | Improved force field parameter assignment: Better diagnostic messages make it easier to find issues and inconsistencies when providing custom force field parameters for residues (Dynamics+). |
22.10.5 | Improved command: 'ConsolePar' supports a new Font=XLarge for everyone who prefers really large fonts. |
22.9.24 | Fixed a graphics problem with gigastructures where the distant objects got shifted incorrectly, and a red error message 'Quad without texture'. |
22.9.10 | Improved command: 'SaveTab' with Format=Text saves all lines with a leading space so that import into Excel and OpenOffice works reliably. Can be disabled with Format=TextNLS (No Leading Space). |
22.8.22 | New highlight: YASARA displays electron density maps in various formats (DSN6, Gaussian Cube, Delphi and YASARA table formats). Most easily with LoadPDB by clicking 'File > Load > PDB file from Internet' and choosing an option with density. Alternatively click 'Options > Table > Load' to load a density file and then 'Options > Table > Show' to create a contour surface. Dynamic or static wire frames can then be added at 'Effects > Show&hide wire frame'. See www.yasara.org/electrondensity (Model+). |
22.8.16 | Improved command: 'FillCellObj' accepts selections of multiple objects, to fill the cell with a group of objects that form a larger structure, like a synaptic vesicle or adhesive proteins that cross-link two membranes. Contributed by Kornel Ozvoldik (Dynamics+). |
22.8.12 | New PetWorld model of the mushroom postsynapse with 140 different objects and 2.4 billion atoms: download.yasara.org/petworld/postsynmushroom . Contributed by Burkhard Rammner. |
22.8.8 | Improved command: The 'OptimizeLoop' algorithm has been improved, which also helps loop building in homology modeling and improves model scores by ~3% (Structure). |
22.8.2 | New PetWorld model of the synaptic gap with 76 different objects and 103 million atoms: download.yasara.org/petworld/syngap . Contributed by Leticia Alves da Silva. |
22.7.25 | Improved command: 'LoadTab' supports new formats when loading tables (DSN6, Gaussian Cube and Delphi), which makes it easy to load X-ray density maps. |
22.7.21 | New PetWorld model of the stubby postsynapse with 150 different objects and 2.4 billion atoms: download.yasara.org/petworld/postsynstubby . Contributed by Burkhard Rammner. |
22.7.17 | Improved command: 'LoadPDB' supports the two new Download parameter values 'LatestEDSurf' (download latest PDB file with electron density surface) and 'LatestEDWire' (with electron density wire frame), and the new 'Contour' parameter to specify a contour level (Model+). |
22.7.13 | Improved macro: 'md_convert' can convert a series of PDB files to the other supported trajectory formats (Dynamics+). |
22.7.6 | New feature: Since Apple stopped bundling Python with MacOS, and also a growing number of Windows users could not get Python installed reliably, YASARA for MacOS and Windows now comes bundled with a minimal Python so that all plugins work from the start. Contributed by Kornel Ozvoldik. |
22.7.4 | Improved command: 'SaveTab' supports new formats when saving tables (DSN6, Gaussian Cube and Delphi), which makes it easy to save modified X-ray density maps. |
22.7.1 | Improved command: 'ShowTab' accepts an improved 'Range parameter' that can now end with 'sigma' to create density contours at a certain standard deviation level, e.g. 'Range=1.5sigma', which is commonly used when visualizing X-ray density maps. The additional 'Center' parameter allows to show non-centered maps, as required to match the corresponding PDB file, which must also have been loaded without centering. For simplicity, the result of ShowTab is now the same in left- and right-handed coordinate systems (Model+). |
22.6.28 | New command: 'Couple' couples the movement of one object to another object if the latter is grabbed. This is e.g. helpful to make sure that an electron density shown with ShowTab moves together with the protein. Click Effects > Move > Objects together. |
22.6.22 | Improved command: The 'Transformation' docs contain an example for calculating the elbow angle in Fab antibody fragments. |
22.6.18 | Improved commands: 'BuildLoop' and 'SampleLoop' accept a new 'BridgeCys' parameter to define if loops should be allowed to form cysteine bridges or not (Structure). |
22.6.16 | New command: 'Uncouple' removes the coupling of object movements again. Click Effects > Move > Objects alone. |
22.6.14 | Improved commands: 'SaveESP' supports a 'Format' parameter to save electrostatic potential maps also in YASARA table format, which can be loaded with the LoadTab command to perform calculations, like averaging ESPs along an MD trajectory. The 'LoadESP' command automatically recognizes the new format (Dynamics+). |
22.6.9 | Improved command: 'Cut' accepts a new 'Cell' parameter to define if the simulation cell is cut or not (Click View > Cut). |
22.6.2 | Improved macros: The 'dock_run', 'dock_runlocal' and 'dock_runscreening' macros calculate the molecular contact surface between receptor and ligand poses and list it in the log file. |
22.5.22 | New 2022 release of all force fields with improvements for unusual amino acids, phospholipids and oligosaccharides. An update is recommended. |
22.5.15 | Improved macro: The MD trajectory player macro 'md_play' has a new button 'Save MP4' to save an MPEG video of the trajectory. |
22.5.3 | New feature: Building of gigastructures has been improved at more spots than can be listed. The packing macros in the PetWorld database have been improved accordingly, please update before building a gigastructure. Joint project with Kornel Ozvoldik (Dynamics+). |
22.4.27 | Improved command: 'SaveYOb' accepts a new 'Transform' flag to undo any coordinate transformations that happened so far (e.g. for an MD simulation). |
22.4.15 | New beginner videos on amino acids ( https://youtu.be/prqX8wHSVXE ), peptide conformation ( https://youtu.be/vpEs806KSUw ) and Ramachandran plot ( https://youtu.be/qjsMRiIoD5E ). Contributed by Reinhard Wimmer. |
22.3.23 | Improved visualization: Bridged cysteines are now always shown, just like the side-chains involved in metal bonds or bound to prostethic groups before. To hide them again, click View > Hide atoms > Residue > Cys. |
22.3.18 | New command: 'ColorHUD' sets the color of the head-up display, click Window > Head-up display > Color. |
22.2.11 | Improved macros: The membrane lipid composition has been changed to a list to support an arbitrary number of different lipids. Phosphatidylglycerol has been newly added now. Contributed by Kornel Ozvoldik (Dynamics+). |
22.2.5 | New command: 'PairObj' sets and gets key/value pairs of an object, which are for example often used in ligand libraries in SDF format to store additional data. Click Edit > Name > Key/value pair and Analyze > List > Key/value pairs. Pairs are only saved in YASARA scenes and objects, SDF, GAMESS and Ghemical files. |
22.1.18 | Improved macro: 'pack_library' has a new function 'PairInMem' to dimerize two transmembrane proteins that link two membranes (e.g. Cadherin). Two parallel membrane meshes can then be filled. |
22.1.4 | New workaround for a bug in AMD Radeon Linux drivers which could cause flickering atoms with the OpenGL renderer. |
21.12.19 | New highlight: The PetWorld Database has been launched at www.PetWorld.vision , containing biomolecular models with millions to billions of atoms for coarse-grained MD simulation and all-atom visualization. Please check the user manual at 'Recipes > Build a gigastructure' to see how you can contribute a giant model of your favorite research project and get YASARA for free in return. We are also planning to submit a joint article with the first 25 contributors. Joint project with Kornel Ozvoldik (Dynamics+). |
21.12.11 | New command: 'ShowPlane' creates a planar polygon mesh, that can serve as a skeleton to assemble a membrane with the new FillCellObj command. Click Effects > Show solid > Plane. Contributed by Kornel Ozvoldik (Dynamics+). |
21.12.10 | New highlight: The 'Shrink' command creates a coarse-grained, shrunken version of a molecule, consisting of 'pet atoms'. This reduces the atom count by about a factor of 50 an enables simulations of giant systems. Visit www.yasara.org/coarsegrained for an example video. Click Edit > Geometry > Shrink. Joint project with Kornel Ozvoldik (Dynamics+). |
21.12.4 | New command: 'ReMesh' recreates a polygon mesh using mostly equilateral triangles with a given side length to serve as a framework for membrane assembly. Employs the Instant Meshes tool by Wenzel Jakob et al. Click Effects > Shape > Remesh. Contributed by Kornel Ozvoldik (Model+). |
21.11.28 | New highlight: The 'Expand' command turns shrunken coarse-grained pet models back into all-atom models for visualization with the Vulkan graphics engine. Please update your reference manager to our new open access article for general YASARA use with Vulkan or coarse-grained work: https://pubs.acs.org/doi/abs/10.1021/acs.jcim.1c00743 . Click Edit > Geometry > Expand. Joint project with Kornel Ozvoldik (Dynamics+). |
21.11.23 | New command: 'LoadDAE' loads a polygon mesh in Collada DAE (Data Asset Exchange) format, for example to build membranes with given shapes. Click File > Load > Polygon mesh. Contributed by Kornel Ozvoldik (Model+). |
21.11.16 | New highlight: The 'BuildGenome' commands builds an entire genome (DNA or RNA, double- or single-standed) including nucleic acid binding proteins (transcription factors, histones, nucleocapsids...). Single-stranded nucleic acids can be built with pre-defined secondary structure using dot-bracket notation. Genomes are built using pet atoms for coarse-grained MD and subsequent expansion to full atomic details. See also www.yasara.org/gigastructures . Joint project with Kornel Ozvoldik (Dynamics+). |
21.11.9 | New command: 'Bend' wraps atoms or a polygon mesh onto a cylinder or sphere. This is helpful when building membranes of relatively small objects (like a synaptic vesicle), then the membrane fragments need to be bent a bit. Click Effects > Shape > Bend. Contributed by Kornel Ozvoldik (Dynamics+). |
21.10.27 | New highlight: The 'FillCellObj' command has been turned into a packing engine, that can fill compartments defined by arbitrary polygon meshes. The meshes themselves can also be plastered with membrane fragments containing transmembrane proteins. Joint project with Kornel Ozvoldik (Dynamics+). |
21.10.19 | New command: 'DeformMesh' deforms a polygon mesh using a sine function of given wave length and amplitude to give polygon meshes (e.g. spheres, planes) a more natural, less regular appearance. Click Effects > Shape > Deform. Contributed by Kornel Ozvoldik (Dynamics+). |
21.10.11 | Improved macro: 'md_analyze' supports a new espmethod parameter to calculate electrostatic potentials in the cell and save them as Delphi maps, which will then be visualized automatically by the md_play macro. Contributed by Kornel Ozvoldik (Dynamics+). |
21.10.3 | New command: 'LoadWOb' loads a polygon mesh in Alias Wavefront Obj format. Click File > Load > Wavefront object mesh. Contributed by Kornel Ozvoldik (Model+). |
21.9.27 | Improved plugins: YASARA uses Python 3 now, since Python 2 has reached the end of life. The 3DM and FoldX plugins have also been prepared for Python 3, an plugin update may be needed if you are using an older version. |
21.9.18 | Improved macros: If macros include each other, error messages now show the line number in the included macro, as well as its filename. |
21.9.13 | New command: 'FileTime' gets the modification time of a file. Contributed by Kornel Ozvoldik. |
21.9.10 | Improved command: 'PointerStyle' accepts a 'Software' parameter to create an additional software-rendered mouse pointer which is visible in screenshots and MPEG movies. |
21.9.7 | Improved charge assignment for metal-oxygen clusters. |
21.8.26 | New highlight: YASARA includes a fast high-quality encoder for MPEG4 movies activated by the 'SaveMPG' command. The new 'LoadMPG' command can stream an MPEG4 movie and use it as a texture just like PNG or JPEG images. See the new example macros at the 'SaveMPG' and 'LoadMPG' commands. Joint project with Kornel Ozvoldik (Model+). |
21.8.20 | New feature: Docking with VINA yields a larger variety of ligand poses, not just the top 20. |
21.8.12 | New workaround for a bug in AMD Radeon Windows drivers that could cause incorrect shadowing, e.g. on Radeon Vega 8 GPUs. |
21.7.27 | Improved command: The 'SaveESP' docs include an example macro for parsing an electrostatic potential map and placing transparent spheres accordingly. |
21.7.20 | Improved macro: 'md_analyze' creates a table *_rmsdres.tab with per-residue RMSF values. Contributed by Kornel Ozvoldik. |
21.7.4 | New tutorial for running YASARA in the Amazon Web Services Cloud using Ray can be found at Essentials > Running YASARA.. > Running YASARA in the cloud. Contributed by Michael Lukesch. |
21.7.1 | Improved macro language: The functions 'lower' and 'upper' return the lower- and upper-case of a string |
21.6.27 | New command: 'ClassRest' classifies selected NMR restraints, i.e. assigns them to a new class (NMRModule) |
21.6.16 | New feature: You can move objects around independently and cut objects open with the free YASARA View, the commands 'Cut', 'Grab', 'GrabNext' and 'GrabPrev' have been made available. |
21.6.12 | New command: 'Memory' sets the amount of memory used by YASARA and exits. See the command docs for hints about memory usage. |
21.6.10 | Fixed a problem of the new ambient occlusion with old Vulkan drivers and MacOS, it now also works with antialiasing enabled, and a red error message on startup is gone. |
21.6.2 | New highlight: YASARA's Vulkan/Metal graphics engine can calculate ambient occlusion per pixel, yielding more realistic lighting and thus improved molecular graphics quality. To best test the effect, press F1, zoom in on atoms closely and then click View > Lighting > Per-pixel ambient light. |
21.5.20 | Improved force field parameter assignment: The parameter cache can detect mirrored molecules parameterized before, so that MOPAC doesn't need to be run again with marginally different results, and mirrored molecules get exactly the same point charges and thus energies. |
21.5.6 | Improved command: 'AddRes' accepts a new 'End' parameter to add nucleotides to the front (5' end) of DNA and RNA. |
21.4.22 | New feature: Memory management now excludes the soup from the memory usage count, so you will be prompted to increase YASARA's memory significantly less often. |
21.4.7 | Improved command: 'Clean' can skip the separation of single-residue oligosaccharides into their building blocks with Skip=SplitRes |
21.3.27 | Improved macros: The function to 'include' other macros now also searches the 'yasara/mcr' folder, so that macros like md_runmembrane also work if copied somewhere else. |
21.3.3 | New workaround for a bug in the Debian Linux kernel that prevented AutoDock from running. |
21.2.20 | Improved command: The 'BumpSum' parameter of the 'SampleDih' command can now be negative to specify the bump reduction required to accept a sampled conformation. |
21.1.23 | Improved commands: 'BuildRes' and 'AddRes' now also invert the chirality of threonine and isoleucine side-chains when choosing 'isomer=D', before only the Calpha was inverted. |
21.1.20 | Fixed a potential error "Couldn't find matching GLX visual" that could prevent YASARA from starting. |
20.12.24 | New highlight: YASARA enters the billion atom world. The 'Instance' command creates copies of an object for visualization, while the number of atoms in the soup remains unchanged. The new Vulkan/Metal graphics engine can display these instances so quickly that interactive visualization of systems with billions of atoms in all common styles from balls and sticks to ribbons is now possible. Click View > Instance and see the command's documentation for examples of Faustovirus, the major vault, tobacco mosaic virus and a bacterial microcompartment. Joint project with Kornel Ozvoldik. |
20.12.20 | New command: 'ColorFar' assigns one or two overall colors to objects at a far distance, allowing to create schematic representations when objects are moved far away. Click View > Color > Far. |
20.12.10 | New highlight: The help movie 'SARS-CoV-2' shows how to build a model of the virus using coarse-grained packing and Cryo-EM results by Yao et al. (2020) Cell 183,730-738. Click Help > Play help movie > SARS-CoV-2. Contibuted by Kornel Ozvoldik. |
20.12.9 | Improved command: 'Oligomerize' can use the new instancing feature to display giant oligomers much faster, and you can color the oligomer members individually at View > Color > Far. Load for example PDB file 6bp7 or 5j7v, then click Edit > Oligomerize > All and tick the box to use instances. This command is now available in the free YASARA View. |
20.12.8 | New feature: The md_runmembrane macros can build membranes with cholesterol, just adapt the 'CLRpercentage' as needed. Contributed by Kornel Ozvoldik. |
20.12.1 | Improved macro: 'md_runbenchmark' allows to choose between the DHFR benchmark for slower systems (up to 8 cores/16 threads) and the STMV (Satellite Tobacco Mosaic Virus with >1 million atoms) for fast systems with more than eight cores. |
20.12.1 | New command: 'Light' defines how ambient light reaches selected atoms, which is helpful to improve lighting of membrane fragments. |
20.11.10 | Improved commands: PosObj, OriObj, PosOriObj, MoveObj, AutoMoveObj, AutoOriObj, RotateObj, AutoRotateObj, RotAxisObj, TransferObj allow to select object instances, just append e.g. 'Instance 1 2 5' or 'Ins 4 6-10' to your object selection. |
20.11.5 | New feature: The limit of 10 objects in YASARA View has been removed to load and explore the SARS-CoV-2 virus model (and all other large models that are on the way) for free. |
20.11.3 | Improved status display: The number of CPU threads used, and the number of the selected GPU are shown in the bottom left corner at 'Pro'. |
20.10.30 | New much faster server infrastructure for building YASARA download links. The limit of one link per day for YASARA View users has been removed. |
20.10.13 | Improved user interface: A YASARA icon can be found at yasara/png/yasaraicon.png, right-click on your Linux YASARA shortcuts to assign this icon (usually you have to pick 'Properties' in the context menu). |
20.10.4 | New highlight: YASARA calculates contact surfaces with the ConSurf command (click Analyze > Surface > between) and shows them with the ShowConSurf command (click View > Show surface > between), rendering the old approximation (the surface of contacting atoms) obsolete. The help movie 'Surfaces II' has been updated to include the new approach (Model+). |
20.10.2 | Fixed some issues: Problems with special non-ASCII characters in the installation path, OpenBabel PDBQT format issues, maximizing the window on highres screens with YASARA View, error 'Object X atom offset not a multiple of 16', error 'VK_SUBOPTIMAL_KHR in function vk_showframe', crash in POVRay for Linux, crash when moving an empty scene around, workaround for a MacOS Cataline bug which could cause YASARA to crash, problem with SwapPosAtom and rings, problems finding Python on Linux distros without 'python', problems with window deminimization in Vulkan, problems enabling Vulkan in Ubuntu 20 with AMDGPU driver. |
20.10.1 | Improved macro: 'dock_play' no longer saves flexible side-chains as an extra molecule, but instead simply updates the conformation in the receptor. |
20.9.23 | Improved selection language: 'outside' selects atoms outside the simulation cell. |
20.9.16 | Improved command: 'ScaleObj' now scales objects without stopping a simulation. This affects the md_runmembrane macros in a non-backwards-compatible way, if you created derivatives of this macro, please update them. |
20.9.11 | New command: 'CysEnergyRes' calculates the energy of cysteine bridges to differentiate between correct and unrealistic distorted bridges. Click Analyze > Energy > Cys-bridge energy (Structure). |
20.9.2 | Improved command: File export with 'SaveSDF2' saves files in SDF 2000 format instead of the default SDF 3000, 'SavePDBQTR' saves rigid structures without branches (e.g. AutoDock receptor) |
20.8.27 | Improved macro: 'md_runmembrane' employs an improved algorithm do detect the transmembrane region and produces more accurate embeddings. |
20.8.23 | New feature: YASARA detects if you have an old, outdated Vulkan driver that crashes already during startup and skips Vulkan initialization in the future, showing a message to update your driver instead. |
20.8.22 | Improved command: If 'Load' opens a file with multiple compounds (e.g. LoadSDF to load a ligand library), the compound names are used as object names. |
20.8.20 | Fixed atom marks and clicks in right-handed coordinate system in Vulkan, problems with Vulkan validation layers, wrong object positions when visualizing MD in right-handed system with OpenGL. |
20.8.14 | Fixed stereo modes in Vulkan and red error messages while using the GUI. |
20.8.10 | New feature: The 'BuildMol' command can build double-stranded DNA and RNA (via the Type parameter), and accepts a sequence directly (via the Sequence parameter), in addition to sequences in files on disk. |
20.8.7 | Improved macro: 'md_runsteered' calculates the total work required to pull the ligand off the receptor. Contributed by Kornel Ozvoldik. |
20.8.3 | Fixed some issues: Vulkan not found on startup, missing hydrogen bonds in Vulkan, parallel projection problems in OpenGL and Vulkan, POVRay Linux segfault on old CPUs without AVX, write permission problems with temporary files in Windows, Pinch and Rotate gestures not working on MacBook trackpads, Mac Mighty Mouse side-buttons not moving along X/Y, the cluster column 'Run' in the dock_runensemble log, simulation stop when window is changed/resized, unexpected movements during undo/redo, graphical issues with cutplanes in Vulkan, APBS failures when combining ShowSurf and ShowESP, crashes when saving multiple objects with SaveCIF, disappearing HD2 hydrogens of Asn in the Twinset, problems with NMR bundles in the Twinset. |
20.8.1 | New feature: 'Clean' detects oligosaccharide super-residues (multiple sugars in a single residue, e.g. the cyclodetrin residue BCD 371 in 1DMB) and separates them so that GLYCAM parameters can be assigned. |
20.7.25 | Improved command: 'Color' accepts a 'ConsMin' parameter to set the minimum sequence conservation when coloring by conservation from a sequence alignment. |
20.7.24 | Improved macro: 'md_analyze' includes an example to look for water-mediated contacts, e.g. for hydrolysis. Contributed by Kornel Ozvoldik. |
20.7.17 | Improved experiment: 'Docking' accepts a 'FailureEnergy' to assign if the docking program encounters a problem. This is used by the virtual screening macro to make sure that screening continues even if one ligand causes a fatal error (e.g. because it is too large for the docking cell). |
20.7.12 | Improved command: 'AlignPDBMol' uses the YASARA method as default, because the RCSB temporarily disabled their webservice. |
20.7.7 | Improved user interface: Now all file formats are supported for drag and drop and as command line arguments on startup. |
20.7.4 | New highlight: After nearly 30 years of service, OpenGL has reached the end of its lifetime as the top API for cross-platform 3D graphics. Its successor is called Vulkan and delivers more performance, control and flexibility. The YASARA graphics engine has been rewritten from scratch for Vulkan and now delivers in real-time what you previously only got from POVRay via slow ray-tracing (e.g. contact hardening soft shadows for improved depth perception). In MacOS, YASARA now uses the Metal API, since OpenGL is deprecated there, the new required minimum is MacOS 10.11 (if you need to run on older Macs, download the 32bit version). The new engine is not yet enabled by default, you need to click Window > Renderer > Vulkan. Vulkan is not available for ancient GPUs, you need at least AMD GCN (2012, Radeon HD7000), nVIDIA Compute Capability 3 (2012, Kepler) or Intel HD 500 (2015, Skylake), and recent graphics drivers. |
20.7.1 | New feature: IMPORTANT! The naming conventions for nucleotides have been changed to the new PDB standard. O1P,O2P,O3P,C5M are now named OP1,OP2,OP3,C7. If you used the old names in macros, you need to update them. Old scenes and YOb-files are converted automatically. SavePDB saves files in Format V3 by default now. This change required new versions of *.sce and *.yob files, which cannot be read by older YASARA versions. If you send such files to colleagues, they also need to update YASARA to read them. |
20.6.28 | Improved command: 'LightSource' accepts new 'HardShadowFPS' and 'SoftShadowFPS' parameters to set the minimum FPS required to draw hard and soft shadows. This allows to automatically reduce the visual quality if needed to keep interactive frame rates on older hardware. |
20.6.23 | New feature: So far each atom could form at most seven covalent bonds. This limit has been removed with the new Scene and YOb file formats. |
20.6.21 | Improved command: When filling a cell with wall boundaries, 'FillCellObj' considers the inaccessible volume close to the cell wall when calculating the number of copies to reach the requested density. |
20.6.20 | Improved experiment: Homology modeling discards alignments that yield models with separate molecules that are not in touch with each other. |
20.6.10 | New command: 'AddESF' adds an electrostatic field to the MD simulation. Click Simulation > Add force field term > Electrostatic field (Dynamics+). |
20.6.6 | Improved macro: 'md_analyzeblock' creates complete analysis reports with all important files linked per trajectory block. Contributed by Kornel Ozvoldik. |
20.5.29 | Improved user interface: Drag&drop has been implemented in Linux, use your file manager to drop files on the YASARA window (Windows and MacOS already worked before) |
20.5.26 | Improved experiment: Homology modeling accepts a 'ReqTemplateRes' parameter to specify required residues (co-factors etc.), otherwise the template will be discarded (Structure+). |
20.5.15 | Fixed a bug in the macro 'md_analyze', where residues interacting with the ligand were shown with a too large distance cutoff of 8 A. This has been changed to 5 A. |
20.5.8 | Improved command: 'Fog' supports a 'StaticA' range to specifiy the static fog range in Angstrom. |
20.4.24 | New highlight: The 'dock_rescore' macro energy-minimizes ligand poses obtained either with YASARA or other software and re-scores them using local docking. This allows to check the numerical stability of docking results. See Recipes > Dock a ligand to a receptor > Re-scoring of ligands the easy way (Structure). |
20.4.15 | Fixed a problem present since 19.12.14, where clicking with the mouse sometimes failed to mark the expected atom. |
20.3.17 | New highlight: The MMLigner structural alignment program developed by J. H. Collier et al. ( http://lcb.infotech.monash.edu.au/mmligner/ ) is available via a YASARA plugin ( https://github.com/vibbits/yasara-mmligner-plugin ). Click Analyze > Align. |
20.3.12 | Improved macro: dock_runcoval can deal with ligands that contain amino acids, also playing back results with dock_play works again. |
20.2.22 | New feature: If you run YASARA with the -txt command line parameter in Windows, you will now get a new terminal to interact with YASARA. |
20.2.21 | Fixed a problem in the md_runsteered macro handling a user-provided pulling arrow that could cause the arrow to point in the wrong direction |
20.2.20 | New feature: The 'AlignPDBMol' command supports a new 'YASARA' method to retrieve structurally similar proteins that are evolutionary related. See the detailed description in the 'AlignPDBMol' documentation. |
20.2.18 | Improved command: If a simulation cell is present, 'NiceOriAll' orients the scene such that the simulation cell is aligned with the axes of the global coordinate system. |
20.1.20 | Improved command: 'BuildLoop' displays in the console from which PDB file each loop sample was extracted. |
20.1.10 | Improved command: The simulation cell properties including volume (Cell command) can be queried at Analyze > List > Cell properties. |
19.12.28 | Fixed the problem that unminimizing the YASARA window yielded a frozen window. |
19.12.14 | New command: The 'Polymerize' commands builds polymers of a given length from any molecule. You can select the two hydrogen atoms that will be removed upon polymerization. Click Edit > Polymerize, or mark two hydrogens and click 'Polymerize' in the atom context menu (Model+). |
19.12.12 | Fixed an IMPORTANT bug in virtual screening with VINA present since 19.1.27, which could cause ligands to be skipped. Fortunately this was easy to see, since all skipped ligands got identical binding energies in the result file. Please check your *.log files that there are no identical energies (unless the ligand library accidentally contained identical compounds). |
19.12.5 | Fixed issues with multiple screens in MacOS. You can now pull the YASARA window from a retina screen to a standard resolution screen without problems, and you can go fullscreen on all your screens not just the first. To maximize the window, keep <Alt> pressed when clicking the green knob. |
19.11.29 | Improved user interface: The current force field is shown in the bottom status line. |
19.11.21 | Improved commands: 'CopyFile' and 'RenameFile' accidentally has twice the same parameter name for the filenames, this has been fixed also in Python. |
19.11.13 | Fixed a problem in the 'Color' command's 'MapCons' option to color by sequence conservation. |
19.11.6 | Fixed a POVRay problem that could stop homology modeling in Windows. |
19.10.23 | Improved force field parameter assignment: carbon nanotubes, graphene layers and buckyballs work out of the box. You can attach functional groups either by replacing hydrogens at the edge, or by adding pseudo-bonds to carbon atoms (see 'Running a simulation the easy way' in the manual). |
19.10.16 | Improved drag and drop: mmCIF files are now supported, also as command line parameter. PDB and mmCIF files are no longer centered automatically so that you can drop them in the same frame of reference. |
19.10.3 | Improved command: 'Clean' allows to skip the addition of incomplete side-chains ('Skip=AddSC'), which helps when screening PDB files for clashes. |
19.9.25 | Improved command: 'LoadPQR' supports PQR files with missing molecule names and transfers atom charge and radius to occupancy and B-factor fields as expected. |
19.9.17 | New macro: The 'Optimize' command contains an example macro for performing a large number of point mutations read from a text file and running an MD on each of the mutants. |
19.9.15 | Improved macro language: The variable 'IndentationLevel' can be used to check if a macro has been included from another macro. All macros have been adapted so that YASARA no longer exits if you include them from other macros. |
19.9.12 | New macro to PEGylate a protein, see the documentation of the PosObj command. |
19.9.5 | Improved experiment: If 'Docking' has to clean a structure, newly added atoms will be kept fixed, so that supplying a structure with incomplete side-chains will not yield flexible side-chains. |
19.8.30 | Improved instructions for calculating Kd values from MD trajectories of weak, unspecific binders, see manual at Recipes > Calculate free energies. Contributed by Kornel Ozvoldik. |
19.8.23 | Fixed issues with surface transparency, missing bonds when loading a structure with hydrogens and loop sampling. |
19.8.11 | Improved structure prediction: The original atom order is now completely restored after structure prediction algorithms that use charge groups (BuildLoop, Optimize*...). |
19.7.20 | Fixed a local docking problem with AutoDock (if you chose method='AutoDockLS' in dock_runlocal.mcr), that caused much higher variation than expected. |
19.7.10 | Fixed a bug in the md_analyze macro which showed a plot with per-atom RMSF values but labeled them per-residue RMSF values. |
19.7.4 | Improved macros: The 'em_run(clean)' macros are now capable to run a full minimization from the command line, including force field selection and saving the result. See example at Recipes > Run an energy minimization. |
19.7.1 | New feature: 'SwapPosAtom' can including bound groups when swapping atoms positions, making it trivial to invert chirality: just swap two bound atoms and their bound groups. |
19.6.21 | Re-implemented support for downloading re-refined PDB files from PDB-Redo, which moved to a new server at www.pdb-redo.eu. |
19.6.6 | Fixed an issue where the YASARA window would not be updated anymore after un-minimizing. |
19.6.3 | Improved macro performance: Removed a performance issue with per-residue analysis in the md_analyze macro, speedups of 20x are possible. |
19.6.2 | Improved command: The 'Format' parameter of 'SaveTab' can include a character to separate table columns, e.g. Format=Text| or Format=Text\t (tabulator) or Format="Text," (comma). |
19.5.23 | Fixed an issue present since version 18.12.7 that could cause red error windows and other problems. Please update if your YASARA version is >=18.12.7. |
19.5.20 | New feature: The md_analyze macro can easily plot per-residue data as a function of simulation time. The report now additionally contains the number of contacts per residue, and the types of contacts made with the ligand along the trajectory. Contributed by Kornel Ozvoldik. |
19.5.19 | Improved commands: 'ListInt' and 'ShowInt' can list/show ionic interactions. The docking pose player (dock_play.mcr) and the ligand explorer (View > Style scene > X+Ligand) now show ionic interactions too. |
19.5.12 | New command: 'CountCon' counts contacts. Click Analyze > Count > Contacts between (Model+). |
19.5.5 | Improved macro: dock_runcoval can deal with ligands that are "covalently" bound via dative bonds to receptor-associated metal ions. |
19.5.3 | Fixed a problem with screen scaling factor 3x (used mainly on very high resolution screens) that caused texture corruption. |
19.5.1 | Improved macro: md_convert allows to interactively set the number of skipped snapshots per converted snapshot. |
19.4.27 | Fixed a problem with the new graphics engine (broken sticks and missing atoms) on older CPUs introduced between 2011 and 2013 with AVX but not AVX2. |
19.4.20 | Fixed a problem with the new graphics engine (black window) in older MacOS versions like 10.8.5. |
19.4.10 | Fixed a problem in the md_runsteered macro that could cause pulling in the opposite direction. |
19.4.2 | New highlight: The new graphics engine that made the Android Virtual Reality Workstation possible is now available for Linux, MacOS and Windows. Especially the display of balls, ball&sticks and sticks now runs 2-3x as fast as previously. Please keep a backup of your old YASARA in case there are issues with your OpenGL graphics driver. |
19.3.28 | Fixed a problem with the GUI that could cause a red error exit "win_freerec: Allocation table corrupted". |
19.3.10 | Improved support for very bad remote desktop connections in Windows without proper OpenGL support. |
19.3.8 | Improved command: 'Wait Key' waits until a character key from 'a' to 'z' is pressed, so that you don't need the mouse during a presentation. |
19.3.5 | New workaround for a MacOS graphics performance issue that affected a small number of Macs (stutter when showing ribbons). |
19.2.22 | Fixed an issue with AutoDock in Windows, please update if you got an error message that AutoDock could not be run. |
19.2.15 | Improved command: 'Clean' provides an option 'Skip=FuseHet' to skip fusing of hetgroups to a protein if they are covalently bound, and keep a TER entry instead. |
19.2.10 | Improved macro: If you want to prevent md_runmembrane from cleaning or modifying your input structure, you can now provide it as a scene (*.sce file), without cell. |
19.1.27 | New highlight: YASARA performs docking of covalently bound ligands using AutoDock's flexible side-chain model. See Recipes > Docking a ligand to a receptor > Covalent docking the easy way. |
19.1.23 | Fixed a problem with MD simulations on nVIDIA's new Volta/Turing GPUs (Geforce RTX 20x0, TITAN V), which are not backwards compatible to previous GPUs. |
19.1.18 | New feature: The 'md_runsteered' macro to run a steered MD simulation can automatically adjust the pulling force as needed and saves a table plus a plot of the pulling force vs separation distance. You can also interactively place an arrow to indicate the pulling direction, see docs at 'Running a steered simulation'. Contributed by Kornel Ozvoldik. |
19.1.15 | Improved MD algorithms: Tuning for AMD Ryzen CPUs raises their performance by 4%. |
19.1.14 | Improved commands: 'LoadPDB' and 'LoadCIF' can now deal with neutron scattering structures that contain a lot of deuterium. |
19.1.12 | Improved selection language: the operators 'with minimum/maximum distance from local/global point' select atoms depending on their minimum or maximum distance from a point specified in local or global coordinates. |
19.1.9 | New command: 'VecOri' calculates the (transposed) rotation matrix corresponding to an orientation. |
19.1.5 | Improved macro: Virtual screening with 'dock_runscreening' automatically excludes broken ligands, you no longer need to run a cleanup macro before. |
18.12.27 | New feature: Icosahedral boranes and carboranes can be simulated out-of-the-box. |
18.12.20 | Improved force fields: The limit of 256 atom types has been removed, allowing to add a few more exotic metal ions to all force fields. |
18.12.15 | Improved command: 'MouseWheel' can reverse the X- and Y-directions independently using the new 'ReverseX' and 'ReverseY' parameters to match your scrolling expectations in MacOS. Click Options > Input devices. |
18.12.10 | Fixed the accidentally unavailable dodecahedral simulation cells and three red error messages: when optimizing side-chains with explicit water (sgl_removefromcube), and when building homology models (multiplicity of object X.., residues plus gaps do not match) |
18.12.7 | Fixed a problem with charge assignment of metal ions that are part of larger residues (e.g. heme) in AutoDock and NOVA force fields. |
18.12.4 | Fixed a problem with the RestrainPot command, that could unexpectedly change the restraint potential to BiHarmonic. |
18.11.30 | Fixed a problem with the Magic Mouse, now swipe movement along the X/Y-axes works again. |
18.11.21 | New feature: The automatic MD trajectory analysis includes plots of the protein secondary structure per residue as a function of simulation time. Contributed by Kornel Ozvoldik. |
18.11.16 | Fixed some issues of version 18.11.10: YASARA for 32bit Linux works again, just like the Connexion controllers in MacOS. A rare hang in homology modeling is gone, and very large MD simulations with millions of atoms don't yield a red error window. |
18.11.12 | Improved command: 'ColorPar' can return the current color parameters. Contributed by Kornel Ozvoldik. |
18.11.10 | New highlight: YASARA for MacOS 64bit has been released to support very large MD simulations and homology modeling projects. You need to update manually at www.yasara.org/update. If you had out-of-memory problems, click 'Options > Memory usage' after updating. Joint project with Kornel Ozvoldik. |
18.11.2 | New feature: YASARA for MacOS supports high-resolution retina displays, you can set scaling factors at Window > Scale and Window > Size. Also tiny stamp-sized windows are possible, allowing to run 12 YASARAs in parallel: www.yasara.org/macosx |
18.10.22 | New 3D cinema experience with FullHD beamers and nVIDIA 3D Vision 2 screens. See www.yasara.org/products.htm#cave and the user manual at Troubleshooting > Something is wrong with the user interface > Quad-buffered stereo. Contributed by Kornel Ozvoldik. |
18.10.11 | Improved support for the MacOS Magic Mouse 2 and trackpads. When YASARA is in fullscreen mode, you can swipe it away (using three fingers on the trackpad, depending on your settings). |
18.9.18 | New SDL2 library used in Linux and MacOS for interfacing with the window manager. This fixed a few issues, e.g. the green fullscreen knob works in MacOS now, and you can still keep Alt pressed to maximize the window without going fullscreen. |
18.9.6 | New compilation infrastructure for MacOS 32bit and 64bit supporting the latest CPU instruction sets. On a MacBook Pro, the MD performance almost doubled. Contributed by Kornel Ozvoldik. |
18.8.21 | Improved support for recent MacBook trackpads. You can use a two-finger pinch gesture to move along X/Y/Z and rotate around Z, plus a third finger to rotate around X/Y. Three fingers thus give you six degrees of freedom on the trackpad. |
18.8.15 | Improved macro: 'dock_runscreening' allows to set the number of best poses to report per ligand (look for 'bestposes') and saves them as SDF and PDB files. |
18.7.20 | Improved force fields: New parameters from GLYCAM.org for simulating Glycosaminoglycans have been included in all force fields (GlcNS_prep_files etc.). |
18.7.12 | Improved command: 'SplitObj' accepts a new parameter 'Keep' to either keep object numbers (default) or atom numbers when splitting (helpful if the order of atoms in the soup is more important than object numbers, which will change as needed). |
18.6.26 | New feature: Python scripts can now run Yanaconda macros, e.g. to quickly dock, run MDs or build models from a Python script without having to translate Yanaconda code to Python. Read Scripts > Python scripts can run Yanaconda macros. |
18.6.14 | Improved experiment: 'Morphing' can create a table of the morphing force per snapshot, see the example at the 'Experiment' command. |
18.6.7 | New command: 'DelVar' deletes a Yanaconda variable and can delete elements from a Yanaconda list. |
18.5.18 | New macro showing how to sample ligands and create multiple energy-minimized conformations, see the documentation of the 'SampleDih' command. |
18.5.3 | New feature: The MD analysis report created by the md_analyze macro includes a plot of the RMSF (Root Mean-Square Fluctuations) per residue. Contributed by Kornel Ozvoldik (Dynamics+). |
18.4.29 | Improved CPU usage when docking with VINA: If the number of docking runs is small (comparable to or smaller than the number of CPU cores), this will no longer result in unused idle cores. |
18.4.24 | New highlight: Virtual Reality arrived on Android (Intel). Please watch the movie about the new YASARA Virtual Reality Workstation at www.yasara.org/androidvr |
18.4.22 | Improved PDB file interface: Molecules/chains may now contain multiple different segment IDs, no TER entries (=split points) will be created at segment boundaries. |
18.4.20 | New help movie: '1.5. Virtual reality' explains how the YASARA Virtual Reality Workstation really works. |
18.4.17 | Improved force field: 'NOVA2' is just like NOVA, but adds knowledge-based packing potentials for energy calculation. (As known from the YASARA/YASARA2 force fields, the NOVA/NOVA2 forces are the same). |
18.4.10 | Improved command: 'Clean' has improved 'Skip' parameters: 'MissBB' also deletes backbones with incomplete backbone, and 'AddCap' adds long peptide bonds instead of caps. |
18.3.29 | Improved command: 'BuildRes' accepts a 'UsepH' parameter to determine if the current pH should influence the residue being built. |
18.3.23 | Fixed a potential crash in MacOS when putting the computer to sleep while the YASARA window was maximized. |
18.3.19 | Fixed potential red error messages during homology modeling about dsa_initinfo and atm_topobbnumtab present since version 17.12.24. If you have an older version, no update is needed. |
18.2.26 | Improved command: 'GroupDistance' can calculate the distance between the centers of mass and the closest atoms of two atom groups. Click Analyze > Geometry > Group distance. |
18.2.13 | Improved command: 'Style' (without parameters) reassigns the current style to all atoms, and (with Hetgroup parameter) styles the het-groups. Click View > Style scene. |
18.2.7 | New highlight: YASARA supports the NMR Exchange Format (NEF) for loading (LoadNEF) and saving (SaveNEF) NMR restraints. Contributed by Geerten Vuister (NMRModule). |
18.2.1 | Improved command: 'Install' can install the 3DM plugin from Bio-Prodict, click Help > Install > 3DM plugin. |
18.1.30 | New force fields: AMBER15FB (the AMBER15 Force Balance Force Field) for general simulations, and Lipid17 for lipids (replaced LIPID14, after updating YASARA all lipid simulations will be run with Lipid17). Contributed by AMBERTools17 (Dynamics+). |
18.1.20 | Improved macros: The nmr_* macros accept restraints in NMR Exchange Format (NEF) (NMRModule). |
18.1.18 | Fixed an error message 'the PSI-Pred program failed in pass 1' during homology modeling. |
17.12.24 | New highlight: The 'md_analyze' macro writes a scientific report about the MD trajectory, including countless plots and figures. See www.yasara.org/mdanalysis for details. Contributed by Kornel Ozvoldik (Dynamics+). |
17.12.20 | Improved macro language: The '**' operator performs exponentation just like in Fortran. |
17.12.15 | New command: 'SavePlot' fully automatically turns an existing table into a scatter or line plot in PNG format. A plot can contain independent graphs. Tickmarks on the axes and placement of the legend are automatic. Click Options > Table > Save as plot. Contributed by Kornel Ozvoldik. |
17.12.10 | Improved command: 'CorrectDrift' now also shifts fixed atoms to avoid sudden large forces between fixed and non-fixed atoms. |
17.12.1 | New highlight: The 'WriteReport' command writes a report in HTML format, composed from headings, text paragraphs, plots and images. Contributed by Kornel Ozvoldik. |
17.11.20 | Fixed the partly corrupted mouse pointer in full-screen mode of MacOS High Sierra. |
17.10.20 | Improved macro language: The built-in function 'isfunction X' checks if X is a user-defined function, 'basename' returns the basename of a path. The 'caller' keyword to access the local variables of the calling function has been extended to 'callerN' to access the scope of the Nth calling function. The variable 'version' contains the YASARA version number. |
17.10.20 | Newly implemented support for 3DConnexion controllers like the SpaceBall in Windows, now also in Windows 64bit. Contributed by Kornel Ozvoldik. |
17.9.20 | Improved command: 'PlayMacro' accepts a new option 'OnStartup' to always run the chosen macro when YASARA starts, making it easy to add custom settings that are not saved in yasara.ini. |
17.9.12 | Improved macro language: The 'not in' operator checks if a value is not in a list. |
17.8.25 | Improved command: The NumberRes docs provide an example macro for transferring the residue numbering scheme between structurally aligned proteins. |
17.8.23 | Improved macro: 'dock_play' provides buttons to save a receptor/ligand complex with the currently shown pose in PDB or YOb format (Structure). |
17.8.21 | New command: 'RunMOPAC' runs the built-in MOPAC program with custom keywords (Dynamics+). |
17.8.19 | Improved macro: 'md_analyze' can cluster the trajectory, set 'rmsdmin' to the minimum RMSD between the representative structures of each cluster (Dynamics+). |
17.8.18 | Improved macro language: The built-in function 'strlen' returns the string length of a variable. |
17.8.16 | Improved macro language: The built-in function 'type' returns the type of a variable, either 'Integer','Float','WeakString' or 'StrongString'. |
17.8.15 | New highlight: The YARIA module combines YASARA with ARIA from Michael Nilges' lab to automatically determine NMR structures with unique quality from their spectra. Developed by Chris Spronk and Benjamin Bardiaux and sold separately, visit www.yasara.org/yaria for details (YARIAModule). |
17.8.10 | Fixed a problem in version 17.7.30 that could cause side-chain prediction to hang indefinitely. If you have version 17.7.30, please update. |
17.8.5 | Improved experiment: After docking, if you want to save receptor and ligand in a single PDB file, you no longer have to uncheck the 'Transform' box and the coordinates all match the original receptor PDB file (Structure). |
17.8.1 | Improved macro: 'md_run' can handle solvents other than water automatically, just save a single molecule as YourStructure_solvent.yob with the approximate density set as the atom property. |
17.7.30 | New help movie: '4.5 Drug Design', a journey through YASARA's drug design functionality. Using an inhibitor for HIV protease as example, this help movie shows how to visualize protein-ligand interactions, predict ligand binding affinities and improve ligands with the small-molecule builder. |
17.7.22 | New workaround for a problem in nVIDIA's Linux driver versions>=375.66 where GPU MD fails with error "Error parsing value of -cl-nv-opt-level= flag". |
17.7.18 | Improved macros: md_run and md_runmembrane provide a 'slow' speed with 2*1.0 fs timestep. |
17.7.12 | Improved commands: 'LoadCIF' and 'SaveCIF' store the remediated molecule/chain names 'label_asym_id' as segment IDs, so that they do not get lost on the way through YASARA. |
17.7.8 | New feature: If you double-click on an atom while holding Ctrl, the entire residue is zoomed in and the central atom of the residue is globally centered. This makes it easy to hop from residue to residue and explore the surroundings. To undo the global centering, see the docs of the 'Center' command. |
17.7.2 | Improved head-up display: If residues/molecules/objects are colored in a single color, the soup browser reflects this color. |
17.6.28 | Fixed the 'AlignPDBMol' command, which stopped working after the RCSB migrated their structure cluster web service. |
17.6.23 | Improved macro: 'dock_runensemble' provides a new 'merge=' parameter to disable the merging of clusters from different receptors. |
17.6.16 | Improved functionality: The clipboard now works in YASARA for Android. |
17.6.11 | Fixed an OpenBabel problem where only the first of multiple molecules in a file could be read, depending on line feed type. |
17.6.2 | Fixed a server problem that was present from May 15 to May 30 and could yield the error message "version `GLIBC_2.14' not found" when installing YASARA for Linux. |
17.5.28 | Improved macro: 'md_run' has built-in support for simulations in vacuo/gas phase, look for 'vacuo'. |
17.5.25 | Improved docking macros: Single ligands can now be provided in SDF format. |
17.5.20 | Improved macro: md_play provides a button to keep the solute centered on the starting structure. |
17.5.15 | New command: 'DrawLine' draws a line in the HUD or in an image. |
17.5.10 | Improved commands: 'LoadPNG', 'LoadBmp', 'LoadJPG', 'ShowImage', 'SwapImage', 'HideImage' and 'DelImage' now work in text mode too. |
17.5.6 | Improved command: 'SwitchObj' can return the current visibilities of selected objects. |
17.5.3 | Improved command: 'SwapRes' adds or deletes a 2' OH-group on the ribose ring when swapping between DNA and RNA residues. |
17.4.29 | Improved commands: 'BindEnergy' 'Energy', 'LoadESP', 'SaveESP', 'ShowESP', 'ShowSurf', 'SolvEnergy', 'SurfESP' create a simulation cell if needed instead of raising an error. |
17.4.24 | Improved command: 'ListBond' accepts a new 'LenMin' parameter to only list bonds with a minimum length, e.g. unusually long peptide bonds. |
17.4.17 | Fixed broken plugins in Windows and a potential crash in MacOS Sierra when pressing the green maximize button. |
17.4.14 | New highlight: An interactive small molecule builder is available, click the left-most benzene icon in the top menu line to (de)activate the builder. Watch the movie at www.yasara.org/smallmolbuilder (Model+). |
17.4.12 | New help movie: '4.1 Building small molecules' has been rewritten and now explains the new small molecule builder. |
17.4.11 | New command: 'BuildGroup' builds one of 53 pre-defined functional groups. Click the benzene icon to activate the small molecule builder and show their structural formulas and names. Click Edit > Build > Group or pick a group in the builder at the bottom directly (Model+). |
17.4.9 | Improved command: 'SwapAtom' can replace atoms (normally hydrogens) with one of the 53 pre-defined functional groups using various attachment points (Model+). |
17.4.7 | New command: 'BridgeAtom' uses one of the pre-defined functional groups to build a bridge between two atoms. Click Edit > Build > Bridge or mark two atoms and click the bridge in the builder at the bottom (Model+). |
17.4.5 | Improved help movie: "3.4. Simulation and QM of small molecules" uses the new molecule builder in section 3. |
17.4.4 | New workaround for a bug in MacOS Sierra where fullscreen mode could fail with a red error message and yasara.ini needed to be deleted. Retina displays work in fullscreen mode, e.g. the new option Window > Size > 2880x1800. |
17.4.2 | Improved macro: 'md_analyzebindenergy' can deal with membrane simulations and either include (meminc='yes') or exclude the membrane from energy calculations (Dynamics+). |
17.4.1 | Improved plugin: CONCOORD has been updated to version 2.1.2 and works with Python 3. |
17.3.30 | New highlight: Small molecules are simulated with the new GAFF2 force field, the new AMBER15IPQ force field is available, AMBER14 includes the OL15 DNA fine-tuning, LIPID14 includes cholesterol. Contributed by AMBERTools16. |
17.3.28 | Improved macro: 'dock_runscreening' can sort ligands by ligand efficiency, i.e. binding energy divided by heavy atoms. This addresses a potential bias towards larger ligands, since the binding energy tends to grow with the number of atoms. Look for 'sortby'. |
17.3.25 | Newly included version of OpenBabel (2.4.1) provides support for import and export of 20 additional molecular file formats. |
17.3.21 | Improved force field parameter assignment for ion binding sites, that can prove helpful when using the md_runfast macro. |
17.3.17 | New feature change: Over the years it turned out that YASARA's feature to automatically sort files into subfolders based on the filename extension caused more pitfalls than it helped, this feature has therefore been removed. |
17.3.12 | Improved commands: 'Radius' and 'GroupBox' accept a new radius type 'Style' to consider the radii of atoms on screen, depending on their current style. |
17.3.11 | Improved commands: 'AddSpring', 'AddAngle' and 'AddDihedral' add force field terms to enforce the current distance/angle/dihedral if no explicit values are specified. |
17.3.8 | Fixed a problem in Android 5+ where changes made by Google prevented OpenBabel and APBS from running. |
17.3.4 | Improved selection language: the 'with arrow to' operator allows to specify a number of arrows, e.g. to select atoms without arrows or metal binding sites with a certain number of dative bonds, see Selections > Selection blocks can be combined > The 'with <>X arrows to' operator |
17.3.1 | Improved command: 'Console' can return the current console mode. |
17.2.27 | New command: 'Resolution' gets or sets the X-ray resolution of selected objects. Click Edit > Renumber > Resolution, or Analyze > Numbers > Resolution. |
17.2.23 | Improved macros: 'md_run' and 'md_runmembrane' delete all waters from the input structure except those connected to metal ions. This ensures that md_analyzebindenergy can easily remove the entire solvent later. |
17.2.21 | Improved command: 'Renumber' has been assigned the shorter name 'Number', also for consistency with the 'Name' command. 'Renumber' still works but is deprecated. |
17.2.18 | Improved command: 'BuildSMILES' makes sure that hydrogen atoms are added right after their heavy atom, and that all heavy atoms get unique names. |
17.2.14 | Improved command: 'Clean' can add most missing backbone atoms, depending on the presence of neighboring residues and a side-chain to infer the coordinates (Dynamics+). |
17.2.12 | Fixed the 'Occup' command which returned occupancies scaled with 100, i.e. percentages. Now the actual occupancy values in the PDB file are returned, 1.0 corresponds to 100%. |
17.2.8 | Improved force fields: Different scaling factors for the non-bonded 1-4 interactions in dihedral angles are supported via SCEE/SCNB parameters, as a result simulations of carbohydrates with GLYCAM better reproduce rotamer populations (Dynamics+). |
17.2.5 | Improved macro: 'md_analyzebindenergy' can extract ligands consisting of multiple residues from the receptor object, and prints the individual energy components in the output table and can handle MM/PBSA solvation if the cell is dodecahedral (Dynamics+). |
17.2.1 | Improved command: The 'BuildSMILES' documentation contains a macro to convert a SMILES library in text format to a 3D library for virtual screening. |
17.1.28 | New highlight: YASARA's graphics engine and user interface have been reimplemented for high and ultra-high resolutions, the new limits for the YASARA Window size are 4K in YASARA View (3840x2160) and 8K in YASARA Model+ (7680x4320). Support for Apple Retina displays fill follow later. Click Window > Size, and Window > Scale. |
17.1.25 | New printed YASARA Science Manual with all our articles about and using YASARA is available. You will receive one with your next order >=275 EUR. Contributed by Kornel Ozvoldik. |
17.1.21 | New IMPORTANT development: Unfortunately Intel decided to leave the smartphone market. If you want to have YASARA and interactive MD simulations on a new smartphone, then you need to order quickly, for example the ASUS ZenFone 2 ZE551ML with 4 cores and FullHD for 180 EUR+ (DHFR benchmark 13 ns/day). |
17.1.19 | Improved macro: 'md_analyze' can additionally visualize the dynamic cross correlation matrix (DCCM) by drawing blue/red cylinders between anti-/correlated residues, just set dccmsel as needed and load *_dccm.yob afterwards (Dynamics+). |
17.1.17 | New support for the latest Android versions (5.0+), including a bug fix for error "win_nextentryoftype: End of window reached". Since write access has been restricted by Google, YASARA is now installed in a different folder /sdcard/Android/data/org.YASARA.app/files |
17.1.13 | Improved experiment: 'Docking' supports ligands with coordinated metal ions without having to manually fix anything, VINA now functions also with exotic metal ions. |
17.1.8 | New feature: YASARA's user interface can adopt the looks of Windows 10 and MacOS ElCapitan/Sierra, click Window > Style. |
17.1.7 | Improved command: 'SampleDih' accepts two new parameters 'DevMax' and 'DevBins' to add a random deviation to the initially chosen dihedrals. |
17.1.2 | Improved command: 'RandomSeed' also sets the random seed for docking and has a new menu entry at Options > Random seed. |
16.12.29 | New highlight: MD simulations of globular proteins run between ~10% (with GPU) to ~20% (CPU only) faster thanks to support for dodecahedral simulation cells in the new 'Cell' command. Click Simulation > Define cell (Dynamics+). |
16.12.27 | New help movie: '3.6. Simulation in dodecahedral cells' explains how dodecahedral cells work in theory and practice. Click Help > Play help movie > 3.6. Simulation in dodecahedral cells (Dyamics+). Contributed by Kornel Ozvoldik. |
16.12.24 | Improved macro: 'md_run' uses a dodecahedral simulation cell by default. Change the 'cellshape' parameter if needed. |
16.12.20 | Fixed a bug in Windows, where minimizing a maximized YASARA window lead to a white unresponsive window after de-minimizing. |
16.12.19 | Improved simulations: When restarting a simulation from a *.sim snapshot with unchanged parameters, YASARA now produces the same simulation trajectory again. You can thus observe interesting events step-by-step again after restarting from the last snapshot before the event (Dynamics+). |
16.12.18 | Improved macro: 'nmr_fold' accepts starting structures in YOb-format, so that you can exclude certain dihedrals from sampling by fixing the two core atoms (e.g. bonds in non-amino acids that mimic peptide bonds). |
16.12.15 | New command: 'AutoPosOri' automatically positions and orients an object in a given number of steps. It thus combines the 'AutoPos' and 'AutoOri' commands in a single call. |
16.12.12 | Improved commands: The names of the 'AutoMoveTo' and 'AutoRotateTo' commands have been changed to 'AutoPos' and 'AutoOri' for consistency and to save key-strokes. The old names are now deprecated. |
16.12.9 | Improved macro: 'md_refine' runs faster and reports the snapshots with minimum energy and best score (the latter in YASARA Structure only). |
16.12.8 | New command: 'ColorMesh' changes the color of polygon meshes liks spheres, cones etc. after the initial creation. Click View > Color > Object mesh (Model+). |
16.12.5 | Improved sequence selector: When searching for a sequence, you can type 'X' for any amino acid. |
16.12.3 | New command: 'ShowCell' creates an object that looks like the simulation cell for visualizing neighboring cells or for other instructive purposes (Dynamics+). |
16.11.29 | Improved command: 'PressureCtrl' offers a new mode 'Manometer2D' that keeps the aspect ratio of the simulation cell in the XZ-plane constant and thus makes sure that an initially square membrane stays a square also after long simulations (Dynamics+). |
16.11.24 | Improved macros: The membrane simulation macros md_runmembrane*.mcr now create square membranes by default and also keep them square during long simulations, unless the 'square' flag is set 0 (Dynamics+). |
16.11.20 | New highlight: YASARA's NMR module supports residual dipolar coupling restraints (RDCs), possibly for multiple alignment media and with interactive visualization (NMRModule). |
16.11.17 | New feature: The NMRFolding experiment has been rewritten, is uses multiple CPU cores and runs orders of magnitude faster for longer proteins (NMRModule). |
16.11.16 | Fixed the broken mouse wheel in Windows and an issue in the 'SupMulti' command, which had problems reordering matched atoms (in this case lots of warnings about mismatching atom names were displayed). |
16.11.15 | Improved command: 'CorrectKnots' uses an improved algorithm and handled more knots simultaneously. |
16.11.12 | New feature: ambiguous dihedral angle restraints are supported, see the 'LoadTbl' command documentation for an example (NMRModule). |
16.11.10 | Improved experiment: 'Morphing' can now easily morph proteins whose sequences differ, if proteins are first aligned and mutated properly, as done by the new example macro at the 'Align' command. |
16.11.7 | Improved macro: 'nmr_fold' uses the new folding performance to fold 'foldmul' structures (set in nmr_setdefaults.mcr) for each ensemble member, keeping only the lowest energy structures. This makes sure that very bad and hard to correct candidates with knots etc. are discarded already before the actual refinement (NMRModule). |
16.11.5 | Improved commands: 'DelRest', 'ListRest', 'RestEnergy', 'SaveTbl' and allow to select RDC restraints with the 'Component' parameter, 'ScaleRest' accepts a new parameter to scale 'RDC' restraints (NMRModule). |
16.11.4 | Improved macro: dock_run calculates the average dissociation constant in each cluster of structurally similar poses. |
16.11.3 | New command: 'AngleVec' calculates the angle between two vectors. |
16.11.1 | Improved command: 'ListRest' outputs and returns information about RDC restraints, and supports a new 'RDCMin' parameter to specifiy the minimum RDC violation (NMRModule). |
16.10.31 | Improved command: 'RestrainPot' now also sets the potential function for RDC restraints using the new parameters 'RDCForceConst' and 'RDCErrorScale', click Simulation > Restrain > Potential (NMRModule). |
16.10.29 | Improved command: 'CopyFile' accepts a new parameter to 'append' to existing files instead of overwriting them. |
16.10.27 | New macro: 'md_analyzeblock' analyzes an MD trajectory in blocks and outputs all results separately for each block. |
16.10.23 | Improved command: 'RenameFile' accepts a new parameter to automatically 'overwrite' existing files without raising an error. |
16.10.22 | Improved command: The 'LabelDis' command accepts a new parameter to specify the 'Radius' of an arrow that is shown between the two atoms, so that you can quickly show many distances with arrows simply by holding <Tab> and clicking on the atom pairs (after labeling a distance once, e.g. from the atom context menu). |
16.10.15 | Improved command: 'Link' displays the newly added bonds in the console, so that you can easily search for potential problems. |
16.10.13 | Improved command: 'FillCellObj' accepts a new parameter 'DisMin' to define the minimum allowed distance between the each object copy and the other atoms (Dynamics+). |
16.10.10 | Improved command: 'ScaleRest' accepts a new parameter 'RDC' to scale residual dipolar coupling restraints (NMRModule). |
16.10.5 | Improved command: 'RestViol' additionally returns the summed and maximum RDC violation (NMRModule). |
16.9.23 | New highlight: The 'ApplyMacro' command automatically applies a macro to a large number of targets or files and makes batch-processing easy. Click Options > Macro & Movie > Apply macro to.. (Model+) |
16.9.21 | New important feature: As requested by the users, the selection operators 'with distance<>X' and 'with minimum/maximum distance' now consider the distance between an atom and itself. This influences existing macros if the same atom is selected on both sides, in which case you now have to use the new operators 'with self-excluded distance<>X' and 'with minimum/maximum self-excluded distance' to get the old behavior. See the manual at Selections > Selections can be combined with... > The 'with distance <>X from' operator for details. |
16.9.15 | Fixed a bug that could cause simulation failures with md_runfast and water molecules bound to other residues using pseudo-bonds (e.g. to restrain metal binding sites involving waters). |
16.9.13 | Improved user interface: The file browser contains an entry 'Recent folders' to quickly jump to recently used folders, and you can go back to the previous folder by holding Ctrl and clicking the folder with the arrow. |
16.9.11 | Improved command: 'MacroTarget' accepts a new parameter to 'Remove' either nothing, the file extension, or everything starting from the last underscore (helpful for docking). |
16.9.7 | Improved force field parameter assignment: Residues with incorrect bond lengths are at least cached temporarily, so that scenes with many incorrect bond lengths of the same type can be parameterized quickly too. |
16.9.4 | Fixed the potentially inconvenient scaling of the YASARA window on high DPI displays in Windows. |
16.8.30 | New command: 'CorrectKnots' automatically disentangles knots and other tight clews during a simulation. |
16.8.27 | New highlight: The Bio-Prodict 3DM protein superfamily data integration platform has become a widely used, indispensable tool for protein analysis and now includes DNA diagnostics, see www.yasara.org/products.htm#3dm (sold separately). |
16.8.20 | Improved command: 'ScaleForce' accepts parameters 'Dihedral1D', 'Dihedral2D' and 'Dihedral3D' to change the weights of the 1D,2D and 3D knowledge-based dihedral potentials in the NOVA&YASARA(2) force fields, which is mostly useful for NMR structure determination (Structure). |
16.8.14 | Improved command: 'RenumberRes' supports fractional residue numbers like 12.4 or 3.23, which may be helpful to implement special numbering schemes. |
16.8.12 | Improved POVRay included in YASARA for Windows: You no longer have to click 'OK' at the license screen occasionally, and you can raytrace from multiple YASARA instances in parallel without conflicts (e.g. when building multiple homology models). |
16.8.3 | Improved user interface: YASARA for Linux supports both clipboards: the primary one (based on the middle mouse button), and the secondary one (based on Ctrl+C,Ctrl+V). |
16.7.28 | Improved macro: 'md_analyzebindenergy' can deal with scenes where receptor and ligand are in the same object, just select the ligand residue with 'ligres'. |
16.7.26 | Fixed a force field parameter assignment problem with pentavalent atoms. If you simulated one of these, check that the geometry was still correct at the end of the simulation. |
16.7.22 | New workaround for Windows 10 bug that prevented the 64bit Twinset from running ('This app can't be run on your PC'). |
16.7.19 | New feature: The abundant memory in 64bit mode allowed to increase the atom number limit of MOPAC to 400, so that larger molecules that do not consist of individual residues can be analyzed and parameterized for MD simulation. |
16.7.10 | Improved command: 'SampleDih' considers fixed atoms when choosing which atoms to rotate when changing dihedral angles. |
16.6.24 | New highlight: A 64-bit version of YASARA for Windows is available, design issues in Windows memory management can no longer cause 'out of memory' errors when building large models or simulating large systems. After updating click Options > Memory usage and set 2000 MB. |
16.6.16 | Improved command: 'RestrainPar' provides a 'ShowAmb' parameter to show all potential assignments of an ambiguous restraint, not just the closest one (NMRModule). |
16.5.13 | Improved command: 'SplitObj' allows to split an object only at selected split points, which often obviates the need to join objects again afterwards. |
16.5.5 | Improved command: 'BuildSymRes' uses a new superposition algorithm to obtain better results if there are significant structural differences between oligomer members. |
16.5.1 | New highlight: The YASARA Structure/WHAT IF Twinset is available also for Windows (64-bit only). To get it, choose version '1.1.1' and 64-bit on www.yasara.org/update |
16.4.30 | Improved commands: 'AlignPDBMol' and 'SaveAli' can save alignments in plain text format with one sequence per line. |
16.4.24 | Fixed a problem with extreme slowness of BLAST on some Windows machines. The NCBI released corrected BLASTs which are now included in YASARA. |
16.4.6 | Improved command: 'SampleDih' rotates the atoms on the lighter side of a dihedral instead of the atoms with the higher number. |
16.4.3 | Fixed a new problem with doubled peptide bonds around unusual amino acids (error message 'Angle parameters for atoms X-Y-Z (c-n1-c3) not found' or 'mob_uncompress: Uncompression failed'). |
16.3.28 | New IMPORTANT feature: A new non-redundant PDB sequence library has been created for YASARA's homology modeling module and BLAST (PDBC), since the NCBI library used so far was not updated reliably any more, missing newly released templates. To see how the new library impacts your models, delete the file (YASARA.app)/yasara/bla/blastdb.txt, create a copy of your existing project folder, then select the copy as macro target and rerun the hm_build macro. Updating YASARA is *NOT* needed, the new PDBC library will be downloaded automatically. |
16.3.24 | Improved commands: 'SaveXTC' and 'SaveMDCrd' can append single snapshots immediately to an XTC/MDCRD trajectory. |
16.3.18 | New features: Labels can be rotated, just keep <Ctrl> pressed and move the mouse while a label is marked. The middle button resets the label orientation. |
16.3.16 | Improved macros: md_run and md_runmembrane contain examples for monitoring properties continuously during a simulation. |
16.3.14 | Improved head-up display: The right-click in the 'Vis' column to show only the clicked unit now also works for molecules, residues and atoms, not just for objects. |
16.3.12 | New command: 'ShiftColor' blends current atom colors with a new target color, e.g. with gray. Click View > Color > Shift. |
16.3.10 | Improved experiment: Homology modeling supports a 'SecStrFile' parameter to provide your own secondary structure prediction or assignment (e.g. from CD spectroscopy). |
16.3.8 | Fixed a new problem in the BuildSymRes command to build symmetry related residues, which is also used by the homology modeling experiment and could cause a red error window (uncompression failed or link not found) |
16.3.5 | Improved the functions to download files from the web, so that they can for example cope with the RCSB's sudden change of the download locations for PDB files. |
16.3.1 | Fixed a problem in the GLYCAM06 force field, which could lead to assignment of the expected net charge instead of GLYCAM's fractional charge for some carbohydrate residues. |
16.2.21 | Improved force field parameter assignment: Metal ions with more than one VdW parameter set are now assigned the most common oxidation state (Cr2+,Fe2+,Cu2+,Ag+,Ce4+,Sm3+,Eu3+,Tl+), unless overridden by the residue name. |
16.2.20 | Fixed a problem in the hydrogen bonding network optimizer that failed to flip rings like the histidine side-chain. |
16.2.19 | Fixed an error message about missing profile files when providing your own templates during homology modeling. |
16.2.18 | New command: 'Brake' enables a simulation brake that slows down fast atoms in unrealistic simulations like NMR structure determination (Dynamics+). |
16.2.17 | Improved force fields: Parameters from Li et al. to simulate the metal ions Pd2+, Ag2+, Sm2+, Eu2+, Yb2+, Rb2+ and Ra2+ have been included (Dynamics+). |
16.2.16 | Fixed an error message in the AMBER14/AMBER14IPQ force fields when trying to simulate non-standard residues bound to standard ones. |
16.2.14 | New highlight: Several new force fields are available: AMBER10, AMBER11 (known as ff99sb*-ILDN), AMBER12, AMBER14 and AMBER14IPQ, see the ForceField command docs for a comparison. Included are GLYCAM06 for carbohydrates, Lipid14 for phospholipids and lots of new ion parameters by Li&Merz (Dynamics+). |
16.2.12 | New macros: IMPORTANT! All simulation macros now use the AMBER14 force field by default, since it performs a bit better than AMBER03. If you want to continue a simulation after updating YASARA, you need to change the force field back to AMBER03 manually in the macro. |
16.2.11 | New feature: IMPORTANT! The fast membrane simulation macro md_runmembranefast runs 25% faster since the time-step has been increased to 5 fs. It is not recommended to continue an old membrane simulation after updating YASARA, since the Lipid14 force field is now used for phospholipids. |
16.2.9 | Fixed a bug in the 'Bind.energy spread' column of the log file created by the dock_run macro. |
16.2.8 | Improved command: 'Clean' can skip the error message about missing backbone atoms (Skip=MissBB). |
16.2.5 | Improved experiment: Homology modeling got several small improvements that sometimes add up to significantly better models. |
16.2.2 | New feature: Force field parameter assignment looks for hexavalent atoms and adjusts equilibrium bond angles to yield an octahedral geometry |
16.1.30 | Improved command: 'AddHyd' can add up to 6 hydrogens per atom. |
16.1.28 | New feature for power users: The 'Install UniRef90H' command downloads a huge, up-to-date version of the UniRef90 sequence database, which requires about 20 GB of free disk space and slows down modeling, but leads to somewhat more accurate homology models. See the documentation of the 'Install' command for details before clicking Help > Install > huge UniRef90. |
16.1.24 | Improved macro language: The variable 'SimWarnings' contains the number of simulation warnings since the start (high temperature, wrong isomers, cis-peptide bonds), which is helpful for NMR protocols. |
16.1.11 | Improved plugins: Custom windows defined at the top of a plugin file can use multiple radiobutton sets. |
16.1.8 | Improved command: 'GroupAngle' accepts a 'Range' parameter to return angles in the ranges 90, 180 or 360 degrees (the latter useful to calculate helix packing angles). |
15.12.30 | New command: 'RenumberAtom' reorders selected atoms, for example by residue number. Click Edit > Renumber > Atom, the documentation contains an example macro for creating a retro-inverso D-peptide. |
15.12.20 | Improved command: 'SurfPar' accepts a 'Unite' parameter to disable the creation of united surfaces during a simulation, so that each object can keep its own surface, surface colors and surface areas. Click View > Show surface > Parameters. |
15.12.10 | Improved command: 'Clean' adds dative bonds to metal ions to stabilize the interaction, and deletes those bonds that are not sufficient to hold the metal ion in place. |
15.12.9 | New feature: Force field parameter assignment looks for pentavalent atoms and adjusts equilibrium bond angles to reproduce the closest trigonal-bipyramidal structure. |
15.12.8 | Improved command: 'AddHyd' can add hydrogens until a maximum number of 7 covalent bonds is reached. |
15.11.26 | Improved macro: 'md_runmembrane' allows to set the phospholipid composition of the two membrane sides independently |
15.11.21 | Improved macro: 'md_convert' provides a checkbox to exclude the water object from conversion. |
15.11.20 | Improved command: 'SavePDB' provides a new 'UseCIF' parameter to disable the saving of mmCIF files if the limits of the PDB format are exceeded, and save somewhat broken PDB files instead. |
15.11.18 | New feature: Python plugins can access persistent storage in YASARA to preserve data until the plugin is run again. See Plugins > Python plugins can access persistent storage in YASARA. |
15.11.16 | Fixed a simulation accuracy problem affecting PME electrostatics of the new 64-bit YASARA for Linux on CPUs with AVX (AVX2 and SSE were fine). Please update if you have an AVX CPU (Intel Sandy/Ivy bridge). |
15.11.9 | Improved scripts: Python scripts can now wait until any button created with 'ShowButton' is pressed: buttonname=yasara.Wait("UserButton"). |
15.11.7 | Fixed a red error message ('scl_calcforcebigroup: Used...') in the 64-bit YASARA AVX code path. CPUs with AVX2 or SSE only were not affected. |
15.10.18 | Fixed error messages when running the neutralization experiment on very small solutes (failed to get contact info), when installing YASARA Structure on MacOS (corrupted layout), when building homology models (exp_retrievetemplate), and when running VINA in a 64-bit Linux. |
15.10.11 | New highlight: A 64-bit version of YASARA for Linux is available, so that you don't need to install extra libraries for backwards compatibility, and memory limits will no longer impair your MD simulation of the ribosome. |
15.10.5 | Improved experiment: 'Neutralization' employs a new, much faster algorithm to place the ions, which had become a bottleneck for simulations of giant structures like the ribosome. |
15.10.1 | Improved command: 'Align' provides a new 'CopyResNum' parameter to transfer residue numbering schemes between aligned proteins. |
15.9.25 | New feature: YASARA includes POVRay 3.7, and thanks to its AGPL license, you no longer need to download it separately. POVRay 3.7 runs much faster, because it uses all CPU threads you assigned to YASARA (Options > Processors). |
15.9.20 | Improved macros: The docking result log and player show the ligand names, which is helpful when analyzing screening runs. A related problem with compound/ligand names introduced in 15.6.7 has been fixed. |
15.9.13 | New macro: 'md_analyzebindenergy' calculates binding energies during a simulation. |
15.9.6 | Improved macros: The nmr_* macros can handle an input structure in PDB format saved as YourProtein_start.pdb, in case a sequence is not sufficient (capping groups, unusual amino acids..). |
15.8.30 | Improved selection language: Selections by BFactor, Occupancy, Property and Charge can leave out the comparison operator and specify multiple values to compare instead. See Selections > Additional selection types > BFactor. |
15.8.23 | New commands: 'ListSMILES' and 'ListSMARTS' identify groups of atoms that match SMILES or SMARTS strings and return them in SMILES/SMARTS order, which allows a direct mapping between string and soup. Click Analyze > List > Atoms matching... |
15.8.20 | New feature: The 'SMARTSRoot' and 'SMARTSMember' keywords allow selections using SMARTS strings. See Selections > Additional selection types > 'SMARTSRoot' and 'SMARTSMember'. |
15.8.18 | Fixed a few issues: Homology modeling no longer pauses if the window in minimized, and no longer crashes when restarting ('new' since version 15.7.25). |
15.8.16 | New highlight: The LoadCIF and SaveCIF commands provide a fast and reliable interface to mmCIF/PDBx and CIF files, allowing to load the new giant PDB structures like 4V8P that are only available in mmCIF format. Click File > Load/Save > PDBx/(mm)CIF format. |
15.8.8 | Improved commands: LoadPDB recognizes (mm)CIF files, and SavePDB saves (mm)CIF files if the PDB file format limits are exceeded. You can thus use LoadPDB/SavePDB without worrying about the actual file content. |
15.8.3 | New feature: the undo/redo functions have been updated, editing giant structures is now 3x as fast as previously. |
15.7.27 | Improved command: LoadPDB ignores cysteine bridges if both cysteines are coordinating metal ions, even though this might cause a loss of newly discovered triple and quadruple bridges ( http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1097-0134/homepage/PROTAprilFool2015.pdf ). |
15.7.25 | New tutorial: A PDF file with step-by-step instructions for protein-ligand interaction analysis is available at https://goo.gl/wgwnZ4 , contributed by Caroline Low. |
15.7.24 | Fixed error messages in Python plugins (e.g. FoldX), and two red error messages (simulation not being active, object out of range) |
15.7.12 | New feature: The 'SaveMDCrd' and 'LoadMDCrd' commands enable support for MD trajectories in AMBER's MDCrd text format (Dynamics+). |
15.7.9 | Improved user interface: The view tabs at the top now have close buttons. |
15.7.6 | Improved command: 'Clean' reorders hydrogens in water molecules to follow the oxygen in the soup, avoiding error messages about water constraints. |
15.7.2 | Improved macros: Support for the AMBER MDCrd trajectory format has been added to all standard macros. |
15.6.7 | New highlight: YASARA allows to create alternative views of the scene, each with its own styles, visibilites, surfaces, arrows etc. Click View > Duplicate, then switch between views using the new View tabs below the top menu line. |
15.6.3 | New feature: To enable support for multiple views and 4-character molecule names (required by the new PDBx file format), YASARA's file formats *.sce and *.yob had to be updated. This included extensive tuning for reduced disk space and faster file access. |
15.6.1 | New instructions for watching YASARA with 3D glasses on a huge 3DTV with 42 inch/107 cm diagonal for just 380 EUR: www.yasara.org/products.htm#3dtv |
15.5.30 | Improved selection language: To select residues within a sequence, you can now provide the sequence in one letter code (e.g. ColorRes CPGDY,Yellow). You can also simply paste the sequence from the clipboard into the 'manually typed selection' box at the bottom of all residue selection windows. |
15.5.27 | New command: 'DuplicateView' creates and shows a duplicate of the current view, which can then be styled independently. Click View > Duplicate. |
15.5.23 | Improved experiment: Homology modeling can automatically oligomerize templates that have been specified inside a custom alignment file. |
15.5.20 | New command: 'ShowView' shows one of the alternative views. Click on one of the View tabs. |
15.5.16 | Improved sequence selector: Place the mouse pointer on top of the sequence selector and press Ctrl+V (=paste) to find the sequence currently in the clipboard. |
15.5.14 | New command: 'DelView' deletes one of the alternative views. Right-click on one of the View tabs, then select 'Delete'. |
15.5.11 | Improved experiment: 'HomologyModeling' accepts a 'TemplateList' parameter to make sure that your favorite templates are ranked first (among those found by YASARA). |
15.5.7 | New highlight: YASARA's internal data structures have been redesigned. Many typical molecular modeling operations run much faster. YASARA now supports 4-character chain/molecule names (as required by the new PDBx/mmCIF format) and up to 7 covalent bonds per atom. |
15.5.2 | New feature: The 'ListRest' command can perform a joint analysis of an entire NMR structure bundle, listing for example only restraints that are violated to a certain extent in a certain number of structures. It also returns the results for automated analysis from macros and scripts. |
15.4.28 | Improved command: 'DelRest' is available for selected molecules, residues and atoms (DelRestMol..DelRestAtom) and provides new parameters 'Class', 'Component' and 'Number' to delete individual restraints. |
15.4.23 | New WHAT IF version included in the Twinset, the various structure validation checks will yield some differences compared to previous versions. |
15.4.20 | Improved commands: SwapRes, AddTer, AddCap, AddRes preserve the current views as closely as possible. E.g. if you swap a side-chain that totally colored blue and has a surface shown, color and surface and be preserved in the new side-chain. |
15.4.18 | New feature: When you use YASARA as a Python module and obtain a portion of the soup with the Atom(),Residue()..All() methods, the bonds and bond orders are now included. See Scripts > A subset of the YASARA soup... |
15.4.15 | New macro for surface patch analysis can be found in the documentation of the 'SwapAtom' command. |
15.4.10 | Fixed a problem in the minimization experiment, which would sometimes not minimize properly if strong bumps were present, so that a subsequent MD simulation could fail. |
15.3.30 | Improved macro language: Depending on the workload, Yanaconda macros run up to 25x faster now. |
15.3.25 | New command: 'BuildGrid' creates a grid of atoms. Click Edit > Build > Atom grid (Model+). |
15.3.20 | Improved user interface: The AutoRotate button in the top menu line disables all automatic rotations (of the scene and individual objects), no matter how they were started. |
15.3.15 | Improved command: 'BuildLoop' accepts an improved 'Mutate' parameter that can specify more precisely how to mutate or not to mutate loop residues. |
15.3.8 | New highlight: YASARA uses GPUs from AMD, nVIDIA and Intel to accelerate MD simulations in Linux and Windows (technical issues preventing GPU acceleration in MacOS have been reported to Apple and will hopefully be solved soon). In the DHFR benchmark (PME, 8.0 A cutoff, correct atom masses), performance increases to 253 ns/day (Core i7 5960X 3.6GHz + Geforce GTX 980) or 150 ns/day (Core i7 4770 3.4GHz + Radeon R9 290X). See www.yasara.org/gpu for details. To enable GPU MD, simply run the md_runbenchmark macro. |
15.3.3 | Improved macro: md_runbenchmark tests MD performance using varying CPU threads and the available GPUs, the best combination is set as the new default for all subsequent simulations. |
15.3.1 | New feature: 'Processors' sets the CPU threads and GPU used by YASARA. It also returns and prints lots of information about the CPU and the available GPUs. Click Options > Processors. |
15.2.25 | Improved macros: md_run(fast) and md_runmembrane(fast) update the pairlist either every 10th (CPU based MD) or every 25th simulation step (GPU based MD). If you need very smooth interactive MD, click 'Simulation > Timestep' and set screen and pairlist update to 1. |
15.2.18 | New Android tablets available to run YASARA, Atom Z3* preferred: Best choice is the ASUS Transformer Pad TF103C(Atom Z3745) with external keyboard for 250 EUR, followed by Lenovo Yoga 2 (Atom Z3745), Lenovo Tab S8-50 (Z3745), Acer Iconia Tab 8(Atom Z3745), Acer Iconia One 7/8(Atom Z3735), Blaupunkt Polaris IC(Atom Z3735), ASUS Fonepad 8(Atom Z3560), ASUS Fonepad 7(Atom Z3530), Prestigio MultiPad Thunder 7.0i(Atom Z2520), Kurio Tab Motion C14100(Atom Z2520), HP 7 Plus G2 1332nn(Atom Z2520). |
15.2.11 | Fixed a problem with the file browser that would not list files on very large Linux partitions in the Terabyte range. As a side-effect, support for ancient Linux distributions had to be dropped, YASARA now requires a Linux from 2007 or later (GLIBC 2.5, e.g. RedHat Enterprise Linux 5). |
15.2.6 | New feature: The 'ShowTab' command includes the 'marching squares algorithm' to show contours of a 2D table using the new 'Contour' style. |
15.2.4 | Improved command: The 'Tabulate' docs include a macro showing how to extract the phi/psi free energy landscape of an alanine dipeptide from an MD simulation and visualize the results using a contour plot. |
15.2.1 | Improved command: The 'CorrectCis' docs include the macro that is behind the YASARA energy minimization server at www.yasara.org/minimizationserver. |
15.1.23 | Fixed a problem with the 'RandomSeed' command, which yielded identical random numbers for 50% of all adjacent seed values. |
15.1.20 | Fixed a problem 'introduced' with version 14.12.2, where certain types of ion binding sites could lead to simulation blowups. |
15.1.17 | Improved command: 'PressureCtrl' provides a new mode 'Manometer1D' to use the 1-dimensional isotropic pressure (average of the three 3D pressure components along X/Y/Z) for cell rescaling. This makes sure that an initially cubic cell stays cubic during the entire simulation. The old 'Manometer' mode has been renamed to 'Manometer3D'. |
15.1.10 | Improved macro language: Yanaconda can now deal with infinity numbers, 'inf' may no longer be used as a variable name. |
14.12.27 | Improved user interface: To better support keyboards without function keys, Alt+1..Alt+8 can be pressed instead of F1..F8 to change the scene style and Alt+9 (like F9) to calculate energies. |
14.12.10 | Fixed a problem with access permission errors in non-English Windows versions. |
14.12.6 | Improved macros and plugins: Atom selections involving only atom numbers have been speeded up significantly, some macros with loops run 100x as fast as previously. |
14.12.2 | New highlight: To celebrate the arrival of Intel's new top CPU Core i7-5960X, YASARA's molecular dynamics algorithms have been partly rewritten to better scale with 8+ CPU cores and 16+ threads. On the Core i7-5960X, the DHFR benchmark now runs at 160 ns/day (no GPU, PME, 8.0 A VdW cutoff, correct hydrogen masses, reproducible trajectory, CPU with 3.6 GHz, no turbo boost, 8 AVX registers). |
14.11.24 | New open access YASARA article, please cite this one for general molecular modeling applications: "YASARA View - molecular graphics for all devices - from smartphones to workstations", Bioinformatics (2014) 30 (20): 2981-2982. http://bioinformatics.oxfordjournals.org/content/30/20/2981.long |
14.11.19 | New feature: Molecular dynamics performance is no longer sensitive to exceeding certain force cutoff values, which was the reason for the non-integral default cutoffs like 7.86432 A or 10.48576 A in the past. The default cutoffs are now increased by 1.7% to 8.0 A (for (Y)AMBER) and by 0.1% to 10.5 A (for NOVA). While this small change has no impact on accuracy, it facilitates performance comparison with other programs (which often use an 8.0 A cutoff in benchmarks). |
14.11.12 | Improved macro: 'md_runbenchmark' displays a comparison graph with other CPUs. |
14.11.8 | Improved command: 'RandomSeed' sets a global random number seed for all operations that involve random numbers, e.g. assignment of initial atom velocities. |
14.11.5 | Fixed the B-factor formula shown in the documentation of the RMSF command, which accidentally scaled B-factors by 10. |
14.11.4 | Improved plugin: Creating animated GIFs is now also enabled in MacOS (File > Save as > Animated GIF), if you have ImageMagick installed as /usr/local/bin/convert. Contributed by Rob van der Kant. |
14.11.3 | New feature: The free YASARA View gets much better graphics performance, since the 'Processors' command to choose the number of CPU threads is now also available in YASARA View. |
14.10.27 | Improved command: The force 'Cutoff' can now be changed during a simulation without stopping it. |
14.10.22 | Improved Python interface: It is now possible to pass Python sets (which can be combined with logical operators) as selection arguments, see the updated section 'Selections > Yanaconda and Python help to define selection subsets and very complex selections'. Contributed by Jon T. Swanson. |
14.10.19 | Improved command: 'LabelRes' supports the new keyword 'CHIRALITYLD' to label amino acids with L/D according to their chirality. |
14.10.12 | New feature: YASARA's secondary structure analysis includes pi helices, following DSSP's alphabetically ordered helix classification 'G','H','I' for helices with hydrogen bonds to residues +3,+4,+5 (3-10,alpha,pi). |
14.10.5 | Improved command: 'SecStr' returns code 'I' for pi helices, and also returns the pi helix content. NOTE that this change is not entirely backwards compatible. |
14.9.28 | Improved support for large files and harddisks: XTC trajectories can now also grow to arbitrary sizes in Windows. |
14.9.21 | New feature: Text consoles no longer pop up in Windows when running MSMS to show surfaces, BLASTing etc. |
14.9.14 | Improved command: 'Duplicate' can duplicate molecules, residues and atoms, not just entire objects. |
14.9.8 | Improved macro: 'dock_run' can calculate the binding energy spread (average and standard deviation) for each cluster (set calcspread=1). |
14.9.2 | New feature: The docking result player 'dock_play' includes buttons to visualize also hydrophobic, pi/pi and cation/pi interactions during cluster analysis. |
14.8.28 | Improved macro language: Comments starting with '#' can be placed also after an instruction, not only at the start of the line. |
14.8.22 | Improved command: The 'pKaRes' documentation includes an example macro to predict pKa values for all snapshots in a simulation trajectory. |
14.8.19 | Improved experiment: 'Neutralization' allows to bypass the reassignment of protonation states after pKa prediction, just set the pH to -1 |
14.8.14 | New command: 'ListDir' gets the list of files that match a given wildcard, so that you can easily loop over certain files in a directory. |
14.8.3 | Improved macro: 'md_analyze' saves the last structure in the trajectory, YourStructure_last.pdb/.sce. |
14.7.17 | Improved command: 'SavePDB' detects non-standard residues with standard names and adds CONECT residues as needed. |
14.7.16 | New warning: If one of your own macros is still using the deprecated 3*1.33 fs timestep, YASARA will display a warning to use the new FixHydAngle command instead. |
14.6.23 | Fixed a potential problem with CONECT numbering in PDB files that appeared in version 14.5.1. Downloading an update is recommended. |
14.6.20 | Improved macro: 'dock_play' provides a new button 'Save this pose' to save the currently viewed complex as a PDB file. |
14.6.15 | Improved force fields: parameters for the noble gases He, Ne, Ar, Kr and Xe are now available by default. |
14.6.10 | Improved commands: 'Rotate' and 'RotAxis' can be used during a simulation, unless entire objects are rotated. |
14.6.5 | Fixed error messages about 'scl_distributenbistatic: Found only..' and 'sim_move: Water temperature invalid', as well as some other minor issues in the new MD algorithms released on May 1. Downloading an update is recommended. |
14.6.4 | New example macro to monitor dihedral angles during a simulation, bin the values and show the probability distribution. See docs of the 'Dihedral' command. |
14.6.3 | Improved macros: md_run* delete long peptide bonds and add internal ACE/NME capping groups instead of closing the gaps. |
14.6.2 | New example macro to monitor kinetic and potential energies (and other features) during a simulation, saving results to a file continuously. See docs of the 'Energy' command. |
14.5.28 | Improved command: The 'Y-parameter' of SaveMPG can be left 0, which tells YASARA to encode a movie with the same aspect ratio as the YASARA window. |
14.5.21 | Fixed an error message about 'Cubestart out of expected range'. |
14.5.16 | Improved the md_runbenchmark macro to run 25% faster, and also report 25% better results. |
14.5.6 | New workaround for Windows&Linux stack management problems that could crash YASARA. |
14.5.5 | Improved macro: 'dock_play' shows the results of receptor ensemble docking and virtual screening in order of binding energy. |
14.5.4 | Fixed a crash during homology modeling. |
14.5.1 | New highlight: YASARA's MD algorithms have been largely rewritten to boost performance. On an Intel Core i7 4770, this YASARA release reaches 81ns/day in the DHFR benchmark, which is almost 3x as fast as previous YASARA versions. |
14.4.28 | New CPU support policy: The new algorithms for much faster MD simulations require to drop support for the ancient Intel Pentium III and AMD Athlon XP CPUs (SSE only), sold between 1999 and 2003. SSE2 - introduced with the Pentium 4 in 2000 - is now the minimum requirement for MD simulations. YASARA View and YASARA Model still support these old CPUs, but you need to select the 'SSE' option explicitly on the download page. |
14.4.26 | New macros: 'md_runfast' and 'md_runmembranefast' pull all tricks to speed up MD simulations. This includes a 5fs timestep with constrained hydrogens and pairlist updates every 10 steps. |
14.4.24 | Fixed a potential error message about 'gl_ProjectionMatrix being deprecated' in the terminal from where YASARA is started. |
14.4.22 | New macro: 'md_runbenchmark' runs the dihydrofolate reductase (DHFR) benchmark and displays the result. This is especially helpful in MacOS 10.9, which currently has technical issues causing slowdowns if too many CPU cores are used or if graphics are shown. So you can potentially gain a lot of simulation performance by leaving one or two threads unused (Options > Processors) and running in text mode (-txt command line parameter). |
14.4.12 | Improved command: 'MouseWheel' accepts a new 'Reverse' parameter to undo Apple's reversed scrolling directions introduced in MacOS 10.7. Click Options > Input devices > Reverse wheel directions. |
14.4.10 | New feature: You can now drag and drop PDB files, YASARA scenes, YASARA objects (all three also .gz or .Z compressed) and YASARA macros, either on the YASARA window (Windows) or the YASARA icon (MacOS). |
14.4.8 | Improved plugin: Reporting bugs and requesting updates from the Help menu now works without sending emails, and thus also behind firewalls. |
14.4.7 | Fixed a problem in MacOS 10.9, where double-clicking on a file in Finder would launch an empty YASARA. You can now also double-click additional files in Finder to send them to an already running YASARA (if you double-click a YASARA scene, this will replace the current scene, but you can use the Undo button if it happened by accident). |
14.4.5 | New highlight: YASARA supports pair lists, which can be updated every Nth step, click Simulation > Timestep ('SimSteps' command). With N=10, simulations run 74% faster. |
14.3.22 | Improved experiment: 'Homology modeling' saves the target and template sequence profiles in compressed FASTA format, so that it's easier to load them in other programs. |
14.3.21 | New command line parameter: '-eta' enables thread affinities and thus binds threads to certain CPU cores. Simulations may run 1-5% faster, but on some broken combinations of kernels and GPU drivers also 50% slower. It is therefore disabled by default now (-dta parameter deprecated). |
14.3.20 | Improved commands: 'AlignPDBMol' and 'SaveAli' support a new compressed FASTA output format ('FASTAComp'), which stores the seed sequence at the top without gaps and may thus discards insertions from the aligned sequences. |
14.3.18 | Improved command: 'ShowWin' can show a 'ColorSelectionWindow' to let the user choose a rainbow or RGB color. |
14.3.16 | New feature: Plugins can include a 'ColorSelectionWindow' to let the user choose a rainbow or RGB color. |
14.3.12 | Improved command: 'Clean' accepts a new 'Skip' parameter to selectively skip some cleaning steps. |
14.3.11 | New highlight: YASARA supports the AVX2 vector instruction set, introduced with the Intel Haswell CPU architecture in summer 2013. MD simulations and many other functions run about 3 percent faster compared to AVX. |
14.3.9 | Improved command: 'SavePrep' accepts a new 'Reorder' parameter to prevent atoms from being reordered in the Prep file. |
14.3.8 | New command: 'DegFreedom' returns the degrees of freedom of the atoms, considering fixed atoms and constraints. Click Analyze > Geometry > Degrees of freedom (Dynamics+). |
14.3.1 | Improved command: 'ShowArrow' has a more useful 'DisFromAtom' parameter, which lets an arrow start or end at a certain distance from an atom, but now in the direction of the other atom instead of the coordinate system origin. |
14.2.20 | Improved selection language: The 'with distance', 'with minimum distance' and 'with maximum distance' operators exclude the self-hit, e.g. 'ListAtom SG with minimum distance from SG' lists the shortest cysteine bridge |
14.2.16 | Improved force field parameter assignment: AutoSMILES can now handle polymers that do not have any sp3 atoms in the backbone. |
14.2.12 | New command: 'CopyFile' creates a duplicate of an existing file |
14.2.8 | New highlight: A mixed multiple timestep algorithm allows to reach a 5fs timestep during MD simulations, check the docs of the TimeStep command for details. |
14.2.2 | New command: 'FixHydAngle' constrains certain critical bond angles involving hydrogens so that a large 5fs timestep can be reached during MD simulation. Click Simulation > Fix > Hydrogen angles. |
14.1.30 | Improved command: 'SaveESP' allows to save the electrostatic potential also when the cell is triclinic, and makes sure that the output is always right-handed |
14.1.29 | New feature: The homology modeling experiment combines manually provided templates with automatically identified ones. To avoid this feature, make sure that the maximum number of templates used equals the number of manually provided ones. |
14.1.27 | Improved command: 'ShowESP' can create contour surfaces of the electrostatic potential with arbitrary resolution and automatically chooses a good contour level if the 'Level' parameter is omitted. |
14.1.26 | New command: 'LoadESP' loads and visualizes an electrostatic potential in DelPhi format |
13.12.28 | Improved command: 'Energy' has a new keyboard shortcut (F9) to interactively calculate the energy during a simulation and display the results in the right simulation HUD. |
13.12.18 | New highlight: YASARA supports the FMA3 vector instruction set for 'fused multiply add operations', introduced with the AMD Piledriver CPU architecture in summer 2012 and the Intel Haswell CPU architecture in summer 2013. |
13.12.12 | Improved macro: The md_convert macro asks interactively for the trajectory formats to convert. |
13.12.5 | Improved command: 'FillCellObj' places solvent molecules with fewer clashes and provides improved step-by-step instructions for fillin the cell with custom solvents including mixtures. |
13.11.25 | Improved command: 'ShowGrid' can show the search grid cubes used by the SolvDensity command if Type=8. |
13.11.20 | New feature: Drawing balls, sticks and balls&sticks runs 80% faster if just two CPU cores are available (performance for 3+ cores stays the same). |
13.11.9 | Improved command: 'BuildSMILES' provides a new 'Sort' parameter to sort the molecules in the SMILES string, largest first. |
13.11.7 | Improved command: 'Load*' creates individual molecules even if the file format does not support them. |
13.10.25 | New highlight: YASARA supports the AVX vector instruction set, introduced with the Intel Sandy Bridge CPU architecture in spring 2011 and AMD Bulldozer CPU architecture in autumn 2011. MD simulations and many other functions run about 10 percent faster compared to SSE4. |
13.10.20 | New command: 'SystemTime' returns the current system time in milliseconds. |
13.10.5 | Improved command: 'LoadPDB' (unless the 'correct' flag is disabled) adds TER entries between hetgroups that should have been present in the PDB file but were omitted. This ensures that a single 'molecule' does not unexpectedly cover several ligands. Waters and metal ions are still treated as single 'molecules'. |
13.10.1 | Improved command: 'KinEnergy' now handled a speciality of YASARA's leapfrog integration algorithm and returns kinetic energies at the current time t (instead of t-dt/2) to match potential energies. The new 'CurrentTime' parameter changes this behavior. |
13.9.20 | Improved command: 'BuildRes' contains an example macro that rebuilds an all-atom model from Calpha only structures. |
13.9.18 | New command: 'BuildSMILES' creates a 3D molecule from a SMILES string, click Edit > Build > Molecule from SMILES string. |
13.9.13 | Improved command: The 'SavePNG' docs include an example macro that creates animated GIFs of rotating proteins in batch mode, from a list of PDB IDs. |
13.9.8 | New price for the YASARA Android tablet RamosW32: 175 EUR for customers in the EU, see www.yasara.org/android. |
13.9.4 | Fixed an issue in the 'Manometer' pressure control mode that affected systems with >65000 atoms and could cause the density to deviate by ~8%. This mode is *not* used by YASARA's standard macros, but if you enabled it manually in your own macro, please use 'SolvDensity' to check the solvent density. |
13.8.20 | New YASARA compatible Android tablets available: the Samsung Galaxy Tab 3 10.1 and the first Android tablet with 2 CPU cores: Asus MeMo Pad Full HD10 (screen resolution probably too high to be convenient). |
13.8.10 | Fixed an issue with the standard AMBER/Aqvist VdW parameters for Potassium, which have now been changed in all force fields to prevent unrealistic aggregation of KCl crystals at higher concentration, see J. Chem. Theory Comput. 2007, 3, 1851-1859 for details. If you manually chose KCl ions, please check the trajectory for aggregates. |
13.7.20 | New feature: YASARA Python plugins can launch YASARA Python modules that control YASARA, e.g. by communicating with a website and coupling YASARA to a browser. Check the docs at Plugins > Plugins can start additional programs that control YASARA |
13.7.10 | Fixed a bug in the preliminary example macro for qualitative prediction of point mutation effects on the binding energy (in the docs of the BindEnergy command). |
13.6.16 | New highlight: A new graphics engine now makes better use of many CPU cores and latest OpenGL functionality. If you have >=4 CPU cores, the speedup is 450% for balls, balls&sticks and sticks. For secondary structure (tubes/ribbons/cartoons) the speedup is up to 300% on AMD cards, and somewhat less on nVIDIA cards. |
13.6.15 | Improved graphics engine note: YASARA for Android already included the new graphics engine from the beginning, so updating YASARA for Android will not yield a speed improvement. |
13.4.21 | New highlight: YASARA for Android has been released, providing the most feature-complete molecular modeling and simulation environment on smartphones and tablets to date. Please visit www.yasara.org/android for movies and information about supported devices. |
13.4.18 | New feature: The CMBI spin-off company Bio-Prodict can cut your research time in half by integrating protein superfamily data with your protein structure, also directly inside YASARA. Click 'Help > Analyze protein families' for more details and videos. |
13.4.15 | New highlight: The 'YASARA molecular modeling tablet' is available, an Android tablet with YASARA preinstalled. 10.1 inch screen, 1 GB ram, 16 GB storage, on sale for 175 EUR. Please visit www.yasara.org/ramosw32 |
13.4.10 | New feature: The Neutralization Experiment provides an 'Ions' parameter to choose between various cations and anions to model ionic strength, the old 'NaCl' parameter is deprecated. |
13.4.8 | Improved user interface: Entering numbers that are out of the allowed range caused them to be marked red. |
13.4.2 | New feature: The ShowTab command can visualize 3D tables with a contour surface |
13.3.26 | New highlight: The 'Keyboard' command creates a virtual on-screen keyboard and makes YASARA fully touchable, offering a unique molecular modeling experience on the new Windows 8 tablets. Watch the YouTube movie at www.yasara.org/windows8. |
13.3.22 | Improved command: 'SaveXTC' accepts an atom selection to save only part of the soup to the XTC trajectory. |
13.3.18 | New feature: The help movie 'Working with YASARA' contains a section with detailed instructions about YASARA's new touch interface. |
13.3.10 | Improved macros: The docking macros no longer mention AutoDock's 'inhibition constant', it is now called 'dissociation constant' to avoid confusion. The values do not change. |
13.2.26 | New command: 'RandomSeed' sets the random number seed for Yanaconda's 'rnd' function, e.g. 'RandomSeed Time' ensures that you get different random numbers each time you run a macro. |
13.2.25 | Improved Python interfaces: Two dozen commands require fewer arguments when run from Python, since additional default values are now considered. |
13.2.24 | New feature: When running an MD using at most 50% of the processors on a hyper-threading enabled CPU, YASARA for Linux can run 30% faster. |
13.2.21 | Fixed a problem with red-cyan anaglyph stereo mode and improved YASARA usability in 10 small but helpful ways. |
13.2.10 | New feature: The standard macros check if YASARA has been run in text mode with the macro as command line argument. If yes, they exit YASARA when finished. |
13.2.9 | Improved macro language: The predefined variable 'RunWithMacro' indicates if YASARA has been run with the current macro as command line argument, and 'ConsoleMode' is >0 when YASARA is running in either fancy or plain text console mode without graphics. |
13.2.8 | New feature: Atoms can be constrained to their initial positions during a simulation with the improved AddSpring command, click Simulation > Add force field term > Spring to current position (Dynamics+). |
13.2.3 | Improved macros: Energy minimization is now performed by em_runclean.mcr and em_run.mcr, giving you the choice to clean the structure before or not. |
13.2.2 | Fixed issues that could prevent VINA and classic AutoGrid/AutoDock from starting on some computers, and a Windows mouse wheel problem. |
13.2.1 | Improved macros: The MD analysis macros md_analyze*.mcr provide a 'refsnapshot' parameter to specify which reference snapshot to superpose on. |
13.1.25 | New highlight: AutoDock VINA has been integrated into YASARA and is now the default choice for the docking experiment, providing highly accurate results significantly faster. Many thanks to Scripps Research Institute (Structure). |
13.1.20 | Improved command: 'StyleWin' accepts the new 'Win8' style to adapt YASARA's look to the new Windows 8. |
13.1.16 | New AutoDock version 4.2.5.1 included in YASARA. According to the AutoDock authors, this version can yield more accurate results due to a bugfix in desolvation energy calculations. We found almost no difference in practice. |
13.1.12 | New feature: 'LoadPDB' provides a 'SeqRes' flag to read the SEQRES sequence of PDB files, align it with the actual structure and add residues missing in the structure (due to a lack of X-ray density etc.) as single Calpha atoms with occupancy 0, shown in light grey in the sequence selector. An example macro shows how to turn these single Calphas into full residues. |
13.1.8 | New command: 'CopyStyleObj' transfers the visualization style from one object to others. Click View > Style atoms > Copy style. |
13.1.4 | Improved command: The 'MarkAtom' command accepts a new 'Zoom' parameter to set the initial size of the mark and returns the numbers of the marked atoms in the same order as they are set. |
12.12.24 | New highlight: The docking experiment allows to keep certain crucial active-site side-chains flexible during docking. To use this feature, provide the receptor as a *.sce or *.yob file and fix the non-flexible atoms (Structure). |
12.12.20 | Improved command: 'Del' supports the keyboard shortcuts <Ctrl>+<Del> or <Ctrl>+<Backspace> to delete with centering. |
12.12.16 | New command: 'PermitAccess' corrects the permissions of the YASARA folder, which is helpful if you copied YASARA from DVD. Click Help > Install > Set permissions. |
12.12.12 | Improved macro language: Yanaconda stops evaluation of logical expressions early if possible, allowing to write shorter code (see docs at Macros > Yanaconda supports the usual operators > Operators with minimum priority 1). |
12.12.8 | New feature: YASARA starts significantly faster since plugins no longer use 'CheckIfDisabled' unless absolutely needed. If not all operating systems are supported, this is now communicated with the 'PLATFORMS:' field in the header. |
12.12.1 | Improved command: 'AddRes' searches for the last residue of the requested type in the selected object before adding another one. |
12.11.25 | New highlight: The homology modeling experiment features a completely new and much more powerful hybridization algorithm to combine models from multiple templates. This includes fusion of domains and reliable replacement of bad segments. |
12.11.19 | Improved experiment: 'Homology modeling' replaces Nickel, Strontium, Barium and Cadmium with the closest standard metals for which Van der Waals parameters are available, instead of just deleting them. |
12.11.17 | Improved commands: 'AddBond' and 'ShowArrow' silently ignore pairs of atoms in different objects, as long as at least one bond/arrow can be created. This facilitates their use when dealing with NMR bundles. |
12.11.15 | Improved command: 'HUD' accepts a new 'FontSize' parameter to choose between small and normally-sized fonts in the HUD. Click Window > Head-up display. |
12.11.10 | Improved command: 'ShowMessage' is no longer length-limited, it can cover the full screen width and additionally turns into a scrolling message if the screen width is exceeded. |
12.10.28 | Improved commands: There is now an official boolean datatype for YASARA commands, which can be one of 'false, off, no, 0' or 'true, on, yes, 1'. |
12.10.20 | Fixed a problem in dock_runensemble.mcr that listed some hits multiple times in the log file and also caused dock_play.mcr to show identical clusters. |
12.10.10 | New feature: The current scene visualization style can be saved as default, click View > Style scene > Save as default. |
12.10.3 | Fixed a problem that could cause an error message 616 during docking or simulations and could affect bond orders in saved *.sce and *.yob files. Please update if you use versions 12.8.26 to 12.9.30. |
12.9.30 | New highlight: The PSSP database is available, which provides the homology modeling experiment with 'P'rofiles from 'S'equence- and 'S'tructurally related 'P'roteins for all templates, allowing to generate more accurate alignments. Make sure to set structprofile='yes' in any private copy of hm_build.mcr (Structure). |
12.9.25 | Improved command: 'ListConRes', 'ListConMol' and 'ListConObj' now consider entire residues, molecules or objects when calculating interaction energies ('Energy' parameter), and not just atoms closer than the specified cutoff. This yields much more useful results. |
12.9.20 | New support for building and simulating graphene layers, see the docs of the 'Force' command for an example. |
12.9.15 | Improved command: 'BuildAtom' accepts a new 'Copies' parameter to build more than one atom, click Edit > Build > Atom. |
12.9.10 | Improved experiment: Homology modeling corrects oligomers that are not ordered properly in the template PDB file and detects if oligomerization interfaces got lost during model building. |
12.9.5 | Improved macro: md_analyze.mcr makes it easier to add your own analysis, it is no longer needed to adjust table columns and the average values are calculated automatically. |
12.9.1 | Improved command: 'LoadPDB' runs infinitely faster when loading gigantic structures with more than a million atoms. |
12.8.29 | Improved selection language: 'SCwithBB' selects side-chain atoms incl. bound backbone atoms (usually Calphas, but also N of prolines), which makes it easy to show side-chains. |
12.8.26 | New highlight: The 'ReplaceRes' command performs a wide range of replacement operations, like transferring a loop between proteins, creating fusion proteins or extending nucleic acids. Click Edit > Replace (Model+). |
12.8.22 | Improved help movie: The 'Domain Replacement' movie explains the new 'ReplaceRes' command, in addition to the step-by-step method for experts. |
12.8.18 | Improved command: 'AddCap' can add C-terminal NH2 caps, which lack the methyl group of NME caps (Model+). |
12.8.14 | Fixed the PDBFinder2 plugin at View > Color > Residue by feature, which stopped working after a CMBI web server change. |
12.8.10 | New feature: When the XTC trajectory format is chosen, the md_* simulation macros additionally save a single restart file in SIM format (which includes velocities and thus allows for a smoother restart). XTC trajectories no longer contain a number in the name, existing ones are renamed automatically (Dynamics+). |
12.8.6 | Improved macros: The md_analyze* and md_play macros automatically detect the trajectory format, so it is no longer required to manually choose between SIM and XTC (Dynamics+). |
12.8.2 | New command: 'RenameFile' moves a file to a different location. |
12.7.28 | Improved macro: dock_runensemble.mcr has been improved to analyze thousands of docking runs quickly, without exhausting memory, also if the ligand is large. |
12.7.24 | Improved macro language: Critical parts of Yanaconda have been reimplemented to improve performance, especially operations with long lists run 20x as fast as previously. |
12.7.20 | Improved Linux plugin: Sampling with CONCOORD now uses the latest version 2.1.1 in 64-bit Linux distributions. |
12.7.18 | New feature: The homology modeling experiment stores the length of loops in the atom's occupancy fields using the formula 'Occupancy=1-LoopLength*0.01'. Coloring a model by occupancy thus visualizes the length of modeled loops, and it becomes trivial to delete unreliable loops beyond a given length. |
12.7.16 | New highlight: The 'ShowInt' command visualizes hydrophobic, pi-pi and cation-pi interactions. Click View > Show interactions > Others. |
12.7.12 | Improved commands: Objects created by 'ShowCon', 'ShowIonSites', 'ShowSurf Static' and 'ShowCavi' are now moved together with their parent object when grabbed. |
12.7.9 | New command: 'ListInt' lists hydrophobic, pi-pi and cation-pi interactions. Click Analyze > Interactions > Others (Model+). |
12.7.6 | Improved commands: 'ListCon' and 'ShowCon' accept a new 'Occluded' parameter. If set to 'no', contacts are ignored if other atoms are between the contacting ones. |
12.7.3 | Improved macro: The ligand explorer at View > Style scene > Cartoon & ligand shows hydrophobic, pi-pi and cation-pi interactions. |
12.6.30 | Improved command: 'ColorPar' accepts the new color schemes 'Hydrophobic', 'PiPi' and 'CationPi' to set the default colors uses when showing interactions of the same same. Click View > Color > Parameters. |
12.6.27 | New graphics engine for protein secondary structure that works around problems in Intel HD graphics drivers, achieving a 150x speedup. AMD Radeons run 50% faster. |
12.6.24 | Improved command: 'LoadJPG' supports JPEG images in grayscale and CMYK format. |
12.6.21 | Improved command: 'ShowCon' to show contacts is now available in also in YASARA View. |
12.6.18 | Improved commands: 'SaveTbl' and 'LoadTbl' accept a 'NameFormat' parameter to choose other atom naming conventions in restraint files than the XPLOR default. This is reflected by the new 'nameformat' parameter in nmr_setdefaults.mcr |
12.6.15 | Improved NMR structure determination: Cysteine bridges are treated as distance restraints during the initial folding step. |
12.6.11 | Improved graphics engine: balls, balls&sticks and sticks with non-standard colors are drawn up to five times faster. |
12.6.7 | Improved macro: 'dock_runensemble' performs the final analysis much faster, with marginal memory usage (Structure). |
12.6.3 | New highlight: The 'Twist' command bends and winds proteins to maximize the number of structurally aligned residues, for example to create sequence profiles for homology modeling. Click Analyze > Align > Twist (Structure). |
12.6.1 | Improved command: 'AddBond' accepts a new 'LenMax' parameter to add only bonds that are shorter than the specified cutoff. |
12.5.25 | New command: 'Name3' converts a protein sequence in 1-letter code to a list of residue names in 3-letter code. |
12.5.20 | Improved command: 'SavePDB' creates SSBOND and LINK records for cysteine bridges and non-standard bonds between residues. |
12.5.15 | New workaround for a bug in NCBI's BLAST+ that could list at most 500 hits (Structure). |
12.5.12 | Improved experiment: 'Homology modeling' includes 15 new tweaks to increase accuracy (Structure). |
12.5.10 | New feature: The homology modeling experiment now (by default) uses re-refined templates from the PDB_REDO database if structure validation indicates that they are better than the original PDB structure (Structure). |
12.5.7 | Improved MD algorithm when using long-range electrostatics: less memory usage and 4% faster (Dynamics+). |
12.5.5 | New feature: The 'LoadPDB' command accepts a parameter 'download=best' which tells YASARA to download re-refined PDB files from the PDB_REDO database if WHAT IF structure validation indicates an improvement, missing CONECTs and reordered atoms in PDB_REDO are corrected automatically. |
12.4.25 | New feature: The NMR macros support explicit solvent refinement in DMSO, the macro nmr_refinewater has been renamed to nmr_refinesolvent. To enable DMSO, change 'solvent' in nmr_setdefaults.mcr. The 'correctoldcisiso' tunes the correction of cis-peptide bonds and wrong isomers (NMRModule). |
12.4.21 | Improved command: 'MarkAtom' accepts atom numbers in a new order to match angle & dihedral selections. |
12.4.17 | New feature: The AlignPar command accepts an 'AngleMax' parameter to specify the maximum allowed angle between the CA-CB bonds of structurally aligned residues. |
12.4.13 | Improved commands: 'RestEnergy' and 'RestViolAll' return summed up results for all selected objects (NMRModule). |
12.4.9 | Improved selection language: Selecting atoms by alternate location indicator supports ordinal names, e.g. 'DelAtom AltLoc !first' keeps only the first atom with a given name in the residue. |
12.4.5 | Improved structural alignments: A virtual Cbeta position is calculated for glycine residues to ensure that only glycines with matching backbone conformation are aligned. |
12.4.1 | New highlight: The 'MakeImageObj' command accepts a new 'Depth' parameter, that extrudes textured 3D objects from 2D images. See second example macro at 'MakeImageObj' (Model+). |
12.3.29 | Improved selection languages: The unique IDs of residues and molecules are now 'Res Atom X' and 'Mol Atom X', which resolves one or two potential pitfalls. |
12.3.28 | New feature: YASARA now uses NCBI's new BLAST+ suite, which does not fail occasionally ('BLAST failed with error 1') and runs much faster, which also speeds up secondary structure prediction and homology modeling (Structure). |
12.3.25 | Improved disk usage: YASARA Dynamics for example now needs 196 MB instead of 257 MB disk space. |
12.3.22 | New workaround for a Linux Mesa OpenGL driver bug that caused an 'X error of failed request' message on startup. |
12.2.19 | Improved macro: 'md_analyzesecstr.mcr' runs much faster, and allows to choose the maximum number of columns in the secondary structure plot (Dynamics+). |
12.3.16 | New feature: The homology modeling experiment accepts a 'LoopLenMax' parameter to skip modeling of long loops (which cannot be predicted reliably) (Structure). |
12.3.13 | Improved command: 'SaveAli' can also return alignments like 'Align' instead of just saving them. This required a non-backwards compatible reordering of the parameters, macros using 'SaveAli' may have to be adapted (Model+). |
12.3.10 | New command: 'AddAngle' enforces a certain angle between three selected atoms by adding an angle term to the current force field. Click Simulation > Add force field term > Angle (Dynamics+). |
12.3.7 | Improved energy function for hydrogen bonds: A few more bonds are found by considering the size of the atoms covalently bound to the acceptor. |
12.3.4 | New command: 'AddDihedral' enforces a certain dihedral between four selected atoms by adding a dihedral term to the current force field. Click Simulation > Add force field term > Dihedral (Dynamics+). |
12.3.1 | Improved macro: 'nmr_analyze.mcr' includes a list of violated restraints in the analysis (NMRModule). |
12.2.22 | New highlight: The 'Inflate' command generates 3D coordinates from nonsense, 1D or flat 2D input structures. The 'Deflate' command converts 3D coordinates back to 2D and allows to style the resulting flat molecules like structural formulas. Click Edit > Geometry. Contributed by OpenBabel. |
12.2.20 | New feature: The new docking macro 'dock_runscreening.mcr' performs virtual screening by docking multiple ligands against the same receptor. See the docs at Recipes > Docking > Virtual screening (Structure). |
12.2.17 | Improved workaround for a bug in Windows that could cause problems when downloading the new UniRef90 BLAST sequence database, e.g. for homology modeling. |
12.2.15 | New feature: 'ShowArrow' accepts a 'Visualize' parameter to draw arrows only between bound atoms, thus visualizing bonds and optionally bond orders. |
12.2.10 | Improved console: Ctrl+A selects the entire content and copies it to the clipboard. |
12.2.9 | New OpenBabel version included, it delivers support for 27 additional molecular file formats, summing up to 135 in total. |
12.2.8 | Improved experiment: 'Homology modeling' detects if N-glycosylation sites get lost and deletes the corresponding sugars (Structure). |
12.2.3 | New plugin: Click 'View > Style scene > Cartoon & ligand' to visualize ligands and their binding residues incl. hydrogen bonds, and 'View > Color > Carbons per object' to apply a color gradient to carbons in different objects. |
12.2.2 | New command: 'Download' retrieves a file from the Internet and saves it locally. |
12.2.1 | Improved selection language: The keywords 'Name' and 'Number' allow to select atoms and residues with names that look like numbers and vice versa. See Selections > Names and numbers with unusual characters can be tagged and quoted. |
12.1.29 | Improved experiment: 'Morphing' has been reimplemented, it can now handle periodic boundaries properly, and provides more reliable morphing strategies for unreliable targets configurable with the extended 'MorphForce' option (Dynamics+). |
12.1.24 | New command: 'ListImage' lists all currently defined images. |
12.1.19 | New highlight: The new NOVA force field has been released, which is more accurate, faster, can automatically parameterize organic molecules and supports multiple CPU cores (Dynamics+). |
12.1.17 | Fixed a problem at the interface between YASARA and AutoDock which could cause suboptimal docking results, depending on ligand flexibility. Please update (Structure). |
12.1.10 | Fixed a problem in the NMR water refinement macro nmr_refinewater.mcr, which focused on the first ensemble member. Please update (NMRModule). |
12.1.6 | A new Models@Home version with CPU multi core support has been released. |
12.1.4 | Fixed a problem from version 11.12.31, where downloading BLAST databases could sometime fail with an error message 706, complaining about size mismatch. |
12.1.2 | Improved command: 'BLAST' performs a PDB-BLAST when searching the PDB with more than one pass (Structure). |
11.12.31 | New highlight: Two new BLAST sequence databases are available: 'pdbc' (the sequences extracted from the PDB coordinate section, which are more useful than the usual SEQRES sequences), and UniRef90, a non-redundant set of all known protein sequences for profile generation (Structure). |
11.12.28 | Improved command: 'BLAST' no longer supports UniProt and TrEMBL searches, since these databases are very redundant and have grown too large to be handled conveniently, use UniRef90 instead. The 'Update' flag is no longer needed and has been removed (Structure). |
11.12.26 | New command: 'SaveESP' saves the electrostatic potential calculated using Particle Mesh Ewald or Poisson-Boltzmann aproaches in Delphi format. Click File > Save as > Electrostatic potential map (Dynamics+). |
11.11.25 | New feature: Yanaconda plugins have full access to selections made in the windows specified in the triple-quote comment at the top of the plugin. See the docs at Plugins > Yanaconda plugins can access a number of predefined variables. |
11.11.23 | Improved command: 'Clean' fuses 'residues' consisting of single atoms, which are sometimes generated by small molecule modeling programs that do not have a concept of residues (Model+). |
11.11.22 | Improved plugins: Plugins hooked into one of the context menus can be rerun quickly by holding down Alt or Tab. |
11.11.21 | New feature: The 'Fog' command can exactly specify the fog range and choose between dynamic and static fog, which can act as a smooth clipping plane, e.g. when creating journal figures. Click View > Lighting > Set fog range. |
11.11.15 | Improved experiment: 'HomologyModeling' delivers slightly improved alignment accuracy, especially when long non-aligned target overhangs are present. |
11.11.10 | Fixed a bug in the 'SampleDih' command present since version 11.1.27 which did not always use the selected sampling method. |
11.11.8 | Improved command: The 'BallStickRadius' documentation includes an example macro showing how to build transparent balls&sticks. |
11.11.7 | Improved commands: All loop modeling functions (BuildLoop, SampleLoop, OptimizeLoop, Homology modeling) deliver increased accuracy. |
11.11.6 | Improved command: 'ShowCone' accepts an 'Alpha' parameter to show transparent cones, pyramids, cylinders and prisms. |
11.11.4 | New feature: Plugins can define custom windows with freely placed widgets, see Plugins > Plugins must stick to format conventions > The menu structure is enclosed in a triple-quote comment > CustomWindow. |
11.11.2 | New highlight: The 'ShowWin' command allows macros, plugins and scripts to obtain user input on the fly. User interface windows can be designed freely by arranging widgets like input boxes, lists, checkboxes and radiobuttons. |
11.10.25 | Improved plugins: The window nomenclature has been changed to common standards. The 'PopUpMenu' is now called 'SubMenu', the 'SwitchBoxMenuX' is called 'RadioButtonWindow', and except for 'PullDownMenu' and 'ContextMenus', all other 'Menus' have been renamed to 'Windows', since these were not really menus. The terminal numbers have been removed: TextInputWindow instead of TextInputMenu4. Note that selection.radiobutton starts counting at 1, not 0 like the old selection.switchbox. |
11.10.20 | New feature: When simulating without PME/long-range electrostatics, an improved switching function is applied to water-water interactions which increases simulation stability. |
11.10.15 | Improved command: 'BLAST' can order PDB hits by PDBFinder2 3D structure quality, so that the best modeling templates are ranked first. |
11.10.10 | New feature: The file 'yasara.def' has been updated with multiple topologies per amino acid, which enables pH-dependent protonation states also for the N- and C-termini of proteins, as well as single amino acid residues. |
11.10.5 | Improved commands: BuildRes, AddRes and BuildMol consider the current pH when building or adding amino acid residues. |
11.10.1 | New feature: When printing text to the HUD, an image or the secondary window, clickable 'action links' can be included that perform any action of choice, see the docs of the 'Print' command. |
11.9.28 | Improved force fields: The element Boron is now automatically supported by all force fields. |
11.9.24 | New command: 'ListBond' lists bonds between selected atoms, including bond order and bond length. Click Analyze > List > Bond. |
11.9.20 | Improved graphics engine: When showing proteins with lots of (throusands of) hydrogen bonds, YASARA runs more than twice as fast as previously. |
11.9.18 | New force field for beta testing: 'NOVABeta' will soon replace the current NOVA force field, see www.yasara.org/novabeta.pdf for details. |
11.9.10 | Improved experiment: 'Homology modeling' can keep unusual amino acids from the template if the target sequence contains an 'X' at the corresponding position. |
11.9.1 | Fixed an infinite hang of the Theseus program in MacOS 10.7 (used by the SupMulti command and homology modeling experiment). |
11.8.20 | New feature: Bond order 2.5 (as in nitric oxide) is supported by commands like 'AddBond' and 'SwapBond', visualized in lime green color. The symbol is ';', e.g. N;O. |
11.8.15 | Improved experiment: 'Docking' supports a 'SetupOnly' parameter to use YASARA for docking setup only (PDBQT files, grid parameter file) and skip the actual docking. |
11.8.10 | New workaround for an Intel HD graphics driver bug (Sandy Bridge CPU) in Windows (version 8.15.10.2509 and earlier). |
11.8.5 | Improved plugin: YASARA can download re-refined PDB files from the PDB_REDO database, click File > Load > PDB file from Internet. Contributed by Robbie Joosten. |
11.7.20 | Improved experiment: The homology modeling report contains hyperlinks to Uniprot, the final alignment is also saved in FASTA format with extension 'alignfinal.fasta' |
11.7.15 | Improved command: the default 'pH' on startup has been changed from 7.0 to the physiological value 7.4, also in all macros like md_run. This ensures that phosphates are completely dissociated by default. |
11.7.10 | Improved atom and bond type assignment in MOL2 export filter. |
11.6.16 | Fixed a problem from version 11.6.13, which slowed down YASARA over time and reduced available memory. |
11.6.13 | Improved commands: 'AddHyd' and 'Clean' more sensibly consider the presence of metal ions when adding missing hydrogens, also without running 'OptHyd' later. |
11.6.12 | Improved macro: 'md_analyze' can calculate and show radial distribution functions. |
11.6.7 | Improved experiment: 'NMRFolding' accepts a 'RandomSeed' parameter to calculate a certain ensemble subset ('start' parameter) |
11.6.1 | Improved commands: When calling 'LogAs' and 'RecordLog' from a Python module, it is now guaranteed that the full output is logged. |
11.5.22 | New feature: The commands 'GDT','Sup','SupMulti' and 'RMSD' provide an improved 'Match parameter' to precisely define which properties should be matched. |
11.5.18 | Fixed a homology modeling alignment problem with templates consisting of large and small domains fused together. |
11.5.14 | Improved macro: 'nmr_analyze' calculates the model quality Z-score, the RMSD from the average structure, as well as ensemble average values of all results. |
11.5.11 | New feature: The commands 'LoadYOb' and 'SaveYOb' can save polygon meshes like static surfaces or solids. |
11.5.6 | Improved plugin: OpenOffice/PowerPoint presentations can be converted to YASARA macros also in MacOS (OpenOffice3 required), click Options > Macro & Movie > Import movie. |
11.5.3 | News: YASARA appears on Belgian television helping cancer research: www.robnet.be/nieuws/doorbraak-kankeronderzoek |
11.5.1 | Improved command: 'Optimize' can now properly optimize side-chains with attached external residues, like glycosylation sites. |
11.4.17 | New highlight: YASARA provides new means to create interactive user interfaces from plugins or macros, including support for Linux touch screens as shown in this YouTube movie: www.youtube.com/watch?v=7WDOapSPe-Y |
11.4.16 | New feature: The md_play macro employs the new user interface capabilities to provide an interactive MD trajectory player (Dynamics+). |
11.4.15 | New command: 'MakeWin' creates a second window that can be filled with text and buttons, and can be used to support a touchscreen (Linux only,Model+). |
11.4.14 | New feature: The dock_play macro employs the new user interface capabilities to provide an interactive docking pose and docking cluster player (Structure). |
11.4.13 | New feature: 'ShowButton' can show buttons also in the HUD, in images or in a secondary window, and perform certain actions when the button is pressed. |
11.4.12 | Improved plugins: The documentation chapter "Python plugins can create interactive user interfaces" provides an example plugin that creates clickable buttons at various locations. |
11.4.11 | New command: 'MakeImage' creates a new image, fills it with a specified color gradient and redirects printing to it (Model+). |
11.4.10 | New feature: To speed up Python plugins and scripts, they can no longer use Yanaconda's explicit evaluators. These were sometimes used as a workaround before YASARA Python commands learned to return results in version 9.1.11, but are no longer needed now. |
11.4.9 | New command: 'PrintWin' redirects printing to the second window created previously with 'MakeWin' (Linux only,Model+) |
11.4.8 | Improved command: 'PosText' can position true type fonts in pixel coordinates when printing to the HUD, images or a secondary window (Model+). |
11.4.7 | New command: 'PrintImage' redirects printing to an image created or loaded previously (Model+). |
11.4.6 | New command: 'ShowURL' opens any URL in the web browser, which is helpful when combined with the new 'ShowButton' command. |
11.4.5 | Improved command: 'PrintHUD' no longer clears the HUD, this can now be done with the 'FillRect' command (Model+). |
11.4.4 | New command: 'FillRect' draws or clears a rectangle in the HUD, the secondary window, or an image (Model+). |
11.4.3 | Improved command: 'Font' can set fonts for printing to the HUD, images or a secondary window, including a monospaced font (Model+). |
11.4.2 | Improved command: 'Go' accepts a 'GoPar' parameter, which becomes a Yanaconda variable when the jump is executed. This helps button creation. |
11.4.1 | Improved macros: The energy minimization and docking macros now optimize the hydrogen bonding network (Structure). |
11.3.30 | Improved command: 'HUD App' shows the application specific HUD created with 'PrintHUD', for example the MD trajectory player (Model+). |
11.3.25 | Improved experiment: The homology modeling reports lists alignment features like percentage sequence identity and similarity. |
11.3.22 | New highlight: The command 'AddDisp' accumulates atomic displacements, the 'DCCM' command calculates the dynamic cross-correlation matrix from the collected data to analyze correlated motions in proteins. The md_analyze macro visualizes the DCCM. |
11.3.18 | Improved macros: The MD analysis macros provide a 'firstsnapshot' parameter to skip an equilibration period. |
11.3.14 | Fixed a problem in the Yanaconda macro language when passing lists longer than 172 elements to a user-defined function. |
11.3.10 | New workarounds for five problems in Intel's Mobile 965 Express graphics chip driver, including a crash on startup. |
11.3.2 | Improved command: 'SwapAtom' returns the numbers of the newly added hydrogens, which makes it very easy to build molecules automatically in a macro. |
11.2.25 | Newly tuned parameters to calculate solvation energies yield slightly more accurate results for the SolvEnergy methods 'BoundaryFast' and 'Empirical'. |
11.2.20 | Improved command: 'AddHyd' returns the numbers of the newly created hydrogens. |
11.2.18 | Fixed a problem from 11.2.15: Sometimes the 'File > Load' selection menus could hang in an infinite loop. |
11.2.14 | New highlight: The 'AlignAtom' command provides various methods to structurally align small molecules like ligands. Click Analyze > Align > Based on structure: Atoms (Model+). |
11.2.12 | Improved commands: 'CorrectCis' and 'CorrectIso' accept an 'Old' flag to only correct newly formed cis-peptide bonds and wrong isomers, but leave existing (presumably correct) ones untouched. The ordering of the 'Proline' flag changed, please check scripts and macros that use 'CorrectCis'. |
11.2.10 | New feature: Adding your own residues for building has become much easier, see the BuildRes documentation. |
11.2.8 | Improved user interface: You can click 'File > Load recent' to quickly reload any of the recent files. |
11.2.6 | New feature: 'Check' supports a new 'ModelQuality' check, which is the weighted average of the Dihedral, Packing1D and Packing3D checks to yield a single model quality value. Click Analyze > Check (Structure+). |
11.2.4 | Improved macro: Energy minimization with em_run.mcr corrects cis-peptide bonds and wrong isomers that are newly formed due to conformational stress, instead of just warning about them. |
11.2.2 | New feature: The homology modeling experiment stores the model quality in the B-factor field, to make coloring by quality trivial. |
11.2.1 | Improved experiment: 'HomologyModeling' supports a 'RequireRes' parameter to discard models that do not cover selected absolutely required target residues. |
11.1.27 | New feature: Sander Nabuurs released the Fleksy Docking program, which combines YASARA and FlexX for induced fit docking. Visit www.cmbi.ru.nl/software/fleksy for details. |
11.1.25 | Improved 3D red/cyan anaglyph stereo quality, especially for magenta colors. |
11.1.23 | New command: 'CompoundMol' sets or gets the PDB compound name for selected molecules. Click Edit > Name > Compound. |
11.1.19 | Improved command: 'SolvEnergy' can calculate solvation energies individually for selected units (except for the PBS method). |
11.1.17 | New command: 'Bound' confines a specified value to a given interval, which can shorten Yanaconda macros considerably. |
11.1.15 | Improved command: 'ShowArrow' accepts a 'DisMax' parameter to show only arrows between close atoms. |
11.1.10 | Improved command: 'SaveWOb' can now also save individual atoms shown as balls or sticks. The two new parameters 'Level' and 'BallZoom' set the tessellation level and ball zoom factors, respectively. |
11.1.7 | Improved plugin: The oligosaccharide builder supports both fructose forms: -pyranose and -furanose. |
11.1.3 | Improved macro: Energy minimization with em_run.mcr outputs the RMSD obtained during minimization. |
11.1.2 | New highlight: The 'Stereo RedCyan' command activates a GPU accelerated high-quality anaglyph stereo mode that tricks the human brain into seeing full color and enables stereo everywhere, also on notebooks. All letters from us now include red-cyan glasses. Click Window > Stereo > Red&Cyan, high quality (Model+). |
11.1.1 | New command: 'SaveWOb' saves selected objects in Alias Wavefront Obj format for use by 3D graphics applications like 3D Studio Max. Click File > Save as > Wavefront object (Model+). |
10.12.19 | Fixed the AlignPDBMol command to cope with the latest alignment format change at the RCSB web server. |
10.12.17 | Improved command: 'TypeBond' accepts a 'HydMissing' parameter to assign bond types differently whether hydrogens are potentially missing or not. |
10.12.12 | New highlight: The homology experiment creates better alignments using sequence profiles, that can optionally be augmented with structure-based profiles of related template structures (structprofile parameter in hm_build.mcr). |
10.12.11 | New help movie: '2.7. Advanced GPU Effects' demonstrates all the features of YASARA's new graphics engine and how to use them in your own animations. |
10.12.10 | Improved ray-tracing of alpha helices with elliptical cross-sections, which previously showed artifacts at the edges. |
10.12.9 | New feature: The 'TempCtrl' command's method 'Reassign' now employs a Lowe-Andersen thermostat, as a potential alternative to the default time-averaged Berendsen thermostat. |
10.12.8 | Improved experiment: 'HomologyModeling' supports a 'FixModelRes' parameter to fix selected conserved side-chains to the original conformation in the template. |
10.12.7 | New command: 'BuildSymRes' builds missing residues using knowledge from symmetry related members of an oligomer. Click Edit > Build > Symmetry related residues. |
10.12.6 | Improved experiment: 'HomologyModeling' can close gaps (caused by missing X-ray density) by copying residues from other oligomer members. |
10.12.5 | New command: 'PolygonPar's 'Smoothness' parameter activates phong shading and hardware tessellation, the 'Reflection' parameter defines how strongly objects reflect the environment (sky sphere or background color and optionally your face saved as yasara/jpg/myphoto.jpg). Click Effects > Polygon appearance > Reflection. Contributed by Jacobus van Meel. |
10.12.4 | New highlight: The 'ShowSkySphere' command loads six cube texture maps and creates a spherical projection at infinite distance, which is reflected by the objects in the scene. Click Effects > Show solid > Sky sphere. |
10.12.3 | Improved macros: md_run, md_runmembrane and md_runsteered can stop the simulation after a given number of picoseconds ('duration' parameter) or when the steering distance exceeds a certain value ('enddis'). |
10.12.2 | New command: 'WebTimeout' sets the timeout for internet connections, which helps at remote connections with slow internet access. Click Options > Internet > Connection timeout. |
10.11.25 | Fixed a potential error message that could stop PsiPred secondary structure prediction in Windows (also during the homology modeling experiment). |
10.11.22 | Improved plugins: Custom options can be added to the new 'SelectionContextMenu', see Plugins > Plugins must stick the format conventions > The menu structure |
10.11.19 | Improved command: 'Processors' supports up to 32 CPU cores. |
10.11.16 | Improved plugins: yasara.workdir contains YASARA's current working directory, so that plugins can save data there |
10.11.12 | Improved command: 'LoadPDB' can read PDBQT files. |
10.11.8 | New highlight: The 'Select' command introduces a new selection mechanism, that also permits to interactively select units within a rectangular box, arbitrary area or 3D sphere. Commands can then be applied directly to the selection. Click Edit > Select. |
10.11.7 | New feature: If the final selection unit is omitted (e.g. 'Color yellow') and if atoms have been permanently selected, then the command is applied to this selection only. See Selections > Possible final selection units. |
10.11.6 | Improved help movie: 'Welcome to YASARA' got a visual makeover and explains the new selection mechanism. |
10.11.5 | New command: 'SelectArea' interactively selects units within an arbitrary area. Click Edit > Select > in arbitrary area. |
10.11.4 | Improved user interface: Interactive selection icons have been added to the top menu line. |
10.11.3 | New command: 'SelectBox' interactively selects units within a rectangular box. Click Edit > Select > in box. |
10.11.2 | New highlight: The 'SecStrPar' command controls a secondary structure morpher, which can seamlessly interpolate the secondary structure between realistic (close to Calpha) and idealistic (perfectly straight strands and helices). Click View > Show secondary structure > Perfection. |
10.11.1 | New command: 'SelectSphere' interactively selects units within a sphere around other units. Click Edit > Select > in sphere around. |
10.10.31 | Improved selection language: 'selected' and '!selected' match all currently (not) selected atoms. |
10.10.30 | New context menu: Right-click on any selected (not marked) atom to modify the selection. |
10.10.29 | New command: 'Unselect' unselects atoms that have been permanently selected before. Click Edit > Unselect. |
10.10.28 | Improved experiment: 'Homology modeling' provides a new 'TemplateExList' parameter to exclude a list of template PDB IDs. |
10.10.27 | Improved user interface: There is now a visual difference between rectangular check boxes (which can be checked individually) and round radio buttons (which permit only a single selection). |
10.10.26 | Fixed an error message 'Atom name "scale" is longer than 4 characters' when manually adding the cell, and OpenGL shader compilation errors raised by some drivers. |
10.10.25 | Improved experiment: 'Homology modeling' recalculates alignment scores instead of using those returned by PsiBLAST, which may have consistency problems. This improves template ranking. |
10.10.24 | New highlight: YASARA Biosciences purchased a license of David Jones' PsiPred program, which now delivers more accurate secondary structure prediction in the homology modeling experiment (Structure). |
10.10.23 | Improved user interface: The maximum path length in file input fields has been doubled to avoid a "Path too long" message. |
10.10.22 | Fixed a crash at the beginning of the 'Welcome to YASARA' help movie on some old graphics chips. |
10.10.19 | Improved command: 'PredSecStr' provides a new 'Method' parameter to choose between the PsiPred and DSC secondary structure prediction methods (Structure). |
10.10.16 | New highlight: YASARA's graphics engine now uses OpenGL shaders to fully exploit the power of your GPU. Click Effects > Polygon appearance to activate exact phong lighting and optionally hardware tessellation, which lets the GPU increase the geometric details. Contributed by Jacobus van Meel. |
10.10.13 | Improved experiment: AutoDock now includes default parameters for almost all chemical elements including commonly found ions like Sodium or Potassium. |
10.10.12 | Improved sequence searches: The built-in BLAST has been updated to the latest version 2.2.24. |
10.10.10 | Improved Python interface: The functions 'Load' and 'Save' provide an interface to OpenBabel file format conversions |
10.10.7 | Improved command: 'Font' supports two new parameters 'Alpha' and 'DepthAlpha' to set the transparency of front, back and side-faces. |
10.10.5 | Improved user interface: The scene content browser in the top right HUD keeps the view even if atoms are modified. |
10.10.4 | Improved command: 'Clean' deletes 'TER' entries between covalently bound residues. |
10.10.2 | Improved command: 'Clean' merges covalently bound residues with the same ID (residue name, number, insertion code, molecule name). |
10.9.29 | New highlight: The macro 'dock_runensemble' docks ligands against a flexible receptor ensemble, each with alternative high-scoring side-chain rotamers. YASARA's AutoDock has been upgraded to the latest version 4.2.3, including an important Windows bug fix that affected docking results in large cells. |
10.9.27 | Improved command: 'ColorPar SecStr' accepts the new targets 'HelixInside', 'SheetSide' and 'Gap' to assign separate colors to the inside of alpha helix ribbons, the narrow side of beta strands and the dots that bridge gaps. Click View > Color > Parameters > Secondary structure. |
10.9.25 | New feature: The 'SecStrPar' command offers a 'Gaps' parameter to change the way how structural gaps (artificially long peptide bonds) are visualized: either open, dotted or closed. Click View > Show secondary structure > Gaps. If you used 'SecStrPar' in a macro or script, you may have to adapt it to the new format. |
10.9.23 | Improved command: 'SecStrPar' offers a 'ColTrans' parameter to switch between sharp and smooth secondary structure color transitions. Click View > Show secondary structure > Color transition. |
10.9.21 | New highlight: The 'SecStrPar' command offers a large number of new options to change the secondary structure style, click View > Show secondary structure > Appearance. Jacobus van Meel contributed elliptical and barbell helix cross-sections, click View > Show secondary structure > Cross section. |
10.9.20 | Improved command: 'FillCellObj' accepts a new 'RandomOri' parameter to randomize the orientations of the objects created to fill the cell. |
10.9.19 | Improved selection language: the 'with arrow to' operator selects atoms which are connected with arrows, e.g. pseudo bonds between metal ions. |
10.9.17 | Improved command: 'SwapAtom' accepts two parameters 'UpdateBonds' and 'UpdateHyd' to selectively update bonds and hydrogens. The old combined 'Update' flag is deprecated and unfortunatly no longer supported in Python. |
10.9.15 | Fixed a raytracing problem, where slightly incorrect colors of some polygons caused a non-smooth appearance. |
10.9.9 | Improved command: 'Align' supports a new method 'None' to extract a structural alignment from already aligned proteins. |
10.9.5 | New example macros to build double and triple stranded DNA (with Hoogsteen base pairing) can be found at the 'AddRes' command. |
10.9.1 | Improved command: 'Label' considers escape codes in strings (e.g. '\n' adds a line feed) and supports a 'Convert' parameter to disable this feature. |
10.8.31 | Improved macros for point mutant analysis can be found in the documentation of the 'SwapRes' and 'BindEnergy' commands. |
10.8.23 | New command: 'LoadJPG' loads an image in JPEG format. Click Effects > Image > Load from JPEG file. |
10.8.22 | New feature: The size of labels can be changed interactively with the mouse while holding down <Ctrl> and the right mouse button. |
10.8.19 | Improved experiment: 'Docking' provides a 'GridPar' command to set custom AutoGrid parameters. |
10.8.16 | New highlight: The 'Optimize' command supports a new 'Structures' parameter to activate a stochastic rotamer network optimizer that generates alternative high-scoring solutions to capture the conformational freedom of side-chains at a given temperature. |
10.8.13 | New feature: The 'CenterAtom' command accepts a 'CoordSys=Global' parameter to center an atom globally, in the middle of the screen and rotate around it as if Ctrl was pressed. Click Center in the atom context menu. |
10.8.10 | New highlight: The 'ShowWire' command displays parts of polygon meshes (surfaces, secondary structure etc.) as wire frames, or converts them to plastic wire frame objects. Click Effects > Show wire frame. |
10.8.5 | Improved support for the newly released POVRay 3.6.2 in Windows. |
10.8.2 | New highlight: The 'AlignPDBMol' command retrieves and aligns structurally related proteins from the PDB using all-against-all FATCAT alignments provided by the RCSB. Click Analyze > Align > PDB neighbors. |
10.7.28 | Improved secondary structure assignment: the new algorithm runs twice as fast and handles a few more special cases. Occasionally, the assignment may differ from the old method (e.g. helices may be one residue longer or shorter). |
10.7.24 | New highlight: The 'Antialias' command supports full-scene antialiasing to create smooth edges without jaggies. Click Window > Antialiasing. Contributed by Jacobus van Meel. |
10.7.20 | Fixed a problem with raytracing of arrows |
10.7.7 | New feature: YASARA plugins and scripts support Python 3.X and 2.X in parallel. |
10.7.6 | Fixed a problem running macros from the command line. |
10.7.4 | New support for automatic simulation of Vanadium-Oxygen clusters like in 3GQI. |
10.6.16 | Improved selection language: Ranges of residues match even if the ends are missing, e.g. DelRes 10-90 deletes a molecule that consists of residues 20-80 only. See Selections > Ranges can be specified. |
10.6.13 | Fixed a problem with some Linux graphics drivers where the entire screen turned black while YASARA started. |
10.6.10 | Improved macros for NMR structure determination: It is now easier to run individual refinement steps manually, see NMR recipes section. |
10.6.7 | Improved command: 'Align' displays both single-line FASTA and multi-line BLAST alignments. |
10.6.4 | Improved command: 'RenumberRes' provides a new 'Increment' parameter to set the residue number increment. |
10.6.2 | New feature: The homology modeling experiment creates a position specific scoring matrix (PSSM) from Uniprot before searching the PDB for templates to increase sensitivity. |
10.5.30 | New workaround for a bug in the BLAST program which makes it occasionally miss a hit. |
10.5.25 | Improved command: 'Clean' deletes 'UNL' residues, i.e. unknown ligands consisting of oxygen only (2HBW,3MPR) |
10.5.21 | New feature: The YASARA manual is now also available as a single PDF file for your eBook reader. See Essentials > Getting started. |
10.5.19 | Fixed a problem with HTTP proxy authentication based on username and password. |
10.5.14 | New command: 'Browser' sets the command used to show HTML files like the user manual. Click Options > Web browser. |
10.4.27 | New convention: To avoid pitfalls when working with homo-oligomers, the commands Sup, RMSD, GDT and the 'with occurrence in' operator now consider the molecule name when matching selections. |
10.4.10 | New plugin mostly for academic users, contributed by Joost van Durme: An interface to the FoldX program ( https://foldx.crg.es ) enables free energy predictions of protein stability, point mutations and interactions. An updated plugin version is available from foldxsuite.crg.eu . A free energy guide has been added to the Recipes section, which is especially important for commercial users. |
10.4.8 | Improved macro: md_run uses a cubic simulation cell by default (unless 'cubic' is set to 0), so that also elongated proteins can rotate freely during long-term simulations without crossing periodic boundaries. |
10.4.7 | Improved macro: md_analyze contains a 'pdbsaved' flag to convert the trajectory to PDB format for further analysis. |
10.4.5 | Improved command: 'AlignObj' supports the new method 'SHEBA' to run SHEBA also from macros, not only as a plugin via the graphical user interface (Linux and MacOS only). |
10.4.1 | New version 1.2.1b of the Advanced Poisson Boltzmann Solver APBS has been included in YASARA. |
10.3.24 | Improved plugins: Options can be added to the HUD context menus in the top right corner, see Plugins > Plugins must stick to format conventions > The menu structure is enclosed.. > HUD*ContextMenu. |
10.3.21 | Improved macro: md_runmembrane places counter ions more safely and keeps water more reliably outside the membrane during the equilibration. |
10.3.20 | Fixed a problem with the activation of quad-buffered stereo in Windows. |
10.3.17 | Improved command: 'Console open' opens the console and waits for input, for example to show results printed from a macro or plugin. |
10.3.14 | Improved experiment: 'HomologyModeling' can build hetero-oligomeric models from homo-oligomeric templates. |
10.3.6 | New feature: The 'WinFont' command accepts a new parameter to adjust the window font size from 8 (tiny) to 12 pixels (normal), click Window > Font > Size. |
10.2.30 | New workaround for an Ubuntu problem where YASARA could hang when resizing the window |
10.2.15 | Fixed a problem with temperature measurements in the NOVA force field present since version 9.9.22. NOVA is normally used for minimization only, which does not depend on the temperature and was thus not influenced by this problem. |
10.2.10 | New feature: The LoadSMILES command can now convert SMILES strings to full 3D coordinates, click File > Load > Other fileformat. |
10.2.7 | Improved command: The Z-scores returned by 'Check' have been renormalized, and are more tolerant regarding deviations from ideal bonds, angles and planarities. |
10.2.3 | Improved commands: 'AutoMove', 'AutoMoveTo', 'AutoRotate' and 'AutoRotateTo' also work in console mode. |
10.2.1 | New highlight: YASARA provides identification, analysis and visualization of internal cavities. The ShowCavi command shows them as newly created cavity objects. Click View > Show cavity. |
10.1.30 | New command: 'FirstCavi' identifies the most prominent atom or residue facing each cavity. Click Analyze > Volume of > Cavity and first. |
10.1.28 | Improved macros: The NMR structure determination macros have been simplified and use the MacroTarget just like other macros. See the updated docs in the Recipes section, you may have to rename the sequence and XPLOR table files of existing projects. |
10.1.26 | New command: 'CaviVol' calculates cavity volumes. Click Analyze > Volume of > Cavity in or at. |
10.1.24 | Improved command: 'ScaleObj' can scale polygon meshes, the 'ScaleMesh' command is deprecated. |
10.1.22 | Improved command: 'CenterObj' can center polygon meshes. |
10.1.20 | Fixed a problem from version 10.1.18 that could prevent YASARA from starting in Windows. |
10.1.18 | New release of the YASARA and YASARA2 force fields: They are now significantly more accurate when dealing with small molecule ligands. |
10.1.16 | Improved experiment: 'HomologyModeling' supports gene fission, where multiple target molecules map to the same template molecule. |
10.1.14 | New feature: The homology modeling experiment supports post-translational backbone modifications, i.e. prosthetic groups that interrupt the peptide chain. See the doc section 'Useful homology modeling hints' for details. |
10.1.12 | Improved macro: 'md_runmembrane' supports porines with a transmembrane water channel. |
10.1.8 | Fixed a BLAST database update problem that could raise the error "BLAST could not be run successfully, it signalled error 1" |
10.1.3 | Improved experiment: 'HomologyModeling' supports a 'Residues' parameter to set the maximum and minimum number of model residues (avoiding very large and small models) |
9.12.27 | Improved experiment: 'Neutralization' keeps water molecules that have been fixed with FixAtom. |
9.12.23 | Improved command: 'Stereo' betters shows fore- and background images, especially when molecules protrude from the screen. |
9.12.13 | New database with now 18000 structures for knowledge-based loop modeling. |
9.12.10 | Improved command: 'ListHBo' accepts a new 'Min' parameter to set the minimum energy threshold for hydrogen bonds, and a 'Results' parameter to return more detailed results for analysis. |
9.12.3 | New downloader for sequence databases etc., that can resume downloads that got interrupted by shaky internet connections. |
9.11.22 | Improved macro: 'md_runmembrane' can use any custom membrane, check the docs at Recipes > Run a molecular dynamics simulation > Running a membrane simulation the easy way. |
9.11.21 | New command: 'CompareBond' finds differences among covalent bonds, click Analyze > Compare > Bonds (Model+). |
9.11.19 | Improved command: SurfDis can additionally return the coordinates of the closest surface point. |
9.11.13 | Improved experiment: The homology modeling report lists the target residues covered by each model. |
9.11.12 | Fixed a homology modeling problem, which caused top scoring templates to be skipped if they shared too much target coverage with others. |
9.11.11 | Improved atom coloring using RGB colors |
9.11.9 | New feature: Side-chain prediction with method SCWALL (also used during homology modeling) runs 30% faster now. |
9.10.25 | Improved macro: 'md_analyze' additionally calculates the average energies and RMSDs. |
9.10.24 | Fixed a problem that could stop a simulation with the error message 'Simulation failure imminent. Minimizing...'. Please update now if you have version 9.9.28 or newer. |
9.10.22 | New command: 'ShowRing' fills rings with polygons, whose colors can optionally depend on the ring planarity. Click Effects > Show rings in (Model+). |
9.10.20 | Improved command: 'ColorPar' accepts a 'Ring' parameter to set the color scheme for ring planarity (applied by the ShowRing command) (Model+). |
9.10.18 | New feature: Multiple monitors are now better supported in Windows, the YASARA window remembers its position on the virtual desktop. |
9.10.13 | Fixed a problem when simulating water molecules without periodic boundaries, please update now if you have version 9.9.28 or newer. |
9.10.12 | Improved display: Antialiasing is now turned off temporarily and automatically to prevent huge slowdowns with certain compressed scenes. |
9.10.11 | Improved macro language: The unit of the predefined Boltzmann constant 'BoltzConst' has been changed from J/K to either kJ/mol*K or kcal/mol*K, depending on the current EnergyUnit, which saves a multiplication with JToUnit. |
9.10.10 | New feature: The homology modeling experiment skips templates if followups cover new parts of the target sequence, allowing to reach full coverage with fewer templates. |
9.10.9 | Improved macro: 'md_runmembrane' can detect membrane anchor lipids to correctly 'embed' proteins without transmembrane regions. |
9.10.8 | Improved command: 'SwitchObj' can be combined with visibility 'OnOff' to sequentially switch objects on and off, creating an animation, e.g. of NMR ensembles or GAMESS output files. Click View > Switch object > On & off. |
9.10.7 | Improved command: 'LoadGAM' loads all conformers of a GAMESS output file as separate objects. |
9.10.5 | New command: 'ShowCon' visualizes contacts and bumps. Click View > Show contacts (Model+). |
9.10.4 | Improved command: 'ColorPar' supports the new keyword 'Contact' to set the color range when showing contacts. |
9.10.3 | New feature: The 'ListCon' command accepts additional parameters to fine-tune the contact selection, and now makes it easy to list bumps. Contacts are now listed in one direction only. Click Analyze > List contacts (Model+). |
9.10.2 | Improved command: 'SaveSim' can also save single snapshots instantaneously, if the steps parameter is omitted. |
9.10.1 | Fixed a system library issue in Windows XP, that caused unexpected Syntax errors in Yanaconda macros. Windows XP users, please update. |
9.9.30 | Improved selection language: '!Metal' and 'Metal' and select all (non-)metal atoms. |
9.9.29 | Improved HUD: If more than one atom is marked, all numbers are shown now in the top left corner. |
9.9.28 | New highlight: The 'FixBond' command constrains bond lengths using the LINCS algorithm. This allows to perform simulations with a larger timestep. Combined with the new MD algorithms they now run between 4.1 times (1 CPU core) and 5.2 times (8 CPU cores) as fast as previously. Click Simulation > Fix > Bond. Fixed bonds are colored sky blue (Dynamics+). |
9.9.27 | New command: 'FixAngle' constrains the bond angles in TIP3P water molecules using the SETTLE algorithm, enabling simulations with rigid water molecules. Click Simulation > Fix > Water geometry. |
9.9.26 | New feature: YASARA supports the SSE4.1 instruction set, increasing performance on 45 nm Penryn-based Core 2 Duo CPUs released in January 2008, and newer CPUs. |
9.9.25 | Improved macro: 'md_run' can use constraints and a larger timestep to speed up simulations, snapshots are now saved every 25ps by default. If the macro is run to continue an old simulation, the old snapshot interval will be kept. |
9.9.24 | New feature: The 'Stereo' command includes preliminary support for anaglyph stereo using red-cyan filter glasses. Note that colors require tuning, click Window > Stereo > Red-cyan & tune colors (Model+). |
9.9.23 | New command: 'FreeAngle' removes bond angle constraints in TIP3P water molecules added with 'FixAngle', click Simulation > Free > Water geometry. |
9.9.22 | New highlight: YASARA's molecular dynamics algorithms have been rewritten. For a typical protein simulation in explicit solvent, they run between 3.2 times (1 CPU core) and 4.3 times (8 CPU cores) as fast as previously, and require significantly less memory. |
9.9.21 | New CPU support policy: The new algorithms for much faster MD simulations cannot run on the 1st generation of AMD Athlon CPUs (3DNow! only), sold between 1999 and 2001. YASARA therefore no longer starts on this CPU and displays an error message instead. |
9.9.20 | New feature: Thanks to the new MD algorithms, the occasional error messages about a 'search grid overflow' are gone forever. |
9.9.19 | Improved command: 'SimSpeed' activates dynamic load balancing to fine tune work distribution among CPU cores. Avoid when possible, since simulations become non-reproducible. |
9.9.18 | New feature: YASARA supports the SSSE3 instruction set, increasing performance on Intel Core 2 Duo and newer CPUs. |
9.9.17 | New command: 'FreeBond' removes bond length constraints added with 'FixBond', click Simulation > Free > Bond. |
9.9.16 | New highlight: The new macro 'md_runmembrane' runs MD simulations of membrane proteins fully automatically. It also identifies the transmembrane region and embeds the protein. See Recipes > Run a molecular dynamics simulation > Running a membrane simulation the easy way (Dynamics+). |
9.9.15 | New feature: The 'PressureCtrl' command supports a 'Manometer' pressure control mode to calculate the pressure from the kinetic energy and virial, which helps simulation of membrane proteins. Click Simulation > Pressure control (Dynamics+). |
9.9.15 | New feature: When loading or saving a scene, this becomes the new 'open document' shown in the YASARA window bar and saved quickly by clicking on the Save icon or File > Save. |
9.9.14 | Improved command: 'ColorPar Element' can set non-standard default colors to improve 3D perception in Anaglyph 3D mode. |
9.9.13 | Improved command: 'SaveMPG' accepts a new 'Frames' parameter to stop encoding after a given number of frames. |
9.9.12 | Improved command: 'Align' with methods LocalSeq and GlobalSeq uses an additional 'Parameter' to disable focusing and return the pure sequence alignment. |
9.9.11 | Improved permission handling: If you change the permissions of the 'yasara' directory using 'chmod -R o-rwx yasara' (or go-rwx), YASARA will keep these setting for newly created files inside the yasara directory. |
9.9.10 | Improved command: 'Label' supports the new keywords 'ATOMELEMENT' and 'ATOMElement' to label with the chemical element symbol. Click Effects > Label > Atom. |
9.9.9 | Improved experiment: 'Docking' allows flexible docking also with atoms that are not bound to the rest of the ligand (normally ions). |
9.9.8 | New selection language featue: The 'with hydrogen bond' operator selects atoms based on hydrogen bonds made. |
9.9.6 | Improved command: 'Align' can return the percentage sequence identity as the second return value if the new 'Results' parameter is set to 4. |
9.8.30 | New selection language feature: 'AminoAcid' and 'Nucleotide' select residues of the corresponding type. 'Protein' and 'NucAcid' no longer select single residues, but require at least two bound amino acids or nucleotides to match. |
9.8.24 | Fixed a Linux problem with some newer X-servers, where it was not possible to leave YASARA's menus by clicking outside. |
9.7.24 | Improved macro: 'md_refine' uses the 'Check' command in YASARA Structure to perform structure validation, making it easier to pick the best refinement snapshot. |
9.7.10 | Improved commands: 'SplitObj' and 'JoinObj' are now also available in YASARA View, click Edit > Join > Object. |
9.7.7 | Fixed a bug in the manual: The Yanaconda section 'Lists can be sorted' contained an incorrect sorting example (Objects-2 instead of Objects-1). |
9.6.17 | Improved command: 'Clean' corrects atom names that appear more than once per residue. |
9.6.16 | Improved command: 'Sim Init' displays newly created topologies without hydrogen numbers, so that they can be copy/pasted into *.fof files. If you need hydrogen numbers for use with other programs, use the 'SavePREP' command. |
9.6.14 | New feature: The 'SMILESRoot' and 'SMILESMember' keywords allow selections using SMILES strings. See Selections > Additional selection types > 'SMILESRoot' and 'SMILESMember'. |
9.6.13 | Improved command: 'CountBond' supports a 'Type' parameter to count only bonds that are free to rotate (Dynamics+). |
9.6.12 | New feature: YASARA command files can be used to execute YASARA commands from your own interactive application. See Essentials > Running YASARA in special environments > Running YASARA from other applications. |
9.6.10 | Fixed a potential BLAST problem in Linux and MacOS, causing the error message 'BLAST could not be run successfully'. |
9.6.9 | New command: 'SurfESP' calculates electrostatic surface potentials, click Analyze > Surface > Area and ESP of (Dynamics+). |
9.6.7 | Fixed a startup problem in the YASARA Dynamics Twinset for Windows. |
9.6.2 | Improved command: The 'Resonate' flag of the Load* command can now be used to disable bond typing. |
9.5.24 | New command: 'SurfDis' calculates the distance from the surface, click Analyze > Geometry > Surface distance of (Model+). |
9.5.23 | New command: 'Transformation' provides access to the coordinate transformation of the last preceding 'Sup', 'Align' etc. command in seven formats (Matrix, Quaternion, Angles...). |
9.5.22 | Improved command: 'Label' supports alternative atom naming schemes using keywords like ATOMNAMEPDB or ATOMNAMEIUPAC. |
9.5.20 | New command: 'SaveSeq' saves the sequence of a selection in FASTA format. Click File > Save as > FASTA sequence. |
9.5.18 | New command: 'Sequence' extracts the sequence of a selection in 1-letter code. Click Analyze > Sequence of. |
9.5.17 | New command: 'GroupBox' calculates the bounding box that fully encloses a selection of atoms. |
9.5.15 | Fixed a problem in the AMBER03 force field, where negatively charged cysteine (CYM) had a non-integral charge. |
9.5.13 | Improved command: 'Boundary' can also return the current cell boundary, either 'periodic' or 'Wall'. |
9.5.10 | New command: 'CountBond' counts covalent bonds between two atom selections. Click Analyze > Count > Bonds. |
9.5.9 | Fixed a user interface pitfall: Clicking Simulation > Timestep during a simulation to change the number of simulation steps per screen update also rounded the default 1.25fs timestep of md_run.mcr to 1.2fs. |
9.5.8 | Improved macro: md_convert has been simplified, it can convert trajectories to a series of PDB files, and can keep a certain atom centered in the cell to remove a drift through periodic boundaries, also from existing trajectories. |
9.5.7 | Improved command: 'Move' can move atoms during a simulation without ending it. |
9.5.6 | Improved command: 'Clean' deletes wrong surplus bonds formed by hydrogens, e.g. in 1A08 revision 2. |
9.5.5 | Fixed an atom type assignment problem which caused planar carbocations to become non-planar during an energy minimization. |
9.5.4 | Improved macro language: The 'sort' function sorts a list, see Macros > Lists can be sorted. |
9.5.3 | New highlight: The 'Stereo' command supports interlaced stereo for 3D screens like the Zalman ZM-M220W, which works with any graphics card and costs just 200 EUR (Model+). |
9.5.2 | Improved experiment: If the homology modeling parameter 'DelTemplateRes' is specified, YASARA will no longer delete waters and buffer molecules, giving full control over which hetgroups to keep. |
9.5.1 | Improved command: 'ShowImage' shows background images also in stereo mode, which helps YASARA movies. |
9.4.30 | Improved experiment: 'Neutralization' supports a 'Vacuum' parameter to define a vacuum region where no water will be placed even if there is a hole, e.g. in a membrane. |
9.4.19 | New workaround for a YASARA window resize problem with ATI fglrx Linux drivers. |
9.4.12 | Improved experiment: 'Minimization' runs initially faster and uses a new convergence criterion. Existing macros that use the 'Convergence' parameter will continue to work, but could be speeded up by adjusting the convergence. |
9.4.11 | New feature: 3DConnexion controllers like SpaceBall or SpaceNavigator are now also supported in Windows (Model+). Contributed by Ahmet Sacan. |
9.4.10 | New workaround for a bug in NCBI's BLAST that still had problems with directory names containing spaces. If you encountered this problem, you can now move the YASARA directory back. |
9.4.9 | Improved macros: dock_run.mcr and dock_runlocal.mcr show progress during the final analysis stage and create consistent filenames also if the MacroTarget ends with a number. |
9.4.8 | New workaround for a problem in Windows' memory manager that could prevent the Twinset with YASARA Structure from building homology models or selecting the YASARA2 force field. |
9.4.6 | New command: 'Accel' gets or sets the acceleration acting on atoms to help steered molecular dynamics simulations. |
9.3.30 | New feature: With the latest PDB format improvements at the RCSB, every PDB file finally contains reliable information about the biologically relevant oligomerization state. The homology modeling experiment therefore no longer uses the PQS database but relies on the PDB only, and automatically downloads new PDB files if the local ones are outdated. |
9.3.28 | New feature: All standard macros like md_run.mcr now use the new, slightly more accurate AMBER03 instead of the older AMBER99 force field. Attention: if you use md_run to continue an old trajectory, this will be done with the new force field. In YASARA Structure, md_run additionally optimizes the hydrogen bonding network. |
9.3.27 | Improved command: LoadPDB stores newly downloaded files in the local PDB if a path has been set, overwriting older, outdated versions. |
9.3.26 | New feature: The homology modeling experiment supports a 'Speed' parameter to build models much faster, but with reduced refinement (which may still be helpful if thousands of models are needed quickly). See the new hm_buildfast.mcr. Note that this parameter was also added to the Python interface. |
9.3.24 | Improved command: 'Oligomerize' chooses new non-redundant molecule names for all copies and also deletes molecules if the selected object contains more than one biomolecule. Proper function may require to download the latest version of some PDB files. |
9.3.22 | New feature: 'BuildRes' and 'AddRes' support a 'Tau' parameter to specify the N-CA-C bond angle. Note that the new parameter has not been simply added at the end, requiring a modification of macros that use the parameters 'Center','End' or 'Isomer' without naming them. |
9.3.21 | Improved command: 'Load*' supports a 'Model' parameter to load only one of many molecules in a multiple-molecule file. |
9.3.20 | New workaround for a bug in Intel Series 4 Notebook chipsets which showed a black screen when the console was opened and experienced slowdowns. |
9.3.15 | New macro: em_run.mcr runs an energy minimization, automatically adding a water shell if a force field other than NOVA is selected. |
9.3.10 | Improved selection language: 'fixed' and '!fixed' allow to select (un)fixed atoms. |
9.3.8 | New feature: 3DConnexion controllers like SpaceBall or SpaceNavigator are now also supported in MacOS (Model+). |
9.3.7 | Fixed a potential pitfall: Changes to alignment parameters are not saved anymore in yasara.ini, so that YASARA always creates the same alignments after a restart. |
9.3.6 | Improved Python modules: YASARA can be used interactively while the module is running, the 'Wait' command no longer returns immediately. |
9.3.3 | Improved command: GrabObj can grab multiple objects for mouse movement even if their positions differ (Model+). |
9.3.2 | New command: 'PosOri' sets/gets object positions and orientations in one go, the output can be copied directly to macros. |
9.3.1 | Improved plugin: The animated GIF/MPEG clip creator makemovie.py now also works in Windows. Contributed by Ahmet Sacan. |
9.2.27 | Improved command: 'Duplicate' can create copies of all objects (including polygon meshes), not just those with atoms. |
9.2.22 | New feature: YASARA's secondary structure assignment algorithm identifies 3-10 helices, named 'G' in the sequence selector and colored yellow by default. The SecStr command returns additional 3-10 helix data. |
9.2.21 | Fixed a Twinset for Windows startup problem (Error 846, Path name too long). |
9.2.20 | Improved sequence selector: for consistency, beta strands are now labeled 'E' instead of 'S'. |
9.2.19 | Improved command: 'Radius' calculates the mass-weighted radius of gyration if 'Center' is set to 'Mass'. |
9.2.18 | Improved plugin: Object sampling with CONCOORD uses a new version that solves convergence problems. |
9.2.15 | Improved command: 'Compare' supports a new 'CheckMol' flag to toggle the comparison of molecule names. |
9.2.13 | Improved force field parameter assignment: YASARA tries to read the oxidation state of metal ions from the residue name (FE2,FE3 etc.) if no matching topology is found. |
9.2.9 | Improved command: The Color command supports a new 'MapCons' parameter to color by conservation in a user-supplied alignment. |
9.2.8 | New commands: 'BinDistance' collects distance statistics, 'RDF' calculates the corresponding radial distribution function (Dynamics+). |
9.2.7 | Improved command: 'FillCellWater' avoids bumps between waters across periodic boundaries to facilitate the following energy minimization. |
9.2.6 | Improved experiment: Homology modeling uses a new loop database which yields better results for loops longer than 20 residues. |
9.2.5 | New feature: The 'BuildAtom', 'BuildRes', 'BuildMol' and 'AddRes' commands are now freely available in YASARA View. Click Edit > Build and watch the help movie 'Building small molecules'. |
9.2.4 | Improved selection language: 'Water' selects H2O, HO-, H3O+ and single oxygens, the 'DelWater' command is now also based on chemical connectivity instead of residue names. |
9.2.3 | Fixed a loop modeling problem from version 9.2.2, please update before building a homology model. |
9.2.2 | Fixed a startup problem of the Twinset for Windows (application failed to initialize, error 0xc000005). |
9.2.1 | Improved experiment: Homology modeling supports a new 'TermExtension' parameter to specify how many terminal residues (that don't align to anything in the template) should be added at most. |
9.1.31 | Improved commands: ShowDoc, SearchDoc and ShowCom open only a single instance of Safari in MacOS, even if issued multiple times. |
9.1.30 | Improved experiment: Homology modeling corrects manually provided alignments to make sure that they make physical sense. |
9.1.29 | Improved command: 'ListHBo' allows to detect cases where a hydrogen can form two H-bonds at the same time. |
9.1.28 | Improved experiment: Homology modeling keeps track on a per-residue basis how the various templates cover the target sequence to improve results for multi-domain targets (these should however still better be submitted separately). |
9.1.27 | Improved force field parameter assignment: YASARA distinguishes between carbanions (pyramidal) and carbocations (planar) based on the geometry and assigns the matching net-charge and atom type. |
9.1.25 | New molecular modeling help movie: '4.4. Domain replacement' shows how to transfer domains or loops between proteins, for example to build hybrid templates for homology modeling. Contributed by Ahmet Sacan. |
9.1.24 | Improved force field parameter assignment for molecules with rings of length 3 and 4 (e.g. beta-lactam) (Model+). |
9.1.23 | New command: 'RotAxis' rotates atoms or objects about an arbitrary axis, click Effects > Rotate about axis. |
9.1.22 | Improved experiment: Homology modeling offers the 'DelTemplateRes' keyword to delete a selection of template residues (e.g. ligands which you do not want to keep in the model) (Structure). |
9.1.20 | Improved command: 'Link' supports a new option to also find dative bonds to metal ions, click Edit > Find bonds in. |
9.1.19 | New command: 'KinEnergy' calculates the kinetic energy, click Analyze > Energy > Kinetic energy (Dynamics+). |
9.1.18 | Improved experiment: Homology modeling puts more emphasis on conserved residues in loop modeling, to better keep ligand binding residues close to insertions/deletions in place. Dative bonds to metal ions are automatically added now (Structure). |
9.1.17 | New command: 'Speed' gets or sets the center of mass speed and velocity vectors of selected units (Dynamics+). |
9.1.16 | Improved force field parameter assignment: The bond angles involving dative bonds to metal ions (ShowArrow/CONECT) are now also restrained, to better keep the structure of complicated prosthetic groups like iron/sulfur clusters during a simulation (Dynamics+). |
9.1.15 | New command: 'GroupCenter' calculates the geometric center or the center of mass (Model+). |
9.1.14 | Improved macro language: Yanaconda contains the predefined variables MassUnit (atomic mass unit), BoltzConst (Boltzmann constant), AvoConst (Avogadro constant) and JToUnit (conversion from J to current energy unit). |
9.1.13 | New highlight: The 'Cut' command creates cut-plane objects that cut polygon meshes (e.g. surfaces) open to look inside. Watch the new molecular graphics help movie 'Cut-Planes' (Model+). |
9.1.11 | New feature: Python plugins can now directly obtain return values from YASARA commands, see Plugins > Plugins can access most YASARA functions. |
9.1.10 | New highlight: YASARA includes APBS, the Adaptive Poisson-Boltzmann Solver by Nathan Baker et al. to calculate solvation energies and electrostatic potentials considering implicit solvent and counter ions (Dynamics+). |
9.1.9 | New feature: The 'SolvEnergy' command supports two new methods to calculate solvation energies, 'PBS' (using APBS, the adaptive Poisson Boltzmann Solver) and 'Empirical', a fast empirical approximation. The dielectric constant parameters are deprecated, use 'SolvPar' instead. Click Analyze > Energy > Solvation (Dynamics+). |
9.1.8 | New highlight: The 'ShowESP' command (now in the View menu) has been replaced with a new version that supports various graphics styles including contour surfaces of the electrostatic potential. Watch the new molecular modeling help movie 'Electrostatic Potentials' (Dynamics+). |
9.1.7 | New command: 'SolvPar' sets solvation parameters for calculation of electrostatic potentials and surfaces, as well as solvation energies. Click Analyze > Energy > Solvation parameters (Dynamics+). |
9.1.6 | New feature: The 'ShowSurf' and 'ColorSurf' commands can color surfaces by electrostatic potential, calculated either with the Particle Mesh Ewald (ESPPME) or the Poisson-Boltzmann approach (ESPPBS). The 'ESP' method is deprecated. |
9.1.5 | New command: 'OriVec' calculates the Euler-like orientation angles corresponding to one or two vector directions. |
9.1.3 | Improved plugins: Menu options (for example long dynamic lists for the ListMenu) can be read from disk, see Plugins > The menu structure is enclosed in a triple-quote comment > ListMenu. |
9.1.2 | New workaround for a bug in Windows Vista which caused the <Tab> key to get stuck when switching between windows. |
9.1.1 | New convention: The commands 'AddBond', 'SwapBond' and 'SwapAtom' no longer update hydrogens and bond lengths by default. This has to be requested explicitly by setting the 'Update' parameter to 'Yes'. |
8.12.31 | Improved macro language: The called function must use a list creator '()' to indicate if a single value or a list should be accepted from the caller, this change is not 100% backwards compatible. See Macros > Calls to user-defined functions must appear one per line. |
8.12.30 | Fixed a download problem with BLAST databases and modeling templates, that could time-out too soon with a bad Internet connection. |
8.12.29 | Improved macro language: The 'caller' keyword allows to access variables in the calling function to implement a general 'call by reference' (See Macros > Calls to user-defined functions must appear one per line). |
8.12.28 | Fixed a problem with undo/redo present since 8.10.15 that caused object positions or orientations to be set incorrectly. |
8.12.27 | Improved macro language: The 'hex' function converts an integer to a hexadecimal string. |
8.12.19 | Improved macro: 'md_refine' now uses the new YASARA force field in YASARA Structure. |
8.12.18 | Improved experiment: Docking supports a new 'DockPar' option which allows to include any parameter you want in the AutoDock docking parameter file. The explicit use of 'ga_num_evals X' etc. is now deprecated, replace with 'DockPar ga_num_evals X'. |
8.12.16 | Fixed two error messages in the homology modeling experiment. |
8.12.14 | Improved command: 'Cell Auto' accepts a selection of atoms to enclose, for example residues in a binding site for docking. Click Simulation > Define cell. |
8.12.12 | Improved experiment: Homology modeling includes the target coverage in the alignment score, so that less homologuous templates are chosen if they cover more of the target. |
8.12.8 | New feature: The YASARA console supports indentation and auto-completion of command names or filenames, just press <Tab>. |
8.12.7 | Improved command: 'BuildLoop' and 'OptimizeLoop' can use the fast access index also if the atom order in the residue does not match the PDB format (N/CA or CA/C flipped). |
8.12.6 | Improved command: 'SwapAtom' supports a 'Rename' flag to skip atom renaming. |
8.12.5 | Improved experiment: Docking allows to set AutoDock's 'ga_num_generations' parameter. |
8.12.4 | Fixed an error message that could show up in side-chain and loop optimization if more than one object was present. |
8.12.3 | New feature: The RCSB unfortunately changed the download location of PDB files without notice today. If you use LoadPDB with download=Yes or run a homology modeling experiment, please update YASARA now. Downloading from the File menu still works. |
8.11.27 | Improved selection language: It is not an error anymore to select residue numbers that don't exist or to select incomplete ranges. |
8.11.25 | Improved command: 'Radius' supports two additional parameters to calculate the nuclear radius and the radius of gyration, also based on the center of mass instead of the geometric center. |
8.11.24 | Improved command: 'LoadPDB' handles dummy atoms correctly again. |
8.11.15 | Improved command: 'ListAtom' lists the chemical element as well. |
8.11.11 | New highlight: The Yanaconda macro language has been rewritten and runs up to 150 times faster, you can now define your own functions (see Macros > Calls to user-defined functions), and work with entire lists at once (vector processing, see Macros > Lists are emulated..). Combined with the new 3D fonts mentioned below, it is a good time to verify (before an important presentation) that your movies still work as expected. All YASARA help movies have been checked and partly received a visual makeover. |
8.11.10 | Improved macro language: The 'zeroed' function returns a zero with the same number of digits as the function argument to help construct matrices. |
8.11.9 | New feature: 'MakeTextObj' and 'Print' create 3D fonts with proper shading and improved True-Type quality. Since the size of characters changed a tiny bit, movies that precisely arrange molecules and 3D letters may need small adjustments (Model+). Contributed by Ahmet Sacan. |
8.11.8 | Improved macro language: The functions 'crack' and 'fuse' allow to analyze and change individual string characters. |
8.11.7 | Fixed an issue present since 8.10.15, where filling the cell with water could crash occasionally. |
8.11.6 | New feature: 'Label' uses a new True-Type font interface to improve label quality on screen and in ray-traced images. Contributed by Ahmet Sacan. |
8.11.5 | Improved Yanaconda macro language: the 'norm' function calculates the length of a vector (=a list of numbers). |
8.11.4 | Fixed an issue where BLAST would hang (un-)reproducibly (depending on the file system used), if YASARA's installation path contained spaces. |
8.11.2 | Improved command: The homology modeling experiment now excludes templates that cover a significantly smaller fraction of the target sequence than others. |
8.11.1 | The Yanaconda operator '//' now performs a floored division, 3//2 still equals 1, but -3//2 now equals -2. This ensures that division results are equally distributed and do not favor '0'. |
8.10.28 | Fixed an issue where downloading re-refined PDB files during the homology modeling experiment could hang indefinitely. |
8.10.27 | New command: 'Scale' multiplies atom coordinates with a scaling factor. Click Effects > Scale (Model+). |
8.10.27 | Improved experiment: Docking can set the AutoDock parameters ga_num_evals, ga_pop_size and dihe0 directly, see Recipes > Dock > Useful docking hints (Structure). |
8.10.27 | New command: 'ScaleMesh' multiplies vertex coordinates in polygon meshes with a scaling factor, click Effects > Scale > Polygon mesh (Model+). |
8.10.26 | Improved support for running multiple YASARAs on a cluster from an NFS volume, no more lock file errors should show up. |
8.10.25 | Improved Python interface: plugins and Python modules can now also use WHAT IF functions in the Twinset using run("SHOSOU") etc. |
8.10.24 | Improved command: 'Console' supports three modes: on, hidden and off which permit to fine-tune the console appearance. Click Window > Console. |
8.10.23 | Fixed an issue present since version 8.10.15, where going to WHAT IF in the Twinset could crash. |
8.10.22 | Improved typing of small molecules, 5 additional difficult cases are handled now. |
8.10.21 | Fixed an issue present since version 8.10.15, where making significant changes to the scene after marking an atom could crash. |
8.10.20 | Improved instructions for using minimal YASARA movies as course lessons (see Recipes > Create your own YASARA movies > Minimal movies can be used to support student courses) |
8.10.19 | Improved splitting of large ligands during force field parameterization now handles most cases automatically. |
8.10.16 | Fixed a startup problem in YASARA for Windows 8.10.15 (Size of struct object is incorrect). |
8.10.15 | New feature: The number of objects in YASARA (Model+) is now unlimited to help with the analysis of thousands of compounds at the same time. Since this feature required changes in every corner of YASARA, don't hesitate to report also the smallest anomalies. |
8.10.14 | New release of OpenBabel included, YASARA now supports 42 additional molecular file formats, 112 in total. Click File > Load/Save as > Other file format. |
8.10.13 | Improved commands: Molecule import and export (Load* and Save*) can handle multiple objects in one file. |
8.10.12 | New command: 'CorrectDrift' removes translational motion of the solute in the cell to prevent it from crossing periodic boundaries. This feature has been included in the md_run macro. Click Simulation > Automatic correction of > Solute drift. |
8.10.11 | Improved commands: 'LoadPDB' and 'SavePDB' preserve COMPND information, 'Label' supports a new 'COMPOUND' tag to insert the per-molecule compound name into labels. |
8.10.4 | New highlight: An interactive oligosaccharide builder plugin is available, including energy minimization of growing sugars. Click Edit > Build > Oligosaccharide (Structure). |
8.10.3 | Fixed a Windows Vista error message when running BLAST and building homology models. |
8.10.2 | New feature: Text files read by YASARA can now be in Unicode format. |
8.10.1 | Improved experiment: Homology modeling detects a wider range of pitfalls when you provide your own template structures. |
8.9.28 | New command: 'SavePrep' creates an AMBER Prep topology file to exchange force field parameters with other programs. Click File > Save as > Other file format (Dynamics). |
8.9.25 | New command: 'LoadPrep' loads molecule coordinates from an AMBER Prep topology file. Click File > Load > Other file format (Dynamics). |
8.9.23 | Improved command: 'Clean' adds internal capping groups to chain breaks. |
8.9.21 | Fixed an incorrect 'out of memory' error message when filling the cell with water (present since 8.9.11). |
8.9.20 | Improved command: 'AddCap' supports a new 'Location' parameter to distinguish between external (chain ends) and internal (chain breaks) caps. |
8.9.19 | Improved command: 'CoordSys' returns the current coordinate system, +1 if left-handed, -1 if right-handed. |
8.9.18 | Improved selection language: The 'with(out) connection to' operator selects atoms depending on their covalent connection. |
8.9.11 | Improved command: The 'FillCellWater' command accepts a new parameter 'DisMax' to create a water shell. |
8.9.10 | Fixed a problem in the Docking experiment, where AutoDock could get trapped in an infinite loop, leading to an out of memory error. |
8.9.9 | Improved command: 'Compare' returns the number of differences found. |
8.9.8 | Improved typing for small molecules, 6 additional difficult cases are handled now. |
8.9.3 | New feature: YASARA supports HTTP proxies for various downloads, read Essentials > Running YASARA in special environments > Running YASARA with web access through an HTTP proxy. |
8.9.1 | Fixed an error message in the HomologyModeling experiment when building hetero-oligomeric models. |
8.8.24 | Improved typing of small molecules, 10 additional difficult cases are handled now. |
8.8.23 | Improved docking: YASARA now reduces the number of energy evaluations for less flexible ligands to speed up docking. Alternatively, the new 'EnergyEvals' keyword can be used to set AutoDock's ga_num_evals parameter. |
8.8.21 | Improved macro language: All YASARA commands return error codes that can be checked, see Macros > Calls to YASARA commands must appear one per line. |
8.8.20 | Improved command: 'LoadPDB' adds missing TER entries if the 'Correct' flag is set. |
8.8.19 | Improved commands: 'Load*' now uses YASARA's bond typer after reading file formats that don't store bond orders. |
8.8.17 | New feature: The 'HomologyModeling experiment' detects gene fusion events where the target sequence covers multiple template molecules and fuses them in the correct order (Structure). |
8.8.11 | Improved command: 'KekulizeBond' and 'Save*' use a new improved algorithm to place double bonds. |
8.8.9 | Improved command: 'TypeBond' considers bond lengths and angles in planar rings to detect molecules with broken aromaticity, and has several other improvements. |
8.8.8 | New highlight: After five years of development, the final YASARA stage 'YASARA Structure' has just been released. You are welcome to join the festive activities by clicking Help > Play help movie > Triple 8 celebration day (Model+). Owners of YASARA View can download the movie from www.yasara.org/movies |
8.8.7 | New help movie: All the new YASARA Structure features are introduced in a new help movie, click Help > Play help movie > What's new in YASARA Structure (Model+). Owners of YASARA View can download the movie from www.yasara.org/movies |
8.8.6 | New highlight: The 'Docking experiment' performs small molecule docking using a tuned version of AutoDock. Click Options > Choose experiment > Docking and read Recipes > Dock a ligand to a receptor (Structure). |
8.8.5 | New highlight: The 'OptHyd' command invokes a new pH-dependent hydrogen bonding network optimizer that fully considers ligands, click Edit > Add > Hydrogens to object & optimize (Structure). |
8.8.4 | New highlight: The 'HomologyModeling experiment' takes all the steps from a target FASTA sequence to a fully refined homology model and writes a scientific report about the modeling. See Recipes > Building a homology model (Structure). |
8.8.3 | New highlight: The 'OptimizeLoop' command performs knowledge-based loop optimization considering the current force field and solvation energies. Click Edit > Optimize > Loop (Structure). |
8.8.2 | New command: 'BuildLoop' quickly scans the PDB for backbone conformations that bridge two anchor points, match certain sequence and secondary structure requirements, and don't bump. Click Edit > Build > Loop (Structure). |
8.8.1 | New highlight: Two new force fields are available: The YASARA force field, which has been derived from YAMBER3 by adding knowledge-based dihedral potentials (one-, two- and three-dimensional), and the YASARA2 force field, which contains additional knowledge based 1D and 3D packing potentials. Click Simulation > Force field (Structure). |
8.7.31 | New help movie: '4.2 Knowledge-based potentials' explains all the details of knowledge-based potentials and their use in YASARA. |
8.7.30 | New command: 'ShowKBP' shows knowledge-based potentials, click Analyze > Geometry > Knowledge-based potential (Structure). |
8.7.29 | New highlight: The 'Check' command performs a new kind of force field based structure validation that works also for ligands, supporting 11 different checks. This number grows to 33 checks in the Twinset. Click Analyze > Check (Dynamics+). |
8.7.28 | New highlight: The 'Optimize Method=SCWRL' command optimizes Side-Chains With a Rotamer Library and very fast dead-end elimination using the SCWRL3 algorithm (Protein Sci. `12`,2001-2014). Additional tuning can be done with 'Method=SCWALL', which performs a minimization of the side-chains in dihedral angle space with implicit solvent. Click Edit > Optimize (Structure). |
8.7.27 | New command: 'SampleLoop' performs the same task for an existing loop (Structure). |
8.7.26 | New highlight: The 'PredSecStr' command employs the DSC method to predict secondary structure (King RD and Sternberg MJE, Protein Sci. 5,2298-2310). Click Analyze > Secondary structure > Prediction (Structure). |
8.7.25 | New highlight: The 'ShowIonSites' command predicts ion binding sites, click View > Show ion binding site (Structure). |
8.7.24 | New command: 'SampleDih' changes dihedral angles, either randomly, systematically, or based on data extracted from the PDB. Click Edit > Sample > Dihedrals (Structure). |
8.7.23 | New highlight: The AMBER03 force field has been included, with tuned protein charges and improved protein backbone energetics, see Duan et al (2003) JCC 24,1999-2012 (Dynamics+). |
8.7.22 | New highlight: The 'BLAST' command runs a built-in (PSI-)BLAST, local sequence databases (PDB,SwissProt,TrEMBL) are updated automatically and augmented with additional validation data to identify the best PDB structure for a given sequence. Click Analyze > Blast (Structure). |
8.7.21 | New highlight: The NMR module to determine protein structures based on distance- and dihedral angle restraints has been released. More details at www.yasara.org/nmr and in the docs at Recipes > Solve an NMR structure (Structure,NMR module). |
8.7.20 | New command: 'DelRest' deletes all NMR restraints assigned to an object (Structure,NMR module). |
8.7.19 | New command: 'ShowRest' shows NMR restraints that involve selected atoms (Structure,NMR module). |
8.7.18 | New command: 'HideRest' hides all NMR restraints that involve the selected atoms and have been shown before (Structure,NMR module). |
8.7.17 | New command: 'LoadTbl' loads a table with NMR restraints in XPLOR format (Structure,NMR module). |
8.7.16 | New command: 'SaveTbl' saves a table with NMR restraints in XPLOR format (Structure,NMR module). |
8.7.15 | New command: 'ListFloat' lists the currently floating assignments in ARIA SaveFloat format (Structure,NMR module). |
8.7.14 | New command: 'ListRest' lists currently assigned NMR restraints and corresponding violation energies. |
8.7.13 | New command: 'RestEnergy' calculates NMR restraint violation energies (Structure,NMR module). |
8.7.12 | New command: 'RestViol' calculates NMR restraint violation statistics (Structure,NMR module). |
8.7.11 | New command: 'RestrainDis' adds a new distance restraint (Structure,NMR module). |
8.7.10 | New command: 'RestrainDih' adds a new dihedral angle restraint (Structure,NMR module). |
8.7.9 | New command: 'RestrainPar' sets/gets the current NMR restraining parameters (Structure,NMR module). |
8.7.8 | New command: 'RestrainPot' sets/gets the current NMR restraining potential (Structure,NMR module). |
8.7.7 | New command: 'ScaleRest' scales NMR restraints (Structure,NMR module). |
8.7.6 | New command: 'IntersectObj' performs collision detection between objects. |
8.7.4 | New convention: due to the increasing number of PDB files with mixed lower- and uppercase chain names (e.g. 1GAV), molecule selections are case-sensitive now. 'Mol a' will no longer select 'Mol A' and vice versa. |
8.7.3 | New feature: Python scripts can interact with Python plugins, see Scripts > Python scripts can interact with Python plugins |
8.7.2 | Improved command: 'Energy' calculates knowledge-based dihedral and packing energies if one of the new YASARA and YASARA2 force fields is chosen (Structure). |
8.7.1 | Improved command: 'SecStr' analyzes and returns secondary structure content also per molecule and object. |
8.6.30 | Improved command: 'GrabObj' can now grab more than one object for interactive movement. Click Effects > Move > Object with mouse. |
8.6.29 | Improved command: 'Clean' replaces selenium and tellurium atoms with sulfur and renames them accordingly. |
8.6.28 | Improved plugin: The object sampling now uses Bert de Groot's Concoord 2.1 and allows to choose different VdW parameter sets. Click Edit > Sample > Object. |
8.6.27 | Improved Yanaconda macro language: the modulo operator '%' now also works on floating point numbers. |
8.6.26 | Improved command: 'Clean' replaces hydrogens that are incorrectly close (e.g. GLN 22 in 1GQV) |
8.6.21 | Workaround for a bug in some new ATI drivers that left the startup screen visible and did not clear the screen. |
8.6.8 | New command: 'SupOrdered' superposes an arbitrary number of selections in an ordered way. Click Analyze > Superpose > Two objects on ordered... |
8.5.29 | Improved selection language: the 'with occurrence in' operator selects atoms that occur in both selections, see Selections > Selection blocks can be combined with explicit operators. |
8.5.27 | New command: 'GDT' calculates the CASP global distance test, i.e. the percentage of atoms that can be superposed below a certain distance cutoff. Click Analyze > Global distance test of (Model+). |
8.5.26 | Improved commands: 'BuildRes', 'SwapRes' and 'AddRes' accept a new 'Isomer' parameter to build also D-amino acids. |
8.5.25 | Fixed a matching problem in 'Sup' and 'RMSD' that occured when more than two objects were superposed with 'Match=Yes', i.e. an RMSD matrix was calculated. |
8.5.7 | New command: 'ElementAtom' gets the chemical element of selected atoms. |
8.5.6 | Improved command: 'RadiusObj' can also obtain the radii of polygon meshes. |
8.4.15 | New command: 'SavePNG' saves a screenshot in compressed PNG format. |
8.3.30 | Improved command: 'Align' initializes the atomic properties to reflect sequence similarity between aligned residues. Coloring by properties thus helps to visualize the structural alignment. |
8.3.27 | Improved command: The minimization experiment supports a new convergence parameter to define how far the minimization should proceed. |
8.3.11 | Improved command: The 'Label' format supports a new 'CHARGE' keyword to display charges of entire units. 'ATOMCHARGE' is deprecated. |
8.3.3 | Improved command: 'Clean' sorts atoms in amino acids in their default order. |
8.3.1 | Reduced CPU usage on some graphics cards, e.g. nVIDIA. |
8.2.21 | Improved selections: the properties 'Ring', 'Aromatic' and 'Visible' are now available in atom selection menus. |
8.2.19 | Improved command: 'SupMulti' now employs the latest version 1.2.7 of Theseus (Linux+MacOS). |
8.2.14 | Improved YAMBER3 force field: Stronger planarity restraints significantly increase structural quality with only a marginal effect on accuracy. |
8.2.10 | Improved typing of small molecules: 27 additional difficulties are now handled. |
8.2.3 | New feature: the 'SolvEnergy' command also calculates the Van der Waals solvation energy and returns it as the second result. A surface area is no longer returned, PLEASE UPDATE macros that use the second return value. |
8.2.2 | Improved macros: The examples macros at the 'BindEnergy' command now include Van der Waals solvation energies and the entropic cost of exposed surface. |
8.2.1 | Improved command: 'Rotate' can now also rotate atoms in the local coordinate system, the order of rotation is now about the X-, Z- and Y-axes. |
8.1.31 | New command: 'GroupLine' calculates the optimal line through a group of atoms, for example to move atoms along a helical axis. |
8.1.30 | Improved command: 'Clean' corrects incorrectly defined chemical elements, like OD2 ASP A 186 in 1F6W. |
8.1.29 | New command: 'GroupPlane' calculates the optimal plane through a group of atoms. |
8.1.28 | Improved command: Per-atom energy calculations with 'EnergyAtom/Res/Mol' add the dihedral energy to the two dihedral core atoms 2 and 3 instead of 1 and 4. This makes sure that the Phi and Psi dihedral energies stay inside the amino acid they belong to. The same holds for bond angles now. |
8.1.26 | Improved macro language: lists can be assigned to each other, e.g. MyOtherList=MyList. |
8.1.20 | New highlight: YASARA supports side-by-side stereo (parallel and cross-eyed), click Window > Stereo (Model+). |
8.1.18 | Improved command: 'AddRes' accepts a new 'End' parameter to add residues also to the front end of a peptide chain. |
8.1.17 | Fixed an issue where LoadSim complained that simulation snapshots created in the second half of 2007 were corrupted. |
8.1.10 | Improved feature: Object names can now be up to 12 characters long. |
8.1.7 | New highlight: A scene content browser with context menus in the top right head-up display allows to easily and quickly navigate and modify the scene. As a side-effect, <Ctrl> needs to be held down when grabbing an object for movement in the HUD. |
8.1.6 | Improved command: 'CheckObj Bumps' no longer considers crystal symmetry to avoid unexpected results. |
8.1.5 | New commands: 'ShowHUD' and 'HideHUD' toggle the display of selected units in the scene content browser. Click Window > Show/Hide in HUD. |
8.1.1 | New workaround for a backward compatibility bug in MacOS 10.5. YASARA now also runs in Leopard. |
7.12.27 | Improved support for non-ASCII characters in filenames (UTF-8 etc.). |
7.12.25 | Improved command: 'StyleWin' can adapt YASARA's look to MacOS 10.5 Leopard. Click Window > Style. |
7.12.22 | Improved secondary structure assignment. |
7.12.18 | Improved command: 'LoadPDB' supports a 'download' flag to automatically download missing PDB files. |
7.12.1 | Improved console: commands typed in can now be longer than the YASARA window. |
7.11.28 | New command: 'ShowPolygon' draws a polygon connecting points or atoms. See Commands > Effects > Polygons. |
7.11.28 | New command: 'HidePolygon' hides a polgon connecting atoms. |
7.11.26 | Improved Python interface: Selection can now be passed as Python lists [] to YASARA functions in Python modules and plugins. |
7.11.25 | New feature: YASARA's treatment of hydrogen bonds has been reimplemented and accelerated, including angle dependence, more details at the ListHBo command. |
7.11.23 | Improved command: 'Print' accepts an additional parameter 'Convert' to toggle the conversion of escape codes in strings. |
7.11.22 | Improved command: 'ListHBo' also lists the energies of hydrogen bonds. |
7.11.18 | Improved selection language: 'Ring' selects ring atoms, 'Aromatic' aromatic atoms. |
7.11.16 | Improved selection language: 'BFactor','Property' and 'Occupancy' calculate averages over the current selection unit. |
7.11.14 | New highlight: YASARA can be used as a Python module, just 'import yasara'. See Scripts > Use YASARA as a Python module. |
7.11.10 | Improved typing of small molecules: 23 additional pitfalls are now considered. |
7.11.3 | Improved selection windows: The 'Belongs to' list on the right side allows to select segments. |
7.11.3 | New command: 'Seg' complements 'NameSeg' (which performs segment inflation now) and sets or gets segment names of selected units, which helps storing complex selections permanently. See also Selections > Yanaconda and Python help to define selection subsets. |
7.11.2 | Improved consistency: ListObj also lists inactive objects. |
7.10.29 | New support for NFS mounted multi-user YASARA installations. See Essentials > Running YASARA in special environments > Running YASARA from an NFS mounted volume. |
7.10.27 | New feature: when a simulation is switched off, YASARA wraps molecules that crossed a periodic boundary such that a maximum number of atoms are placed inside the cell. |
7.10.26 | Improved command: MUSTANG based structural alignments using 'Align' have been speeded up by an order of magnitude in Windows. |
7.10.18 | New guide and features for running YASARA on clusters: read Essentials > Running YASARA in special environments > Running YASARA on a cluster. |
7.10.15 | Improved command: 'Align' accepts an additional parameter to help MUSTANG align difficult oligomers. |
7.10.12 | New behavior: LoadSce now only sets surface parameters if a change of settings is requested with 'Settings=Yes'. |
7.10.10 | Improved command: pKaRes can determine the pKas predicted during a neutralization experiment. |
7.9.9 | New macro: md_runsteered.mcr runs a steered molecular dynamics simulations. More details in the user manual at Recipes > Run molecular dynamics simulations. |
7.9.5 | Improved commands: 'SaveSim' and 'LoadSim' protect the simulation snapshots with a checksum to minimize problems with disk data corruption. |
7.9.2 | New highlight: YASARA includes Arun S. Konagurthu's MUSTANG program to create pairwise and multiple structural alignments. Click Analyze > Align > Objects with MUSTANG. |
7.8.28 | Improved command: 'Tabulate' can add strings to a table. |
7.8.20 | New command: 'SaveAli' saves structural or sequence alignments in YASARA or FASTA format. Click Analyze > Align > Save alignment. |
7.8.15 | New highlight: YASARA supports local Smith&Waterman and global Needleman&Wunsch sequence alignments. Click Analyze > Align. |
7.8.10 | New command: 'AlignPar' sets various alignment parameters. Click Analyze > Align > Parameters. |
7.7.31 | New highlight: The 'SupMulti' command superposes multiple objects together using the Theseus maximum likelihood approach developed by Douglas Theobald. This puts more emphasis on structurally conserved regions, allowing to superpose NMR bundles automatically without having to specify a target region. Click Analyze > Superpose > Multiple objects. |
7.7.28 | Improved force field parameter assignment for 3- and 4-rings. |
7.7.26 | New feature: The radii of sticks in balls&sticks and sticks alone can now be set independently. Click View > Stick > Parameters. |
7.7.10 | Improved command: 'Clean' deletes water molecules that overlap with other atoms or each other. |
7.7.4 | New feature: YASARA builds nucleotides, DNA and RNA in all conformations. The 'BuildRes' command builds the first nucleotide, 'AddRes' appends at the 3' end, 'BuildMol' builds an entire nucleic acid based on a sequence. |
7.7.3 | Improved commands: 'ShowTorus' and 'ShowSphere' support a new 'Alpha' parameter to create transparent objects. For 'ShowSphere', this change is not entirely backward compatible. |
7.7.2 | Improved command: 'ListHBo' provides more intuitive output by listing atoms in the first selection that are hydrogen bonded with atoms in the second selection (i.e. bonds are listed in only one direction now). |
7.7.1 | Improved Yanaconda macro language: the 'in' operator checks if a list contains a certain value, the priority of the bitlogical operators has been set higher than comparisons, just like in Python. The variables 'FirstObj' and 'LastObj' store the number of the first/last *active* object and -1 of no object is active. |
7.6.29 | Improved commands: 'ListRes', 'ListMol', 'ListConRes', 'ListConMol', 'ListHBoRes' and 'ListHBoMol' now return unique residue and molecule ids instead of potentially ambiguous residue numbers and molecule names. |
7.6.19 | New feature: Commands like 'SavePDB' now support the forthcoming new PDB format V3.0. Since it is less consistent and likely to cause problems with other programs, the original PDB format stays the default. |
7.6.17 | New commands: 'AddPos' adds atom positions to an internal table, 'AveragePos' and 'RMSF' use these data to calculate average positions and root mean square fluctuations. |
7.6.10 | Improved macro: 'md_analyze' calculates B-factors and the time-average structure from the simulation trajectory. |
7.6.5 | Improved macro: 'md_analyzeres' also calculates per-residue fluctuations |
7.5.30 | Improved command: 'SolvEnergy' is significantly faster, and the results have been optimized for accuracy. |
7.5.20 | Improved command: 'Clean' deletes residues that overlap significantly with other residues and are most likely slightly different ligands bound to the same active site, like BTN/BTQ in 2F01. |
7.5.14 | Improved command: 'Wait' can wait until the users marks an atom, distance, angle or dihedral. |
7.5.11 | Improved command: 'MarkAtom' returns the numbers of the currently marked atoms. |
7.5.8 | New command: 'CorrectConv' corrects errors in naming conventions (CH2 groups, Val/Leu side-chain flips) during a simulation to aid high-temperature NMR structure determination protocols. Click Simulation > Automatic correction of > wrong naming conventions (Dynamics+). |
7.5.4 | New feature: The 'Check' command performs a new 'NameConv' check of naming conventions (CH2 groups, Val/Leu side-chain flips) and also handles the checks for cis-peptide bonds and wrong isomers. The old commands 'CheckCis' and 'CheckIso' are now deprecated. |
7.5.3 | Improved command: 'ShowHBo' supports a new 'Extend' flag to extend selections to hydrogen bonding partners, making it easy to show hydrogen bonds involving selected atoms. Click View > Show hydrogen bonds. |
7.4.29 | New movie: Proteins for beginners, NMR structure determination, information content of NOE restraints, refining NMR structures and error detection by Sander Nabuurs, separate download from www.yasara.org/movies |
7.4.27 | Improved commands: 'Label' and 'Unlabel' can now also (un)label individual segments. |
7.4.26 | New movie: Methionine synthase, example for visualizing enzymatic mechanisms with YASARA, by Richard Deth, separate download from www.yasara.org/movies |
7.4.24 | Improved command: 'Clean' renames left-over single OT1/OT2 atoms to O. |
7.4.22 | New highlight: YASARA now features an accurate and fast, multi-threaded algorithm to calculate molecular surfaces in real-time including all cavities. Click View > Show surface > Parameters > Numeric. |
7.4.18 | Improved feature: molecular surface calculations using the Gaussian approximation have been calibrated to reproduce the results of the new, more accurate molecular surface algorithm above. |
7.4.16 | New macro: md_analyzesecstr creates a 3D plot and text table of the secondary structure changes during a simulation. |
7.4.13 | Improved speed: YASARA is now compiled with a higher optimization level. |
7.4.1 | New plugin: The ConSurf interface developed by Joost Van Durme and Sebastian Maurer-Stroh colors proteins by sequence conservation (using the ConSurf server by Landau et al.). Click View > Color > Molecule by ConSurf. The similar PDBFinder2 color mapping has been moved to View > Color > Residue by feature. |
7.3.30 | Improved surfaces: Calculations involving surface environments have been speeded up by 25%, surfaces also require significantly less memory. |
7.3.28 | Improved command: 'Transfer' supports three different ways of handling local atom coordinates during an object transfer. When an object is transferred into the simulation cell, its CRYST1 record is set, so that the simulation cell can be saved in PDB files. Click Effects> Transfer. |
7.3.21 | New feature: The 'SurfPar' command allows to choose between two sets of radii for molecular and solvent accessible surfaces. Standard VdW and more realistic effective solvation radii. Click View > Show surface > Parameters. |
7.3.20 | Improved command: 'Dihedral' also sets and gets improper dihedrals if 'bound' is set to 'yes'. |
7.3.15 | New workarounds for many bugs in Linux OpenGL drivers, especially for older video cards like e.g. Radeon 9X00, Intel integrated chipsets, Matrox G400. |
7.3.11 | New highlight: YASARA has been ported to Mac OS X, including special support for Mac gadgets like the Mighty Mouse. Watch the help movie 'Working with YASARA' for details. |
7.3.4 | New command: 'SeqSelector' toggles the display of the sequence selector at the bottom. Click Window > Show sequence. |
7.2.26 | Improved support and workarounds for MESA indirect software rendering in Linux. |
7.2.25 | Improved command: 'FramesPerSec' can also deactivate screen redraws when YASARA is idle to save CPU power. The SavePower command is deprecated. |
7.2.24 | New feature: Hydrogens can be selected by their name according to many different nomenclatures. See Selections > Additional selection types allow to filter for various properties > 'PDB', 'PDBRev'... |
7.2.22 | Improved command: 'LoadPDB' corrects the hydrogen nomenclature unless 'Correct' is set to 'No'. |
7.2.20 | Improved command: 'AddHyd' adds amide and guanidine hydrogens matching PDB naming conventions. |
7.2.18 | New command: 'AtomSymbol' toggles the display of the chemical element symbol inside atoms that are cut open. Click Effects > Atom appearance > Element symbol. |
7.2.15 | Improved command: 'Clean' swaps amide and guanidine hydrogens to match PDB naming conventions. |
7.2.10 | Improved support for ATI Radeon cards in Linux: if driver >=8.X.Y is installed, graphics run significantly faster. |
7.2.7 | New feature: Compressed files with '.Z' extension can now be loaded directly just like '.gz' files. |
7.2.6 | Improved command: 'CD' allows to always change the working directory on startup, click Options > Change directory. |
7.2.5 | New command: 'ShowButton Continue' shows a continue button and sets the Yanaconda variable 'ContinueButton' to true if pressed. |
7.2.4 | Improved command: 'List' accepts a new 'Compress' parameter to return a compressed selection list, see Commands > Analyze > Scene content > List. |
7.2.3 | New feature: The 'Charge' command has improved capabilities to not only set net charges but also individual atom charges. This change is not entirely backward compatible. |
7.2.2 | Improved user interface: file selection menus provide various shortcuts to Home, Documents, Pictures etc. |
7.2.1 | New command: 'Install' automatically installs POVRay or Python, click Help > Install. |
7.1.30 | Improved command: 'Raytrace' creates PNG images by default to save disk space. |
7.1.28 | New feature: The neutralization experiment allows to request a certain NaCl contration and thus add more salt ions than needed to neutralize the cell (click Options > Experiment > Neutralization). |
7.1.27 | Improved command: 'Mass' also lists the summed up mass. |
7.1.26 | New command: 'ShowTorus' draws a ring-, horn- or spindle-torus. Click Effects > Show solid > Torus (Model+). |
7.1.25 | Improved window manager: if all animations are disabled, clicks on icons and buttons now provide more visual feedback. |
7.1.24 | Improved Yanaconda macro language: the 'rnd' function can randomize strings, e.g. to create random RGB colors. |
7.1.17 | Improved command: 'JoinObj' can now also join polygon meshes like arrows, spheres, boxes etc. |
7.1.14 | New feature: Dummy atoms (element 0) can now be included in a simulation without causing an error message. |
7.1.10 | Improved command: 'SavePower' now reduces YASARA's CPU requirements to truly 0 if no input is made. Click Window > Save power. |
7.1.9 | Improved command: 'Wait' supports the new unit 'Femtoseconds' to make waiting during a simulation more straightforward. |
7.1.7 | New highlight: YASARA's graphics engine now supports diffuse shadows and ambient lighting for balls to sticks, even on very old video cards. Watch the new help movie 'Lighting and shadows'. |
7.1.6 | Improved commands: 'Sup' and 'RMSD' have improved flipping capabilities for equivalent atoms to minimize the RMSD: Hydrogens are now also considered and flipped atoms are listed in the console. |
7.1.5 | Improved selection language: 'Segment' switches to a selection of macromolecular segments, read Selections > Additional selection types > Segment. |
7.1.4 | New command: 'UndoLevels' sets the number of undo levels without having to edit yasara.ini. Click Options > Undo levels (Model+). |
7.1.3 | Improved command: 'LoadPDB' allows to configure the path of a local PDB installation, click File > Load > PDB file from local PDB. |
7.1.2 | Improved command: The 'Lightsource' command now also configures ambient lighting and shadows, the 'Shadow' command is deprecated. |
7.1.1 | New highlight: YASARA now has a newly styled look, that also adapts to your current operating system, see www.yasara.org/looks. Click Window > Style (Model+). |
6.12.31 | Improved commands: 'LoadSce' and 'SaveSce' now also load/save the projection, antialiasing, point & line appearance, fog and hbond colors, lighting parameters, surface parameters and cell boundary. |
6.12.30 | Improved command: 'WinFont' now allows to choose between 6 different fonts, click Window > Font. |
6.12.29 | Improved command: The 'HUD' command can show the head-up display with an antialiased font, click Window > HUD > Antialiasing. |
6.12.28 | Improved command: The 'ConsolePar' command can show the console with an antialiased font, click Window > Console > Parameters. |
6.12.27 | Improved command: 'AnimateWin' command supports a new 'tilting' animation, click Window > Animation > Tilt. |
6.12.26 | Improved plugins: The 'CheckBoxMenu' allows to set the default checkbox states by appending '(Checked)' to the box text. |
6.12.19 | New feature: While a window is on screen (e.g. to interactively adjust dihedral angles), the scene can still be moved and rotated by holding down a mouse button outside the window. |
6.12.17 | New feature: When specifying a macro as a command line argument, it is now possible to add variables, see Essentials > The command line parameters. |
6.12.13 | Improved selection language: The 'with bond angles to' operator analyzes second neighbors in the molecule. See Selections > Selections can be combined.. > The 'with <>X bond angles to' operator. |
6.12.10 | Improved typing and force field parameter assignment for small molecules. |
6.12.8 | Improved commands: Load* and Save* now support many more OpenBabel based fileformats. |
6.12.3 | New highlight: The 'Processors' command activates support for multiple CPU cores, heavily speeding up molecular simulations, see www.yasara.org/parallelmd and click Options > Processors (Dynamics+). |
6.12.1 | Improved commands: 'Fix' and 'Free' are now included in the undo/redo history. |
6.11.29 | New feature: Up to four bond lengths, bond angles and bond dihedrals can now be changed together interactively. Mark two atoms, then click Geometry > Bond .. in the atom context menu. For more details, check the 'Distance', 'Angle' and 'Dihedral' commands (Model+). |
6.11.27 | Improved support for Windows Vista. |
6.11.24 | Improved command: 'LoadPDB' accepts a 'Model' parameter to load only one model from an NMR bundle. |
6.11.22 | New command: 'SwapBond' changes an existing bond order, the use of 'AddBond' for this purpose is deprecated. Click Edit > Swap > Bond. |
6.11.21 | Improved Yanaconda macro language: the 'join' function concatenates a list to a single weak string. |
6.11.20 | Improved selection language: the 'without contribution to .. surface' selects buried residues that do not contribute to a certain surface. |
6.11.11 | New command: 'MoveMesh' moves a polygon mesh in the local coordinate system to facilitate rotations around certain points. |
6.11.5 | New feature: YASARA's assembly language core now supports the SSE3 instruction set found in PentiumIV Prescott, Athlon64 Venice, Opteron 90nm and newer CPUs. On AMD Opteron, the speedup for MD simulations is ~10%. Make sure to either select 'Many' or a CPU architecture with SSE3 on the download page. |
6.11.3 | Improved command: 'Temp' accepts a new 'reassign' parameter to toggle the reassignment of atom velocities according to a Maxwell-Boltzmann distribution. |
6.11.1 | Improved command: 'LoadPDB' automatically adds missing CONECTs if the 'Correct' flag is set. Using LinkAtom is no longer needed. |
6.10.30 | New example macro: md_refine.mcr refines a homology model and analyzes individual snapshots, check the docs at Recipes > Refine a homology model. |
6.10.28 | Improved command: 'Link' does a better job ignoring bumps instead of assigning covalent bonds. |
6.10.26 | Improved command: 'ListObj' now also lists those objects that do not contain atoms. |
6.10.24 | New feature: The new parameter 'SetPar' of the 'ForceField' command allows to set optimal default simulation parameters, click Simulation > Force field (Dynamics+). |
6.10.19 | Improved simulations: If the simulation cell includes only a small part of the protein, the simulation runs much faster now with (Y)AMBER force fields. |
6.10.8 | New highlight: The 'Crystallize' command fills the unit cell with symmetry related copies of the selected object. Click Edit > Crystallize (Dynamics+). |
6.10.4 | Improved macro language: the 'chr' function converts an ASCII number to a character string. |
6.9.22 | New feature: Amino acid side-chains bound to ligands or metals are now shown when choosing one of the trace, ribbon or cartoon scene styles. |
6.9.20 | Improved commands: 'LoadPDB' and 'SavePDB' preserve the crystallographic symmetry REMARK 290. |
6.9.18 | New command: 'Compare' finds differences between atom and residue selections. Click Analyze > Compare. |
6.8.19 | Improved command: 'NiceOri' can choose a nice orientation for the entire scene. Click Effects > Orientation > Set nicely for scene (Model+). |
6.8.13 | Improved command: 'SwapRes' can swap nucleotides to Uridine and handle nucleotides like ATP or GDP. |
6.8.6 | Improved command: 'BuildRes' supports a 'Center' flag to disable centering of the newly built residue. |
6.8.1 | Improved command: 'SwapRes' keeps all useful side-chain dihedral angles to minimize reorientations (Model+). |
6.7.25 | Improved command: 'RayTrace' supports a new 'Background' parameter to create transparent backgrounds. |
6.7.15 | New highlight: The YAMBER3 force field provides another improvement in force field accuracy (Dynamics+). |
6.7.10 | Improved command: 'SurfPar' can display the current surface parameters. |
6.7.8 | Improved graphics: Lines are now drawn with antialiasing if requested (Window > Antialiasing) and supported by your OpenGL driver. |
6.7.6 | Improved command: 'ColorPar' allows to choose all rainbow colors for the secondary structure elements. Click View > Color > Parameters > Secondary structure. |
6.6.25 | Improved selection language: the 'with distance >X from' operators provide more intuitive results for 'Res', 'Mol' and 'Obj' selection units. |
6.6.19 | New feature: MD simulations with solvents other than water are now much easier. Check the documentation of the commands 'FillCellObj' and 'PressureCtrl' (Dynamics+). |
6.6.18 | New command: 'Mass' sums up atomic masses, click Analyze > Mass of. |
6.6.17 | Improved command: FillCellObj allows to specify a density to easily fill the simulation cell with special solvents. Click Simulation > Fill cell with (Dynamics+). |
6.6.16 | New command: 'SolvDensity' measures the density of any solvent, the 'WaterDensity' command is now deprecated. |
6.6.12 | New feature: The current energies are displayed in the simulation HUD on the right side and can be quickly recalculated by pressing the key left to '1'. |
6.6.11 | Improved commands: 'CorrectCis' and 'CorrectIso' can now also correct unusual amino acids. |
6.6.10 | New feature: Having grabbed a single object for movement, it is now possible to grab the entire scene again by clicking a second time on the object name in the top right HUD. |
6.6.9 | Improved commands: 'Sup' and 'RMSD' can now perform full matching of atom and residue names. |
6.6.6 | New highlight: YASARA can now calculate force field energies individually for objects, molecules, residues and atoms. This makes it easy to localize regions of high-energy. Click Analyze > Energy (Dynamics+). |
6.5.29 | New feature: The commands 'Sup' and 'RMSD' can now also shuffle atoms around within a residue to easily superpose molecules with different atom orders. |
6.5.20 | New default: The 'CorrectCis' command does not correct cis-prolines by default now. |
6.5.15 | Improved command: 'TransformObj' supports a flag to keep the global object position after transformation of atom coordinates. This is now the default. |
6.5.7 | New command: 'RenumberObj' reorders the objects in the scene, helpful to close gaps in the HUD if objects have been deleted. Click Edit > Number > Objects. |
6.4.30 | Improved command: 'Clean' adds cysteine bridges between close CYS SG atoms. |
6.4.29 | New feature: Atoms causing an error message are now automatically highlighted. |
6.4.28 | Improved command: 'LoadPDB' supports a 'correct' option to automatically delete unusually long CONECT bonds. |
6.4.27 | Improved command: 'Clean' detects alternate conformations of entire molecules put on top of each other and deletes the one with the lower occupancy. |
6.4.26 | Improved commands: 'LoadPDB' and 'Clean' detect and correct shifted atom names. |
6.4.25 | Improved commands: Virtually all YASARA commands now support compression when reading or writing files whose names end with '.gz'. |
6.4.23 | Improved commands: 'Sup' and 'RMSD' display a warning when trying to superpose atoms with different names. |
6.4.21 | Improved plugin: The PDBFinder2 interface retrieves data from a new server and better handles proteins with chain-breaks. Click Analyze > PDBFinder2 properties. |
6.4.15 | Improved command: 'Clean' sorts backbone and side-chain atoms within each residue. |
6.4.9 | Improved commands: 'BuildRes', 'AddRes' and 'SwapRes' can now select specific Asp, Glu, His and Cys protonation states via special residue names. |
6.4.8 | Improved command: 'Tabulate' now also adds string return values to a table, e.g. 'Tabulate NameRes all' tabulates all residue names. |
6.4.7 | Improved experiment: The minimization checks for regions with strong bumps and performs a local steepest descent minimization without electrostatics first to avoid nuclear fusion caused by Coulomb attraction exceeding VdW repulsion. |
6.4.5 | Improved command: 'Energy' explicitly returns a planarity energy also for the NOVA force field to identify severe planarity problems. Total NOVA energies therefore change a bit. |
6.4.3 | New feature: YASARA now calculates solvent accessible surfaces using optimized 'effective' Van der Waals radii that implicitly consider hydrogen bonds. For best results, the probe radius should be set to 1.4 A (click View > Show surface > Parameters). |
6.3.27 | Improved command: 'List' supports a new 'Format' parameter to also get names in specific formats, not only numbers. |
6.3.26 | New commands: 'PosMol' and 'PosRes' set and get the position of the geometric center of molecules and residues, click Effects > Position. |
6.3.25 | Improved command: 'SecStrRes' returns the secondary structure as a list of character strings 'H','E','T' and 'C'. Numerical codes are deprecated. |
6.3.24 | New highlight: the commands 'GroupDistance', 'GroupAngle' and 'GroupDihedral' calculate the distance between geometric centers and the angles between lines and planes optimally fit through groups of atoms, e.g. the angles between two helices or phenyl rings. Click Analyze > Geometry (Model+). |
6.3.23 | Improved command: 'SaveMOL2' stays closer to the file format when saving proteins. |
6.3.20 | New feature: The 'Surf' command supports a new 'unit' parameter to calculate surface areas per molecule, residue or atom. |
6.3.16 | Improved command: 'Color' accepts multiple sequence alignment also in FASTA format when coloring by sequence conservation. |
6.2.12 | New command: 'Name' sets or gets the names of objects, molecules, residues and atoms. The 'Rename' command is now deprecated. |
6.2.10 | New command: 'UnlabelDis' deletes distance labels between selected atoms. Click Effects > Unlabel > Distance. |
6.2.7 | New workaround for flickering problems on Intel GMA 9xx graphics chips when running YASARA fullscreen. |
6.2.5 | Improved command: When 'Raytrace'ing with outlines, black labels are excluded to allow proper labeling of schematic figures. |
6.1.24 | Improved bond typing: A weighted average of bond length and bond angle deviations is now used to determine hybridization states. |
6.1.23 | Improved command: 'SwapAtom' knows all standard (order dependent) bond lengths between organic elements and updates them accordingly. |
6.1.22 | New feature: 'Check WaterPos' calculates normality Z-scores for water molecules to identify those at unlikely positions, e.g. a hydrophobic protein cavity. Click Analyze > Check (Dynamics+). |
6.1.19 | Improved experiment: Neutralization uses an improved algorithm to avoid placing water molecules in cavities where a vacuum would be energetically more favorable. |
6.1.17 | Improved macro language: the 'dirname' function extracts the directory name from a string. |
6.1.15 | New improved algorithm to remove center-of-mass-motion from a simulation, solutes are now less likely to pass periodic boundaries, which makes visualization easier (Dynamics+). |
6.1.14 | Improved command: 'Sim Pause' can now be used to pause a simulation after a given time. Click Simulation > Simulator > Pause in... |
6.1.13 | Improved commands: 'Label' and 'Unlabel' are now restricted to create and delete labels of a given unit type. Click 'Effects > Unlabel > All above' to delete all labels at once. |
6.1.12 | Improved commands: 'Sup' and 'RMSD' can determine the chemical equivalence of molecules with exotic atoms to minimize the RMSD via the 'flip' flag. |
6.1.11 | Improved command: 'ForceField' allows to set the charge assignment scheme: AutoSMILES, AM1BCC or AM1 (for comparison and validation only). |
6.1.10 | New feature: The 'AutoSMILES' algorithm automatically splits long aliphatic lipids that contain too many atoms for QM charge derivation (Dynamics+). |
6.1.9 | Improved command: 'Clean' makes external single atoms bound to a residue part of this residue, e.g. three oxygens bound to Cys SG atoms. |
6.1.8 | Improved command: 'Experiment' automatically cleans the soup in case hydrogens are missing, 'Neutralization' does a better job removing waters from the protein core. |
6.1.7 | Improved command: 'Clean' deletes terminal residues with incomplete backbone, which are usually X-ray artifacts. |
6.1.6 | Improved feature: automatic force field parameter assignment and QM optimization in water are now 6x faster in YASARA for Windows. |
6.1.1 | New highlight: The 'AutoSMILES' algorithm fully automatically parameterizes organic molecules for simulation, including assignment of point charges by combining the high-throughput AM1BCC approach with a large SMILES-based library of optimal RESP charges, making it possible to run MD simulations of most PDB files at the touch of a button. See www.yasara.org/autosmiles or Recipes > Running molecular dynamics simulations > Preparing the force field > Deriving new (Y)AMBER parameters (Dynamics+). |
5.12.31 | Improved typing of double bonds outside rings. |
5.12.30 | Improved selection language: the 'Charge' operator allows to select by net charge. Look at the end of the 'Belongs to or has' list or read Selections > Additional selection types > Charge. |
5.12.29 | New help movie: '3.4 Simulation and quantum mechanics of small molecules' introduces fractional bond orders and pH-dependency, shows how to build and simulate small molecules, and how to use quantum mechanics to optimize geometries and compare tautomers. Click Help > Play help movie > Simulation and QM of small molecules. (Dynamics+) |
5.12.28 | Improved command: 'LabelDis' accepts a new 'bound flag' to label only distances between bound atoms. |
5.12.27 | New highlight: The 'QuantumMechanics' command activates the semi-empirical MNDO, AM1 or PM3 quantum chemistry methods provided by the built-in YAPAC, a customized and validated derivative of MOPAC. Click Options > Quantum mechanics (Dynamics+). |
5.12.26 | Improved command: 'Label' supports two new format options 'ATOMTYPE' and 'ATOMCHARGE' to label with atom type and charge respectively. |
5.12.25 | New feature: 'pH' sets the implicit solvent model used in quantum chemistry calculations, either none when working in vacuo or COSMO by A.Klamt when working in solution. |
5.12.24 | Improved command: 'Sim Init' automatically adds springs to enforce virtual bonds to metal ions (i.e. headless arrows added by ShowArrow or by CONECT records in the original PDB file) (Dynamics+). |
5.12.23 | New highlight: The 'Optimize' command tunes the geometry of molecules containing up to ~100 atoms using semi-empirical quantum chemistry. Click Edit > Optimize. |
5.12.22 | Improved command: 'AddBond' accepts a new 'bound flag' to modify only existing bonds. Click Edit > Add > Bond. |
5.12.21 | New command: 'FormEnergy' calculates the heat of formation using semi-empirical quantum chemistry. Click Analyze > Energy > Formation. |
5.12.20 | Improved command: 'AutoMoveImage' supports two ways of repeating the automatic image movement: 'Cycle=MoveBack' and 'Cycle=JumpBack'. |
5.12.19 | New command: 'TypeAtom' retrieves the currently assigned force field atom types, for example to label atoms accordingly. |
5.12.18 | Improved command: When importing molecules with OpenBabel using 'Load*', the 'Resonate' flag allows to automatically replace alternating single/double bonds with the proper resonance form. |
5.12.16 | Improved command: 'Clean' replaces seleno-methionine with methionine and deletes NMR dummy atoms (element 0). |
5.12.15 | New highlight: The new General AMBER Force Field (GAFF) provides force field parameters for any organic molecule. |
5.12.14 | Improved typing of bonds and handling of alternate atoms. |
5.12.10 | New WHAT IF released as part of the Twinset. WHAT IF's homology modeling module now also works in the Twinset. |
5.12.7 | Improved handling of cyclic peptides: Traces, tubes and ribbons are now drawn without a gap, provided that the cyclic peptide bond is indicated with a 'CONECT' in the PDB file. |
5.12.3 | New command: 'KekulizeBond' converts resonance bonds with fractional bond orders to alternating single/double bonds. Click Edit > Adjust bond orders > Kekulize bond. |
5.12.2 | Improved command: 'RMSD' accepts a 'flip' flag like 'Sup' to minimize the calculated RMSD by flipping chemically equivalent atoms. |
5.12.1 | New command: 'ResonateBond' converts alternating single/double bonds to the proper resonance form. Click Edit > Adjust bond orders > Resonate bond. |
5.11.26 | Improved command: 'ShowTrace' displays a trace also for Calpha only proteins when you press <F4>. |
5.11.25 | Improved command: 'Clean' detects residues with missing bonds and invokes 'Link' to find them before adding hydrogens. |
5.11.24 | Improved command: 'LoadPDB' automatically searches and types links in standard residues with non-standard atom names. |
5.11.23 | New workaround for a new ATI Radeon OpenGL Linux driver bug (missing secondary structure), updated installation hints at Troubleshooting > YASARA runs slowly > You are running Linux with an AMD Radeon. |
5.11.22 | Improved command: 'Link' uses a new algorithm to find also large numbers of bonds quickly. |
5.11.20 | Improved command: The tubes and ribbon created by 'ShowSecStr' stay correct when the protein crosses a periodic boundary. |
5.11.19 | Improved command: 'PosAtom' can now set and get the mean position of an atom selection. |
5.11.18 | New highlight: The improved 'TypeBond' command employs a new algorithm combining graph theory with chemical knowledge on valence ambiguities and preferred tautomers to type complicated hetero-polycycles, e.g. in PDB file ligands. See www.yasara.org/typing or click Edit > Type bonds. |
5.11.14 | Improved command: 'LoadPDB' provides special support for ancient but still official PDB files with weird atom names. |
5.11.10 | Improved plugin: the OpenOffice Impress import filter now supports OpenOffice 2.0. Click Options > Macro & movie > Import movie |
5.11.6 | New Yanaconda function: 'ord' returns the summed ASCII code of the given string |
5.11.4 | Improved command: 'Dihedral' can now change improper dihedrals, also interactively from the atom context menu. |
5.11.3 | New command: 'Dipole' calculates the electric dipole moment. Click Analyze > Dipole moment of (Dynamics+). |
5.11.2 | Improved selection language: the operator 'within sequence' selects units belonging to a given sequence, e.g. ColorRes Lys within sequence Arg Lys Phe,yellow. |
5.11.1 | New workaround for a Mandriva Linux 2006 AMD64 problem, which is lacking the library 'libncurses'. |
5.10.15 | Improved selection language: Single or double quotes can be used to span unusual atom/residue/object names with special characters like spaces. |
5.10.9 | New highlight: Structural alignments using the CE, Multiprot and Sheba methods are available for Windows and Linux. Click Analyze > Align. Contributed by Emmanuel Bettler and Mikael Roche. |
5.10.8 | Improved command: 'BuildAtom' allows to define the position of the new atom, which helps to place dummy atoms e.g. in the center of a phenly ring to measure distances. |
5.10.7 | New command: 'pKaRes' assigns pKa values to selected residues that override the predictions made during the neutralization experiment. Click Options > Residue pKa. |
5.10.5 | Improved command: 'SwapRes' can swap residues to Uracil and keeps the chi1 dihedral intact. |
5.10.1 | New highlight: The commands 'ShowSphere', 'ShowBox' and 'ShowCone' display solid spheres, ellipsoids, cubes, boxes, cylinders, cones, prisms and pyramids. Click Effects > Show solid. Click Help > Play help movie > 'Buckynut Island' for a demonstration (Model+, download from www.yasara.org/movies in YASARA View). |
5.9.25 | New Yanaconda function: 'trunc' returns the integer part of a number, rounded towards zero. |
5.9.18 | New command: 'MoveMesh' translates a polygon mesh in its local coordinate system to allow off-center rotations. Click Effects > Move > Mesh. |
5.9.15 | New command: 'SearchDoc' searches the YASARA user manual. Click Help > Search user manual. |
5.9.10 | Improved experiment: Neutralize does a better job at keeping original water molecules very close to metal ions instead of replacing them with newly added ones. |
5.9.6 | Improved command: 'Link' now uses the atomic bond radii and an 'allowed deviation' parameter to find bonds. The bond orders are also assigned automatically. |
5.9.2 | New highlight: The 'pH' command sets the default pH, YASARA now has extensive knowledge about pH-dependent bond orders and protonation patters of organic molecules and assigns bond orders and hydrogen atoms according to the chosen pH. See Commands > Options > Default pH (Model+). |
5.8.30 | Improved command: 'SampleLoop' allows to select the preferred secondary structure. |
5.8.24 | Improved command: 'LoadPDB' automatically topologyfies ligands in PDB files and assigns bond orders. |
5.8.21 | New highlight: The 'TypeBond' command analyzes any organic molecule and assigns fractional bond orders, making it easy to add hydrogen atoms. It is no longer required to manually add topologies for unknown molecules to yasara.def. See Commands > Edit > Bonds > TypeBonds. |
5.8.19 | Improved command: 'AddHyd' contains a new 'update' parameter to adjust bond orders to the newly added hydrogens. |
5.8.15 | New feature: Bonds to metals (which are not considered real bonds by MD force fields) are converted to virtual bonds and shown as cylinders when reading/writing PDB files. See Commands > Edit > Bonds > AddBond. |
5.8.10 | Improved command: 'AddBond' now accepts fractional bond orders to express resonance effects and a parameter to update hydrogens. See Commands > Edit > Bonds > AddBond. |
5.8.2 | New highlight: The POVRay interface has been heavily improved and now includes fog, textures (MakeImageObj), fore- and background images (ShowImage), exact background colors and the ability to add outlines for comic style graphics. See Commands > File > Screenshots > Raytrace. |
5.8.1 | Improved command: 'Color' accepts RGB atom colors and finds the closest matching color in YASARA's own color scheme. |
5.7.30 | New command: 'SaveMacro' creates a macro that restores selected parts of YASARA's current state: scene, visualization parameters, images, simulation parameters, window parameters. Click Options > Macro & Movie > Save macro. |
5.7.29 | Improved command: 'PressCtrl' can exclude axes from rescaling. |
5.7.28 | New highlight: The 'Projection' command toggles between perspective and parallel projection. Click View > Projection. |
5.7.21 | Improved command: 'RayTrace' and 'SavePOV' now also include the black outline of the comic atom texture (View > Atom appearance > Texture > Comic). |
5.7.20 | Improved command: 'AddHyd' automatically corrects bond orders and atom names of carboxyl groups. |
5.7.19 | Improved command: 'SaveXTC' and 'LoadXTC' have improved LFS support to handle trajectories larger than 2 GB in Linux. |
5.7.18 | New highlight: A new plugin automatically converts OpenOffice/PowerPoint presentations to YASARA movies, which makes it easy to augment them with hi-quality molecular animations. See Recipes > Create your own YASARA movies > Movies can be imported from OpenOffice and PowerPoint (Model+). |
5.7.17 | Improved command: 'Clean' corrects bond orders and atom names of carboxyl groups. |
5.6.30 | Improved command: 'AddBond' now gained the 'UpdateHyd' option to suppress the update of hydrogen atoms. |
5.6.29 | Improved plugins: Error reports and update requests now function without having to add an email server in plg/reporter.cnf |
5.6.23 | Improved command: 'ScaleForce Planarity' now includes not only improper dihedrals, but also normal dihedrals in planar systems. |
5.6.21 | Improved multi-monitor support: Set 'CorrectWin' in yasara.ini to 0 to disable the window size correction, which helps if the YASARA window is on monitor 2. |
5.6.16 | Improved command: 'WaterDensity' works better in non-periodic cells, where the vacuum layer between cell wall and atoms (caused by repulsive wall forces) is now excluded from the density calculation. |
5.6.14 | Improved command: 'PressureCtrl' now rescales only the simulation cell and not the atom coordinates if there are atoms outside a non-periodic cell. |
5.5.25 | Improved command: 'BuildMol' now also reads FASTA sequences to build a linear peptide chain (Model+). |
5.5.22 | New highlight: The 'Volume' command calculates VdW, molecular and solvent accessible volumes. Click Analyze > Volume of (Model+). |
5.5.20 | New command: 'ScaleForce' scales bond, angle, dihedral, planarity and non-bonded forces during a simulation. Click Simulation > Scale forces. The commands ScaleBSFC and ScaleNBI are now deprecated (Dynamics+). |
5.5.18 | New feature: Yanaconda macros can contain 'include' statements to include other macros (read Macros > Yanaconda macros can include each other). |
5.5.16 | Improved commands: 'CorrectIso' and 'CorrectCis' use a new dihedral-angle based algorithm to enforce correct stereochemistry during high temperature simulations. |
5.5.13 | New command: 'NiceOri' orients an object nicely (along its major axes). Click Effects > Orientation > Set nicely for object (Model+). |
5.5.12 | Improved command: 'CorrectCis' allows to exclude proline residues from cis-peptide bond correction. |
5.5.9 | Improved command: 'Clean' swaps methylene bridge hydogens to match PDB/XPLOR conventions for stereoassigned NOEs. |
5.5.1 | Improved force field parameter assignment for DNA/RNA bases. |
5.4.5 | New IMPORTANT feature: YASARA's internal force field representation has been changed. If you modified force fields, recompile them with 'yasara -upd' now. |
5.3.31 | Improved command: OpenBabel export with 'Save*' now offers a 'transform' option to restore original atom coordinates and a 'nameformat' option to choose among different atom naming conventions. A few OpenBabel for Windows issues have been fixed. |
5.3.30 | New feature: the order of covalent bonds can be shown in Ball&Stick style with 'ColorBonds Order'. |
5.3.28 | Improved command: 'SavePDB' allows to select the YASARA PDB format variant in addition to PDB standard and Xplor. |
5.3.20 | New IMPORTANT feature: The conventions for triclinic (=non-rectangular) simulation cells have been changed to match the PDB format. .sce or .sim files with non-rectangular cells have to be converted. Please update YASARA Dynamics (as a bonus, the PME code runs a bit faster now). |
5.2.28 | Improved detection of unusual DNA/RNA bases to display them as part of the DNA/RNA backbone. |
5.2.26 | New command: 'SecStr' assigns a custom secondary structure and analyzes the secondary structure content. The commands 'ShowSec' and 'HideSec' changed their names to 'ShowSecStr' and 'HideSecStr'. Click Analyze > Secondary structure of. |
5.2.24 | New feature: OpenBabel has been updated to version 1.100.2, the command 'Save*' now also exports atom charges assigned by the current force field. Click File > Save as > Other fileformat. |
5.2.17 | Improved command: If there are residues with alternate locations, 'Clean' keeps only the one with highest occupancy. |
5.2.13 | New highlight: The 'Check' command performs 20+ different WHAT_CHECKs of protein structures: bonds, angles, torsions, omega angle, Ramachandran plot, side-chain rotamers, proline rings, chirality, planarity, backbone conformation, peptide-plane flips, bumps, 3D packing quality, inside-outside distribution, unsatisfied H-bonds, flipped Asn/Gln/His side-chains, B-factors and atom occupancies. Click Analyze > Check (Twinset). |
5.2.11 | New command: 'PointPar' sets the style and thickness of point/wireframe objects (ShowESP,ShowGrid,WHAT IF MolObjects). Click Effects > Point & line appearance. |
5.2.9 | New highlight: The 'Align' command performs a structural alignment with the MOTIF algorithm. Click Analyze > Align (Twinset). |
5.2.7 | Improved command: 'LoadPDB' now searches a local PDB automatically if 'PDBPath' is defined in yasara.ini |
5.2.5 | New highlight: The 'OptHyd' command optimizes the hydrogen bonding network and flips Asn/Gln/His side-chains if that improves the network. Click Edit > Add > hydrogens to: object & optimize (Twinset). |
5.2.3 | Improved command: 'SaveMPG' now uses a quality instead of bitrate setting, which avoids encoding failures with some animations. |
5.2.1 | New highlight: The 'Regularize' command optimizes bond lengths, angles and chirality. Click Edit > Geometry > Regularize (Twinset). |
5.1.30 | Improved commands: 'Raytrace' and 'SavePOV' now also work in console mode, e.g. on a web server creating molecular graphics with YASARA. |
5.1.28 | New highlight: The 'ShowRota' command shows the backbone dependent rotamer distribution for selected residues. Click Analyze > Rotamers (Twinset). |
5.1.21 | Improved command: 'ScreenSize' also works in console mode and defines the aspect ratio of ray-traced output. |
5.1.20 | Improved selection language: the 'Property' operator selects atoms by their property value. |
5.1.19 | Improved command: 'ColorPar' can change the default color range for atom properties. |
5.1.18 | New command: 'Prop' gets and sets the new atomic property value that maps to WHAT IF's 'atomic value' and becomes very helpful in the Twinset. |
5.1.17 | Improved command: 'PosAtom' now also gets/sets atom positions in the global coordinate system. |
5.1.12 | Improved command: 'SaveXTC' wraps molecules around periodic boundaries to avoid saving 'broken' ones with bonds that span the simulation cell. |
5.1.11 | Improved command: 'TransferObj' can now also correctly transfer static surfaces and similar geometry to another coordinate system. |
5.1.10 | Improved commands: 'LoadSim' and 'LoadXTC' now have an option to disable secondary structure reassignment. |
5.1.9 | Improved commands: 'RayTrace' and 'SaveMPG' allow to disable the POVRay window. |
5.1.5 | New highlight: The 'SaveMPG' command creates MPEG movies, plain or ray-traced. Click File > Save as > MPEG movie (Model+). |
4.12.31 | Improved support for resolution independent movies. See Recipes > Create movies > The look of the movie. |
4.12.29 | Improved command: 'LoadXTC' applies the transformation history of the target object to avoid unwanted shifts. |
4.12.25 | New highlight: The 'SolvEnergy' command calculates solvation energies using a fast boundary element approach. Click Analyze > Energy > Solvation (Dynamics+). |
4.12.19 | Improved commands: 'AddHyd' and 'Clean' make better choices when inventing hydrogen names. |
4.12.17 | Improved command: 'Label' supports new format components: OBJNAME,OBJNUM,ATOMNAME and ATOMNUM. Click Effects > Label. |
4.12.15 | New highlight: YASARA now supports copy&paste, the console at the bottom has been heavily improved with history and selections. Click Essentials > The keys and mouse buttons > Using the console. |
4.12.13 | Improved commands: 'ListCon' and 'ListHBo' now also return the selected units, e.g. atomlist()=ListConAtom Mol A,Mol B. |
4.12.11 | New command: ConsolePar changes the size and font of the extended console (press <Space> twice to bring it up). Click Window > Console > Parameters. |
4.12.9 | Improved selection operators: 'with distance' and 'with atoms among' now consider periodic boundaries during a simulation. |
4.12.7 | Improved experiment: Neutralization does a better job at reaching the requested water density. |
4.11.30 | Improved secondary structure assignment for double beta bulges. |
4.11.29 | Improved support for hires notebook screens up to 1680x1050. |
4.11.24 | New feature: hydrogen bonds can now inherit the color of the bound atoms, click View > Color > Hydrogen bonds. |
4.11.23 | Improved quad-buffered stereo and ray-tracing of stereo images. |
4.11.14 | New command: 'FlipTab' flips a pair of table axes (columns, rows, pages). Click Options > Tables > Flip. |
4.11.13 | New feature: YASARA can now work with 250 objects at the same time (Model+) |
4.11.12 | Improved commands: 'Sup' and 'RMSD' calculate all permutations if several objects are selected and support a 'unit' parameter. Averages and standard deviations are no longer returned. |
4.11.11 | New Yanaconda functions: 'mean' and 'stddev' calculate the average and standard deviation of a list. |
4.11.10 | Improved command: 'Center' now also allows to center on atoms, residues and molecules. E.g. click Center > Atom in the atom context menu. |
4.11.9 | New highlight: Tables have been reimplemented and heavily improved. They can now be one-, two- or three-dimensional. The 'ShowTab' command visualizes tables using various styles. Click Options > Table > Show. |
4.11.8 | New command: 'MakeTab' creates a new table with one to three dimensions. Click Options > Table > Make. |
4.11.7 | New command: 'DelTab' deletes tables. Click Options > Table > Delete. |
4.11.7 | New command: 'Tab' sets or gets table cells, columns, rows, pages and entire tables. Click Options > Table > Set/get cells. |
4.11.6 | New command: 'Tabulate' adds new cells to a growing table and replaces the deprecated 'AddTab' command. |
4.11.6 | New command: 'SelectTab' selects a table for use by the new 'Tabulate' command. Click Options > Table > Tabulate. |
4.11.5 | New command: 'LoadTab' loads a table in plain text format from disk. Click Options > Table > Load. |
4.11.5 | Improved command: SaveTab allows to select a table, which supports the forthcoming release of heavily improved tables. This is one of the rare changes that are not backwards compatible but required for consistency. |
4.11.4 | Improved plugin: An interactive check for updates is available, click Help > Check for update. Contributed by Emmanuel Bettler. |
4.11.3 | Improved command: 'Link' now also assigns the order of covalent bonds for residues with topology information in yasara.def. |
4.11.1 | Improved command: 'FillCellObj' allows to define the maximum allowed sum of bumps. |
4.10.31 | New Yanaconda functions: 'sum' and 'average' sum up list elements and calculate the average. |
4.10.30 | Improved windows: all load/save dialogs have been enlarged so that long filenames are easier to read. |
4.10.29 | New command: 'Radius' calculates Van der Waals radii. Click Analyze > Radius of. |
4.10.28 | Improved commands: 'Occup' and 'BFactor' now allow to set unusual atom occupancies and B-factors from -99.99 to 999.99 for programs that expect different data like charges and radii in these columns of the PDB file. |
4.10.24 | New feature: YASARA now reads gzip compressed files (.gz extension) transparently. Time to compress your local copy of the PDB? |
4.10.21 | New command: 'MouseWheel' assigns one of four functions to the mouse wheel. Click Window > Mouse wheel command. |
4.10.20 | New command: 'SavePower' enters a special power saving mode for notebooks running on battery. Click Window > Save power. |
4.10.19 | New command: 'WinFont' changes the fonts used by YASARA's window manager. Click Window > Font. |
4.10.16 | New highlight: The 'FirstSurf' command combined with the new selection operators 'with distance from surface' and 'with contribution to surface' enables very flexible surface analysis. See Commands > Analyze > Surfaces > FirstSurf (Model+). |
4.10.15 | Improved command: 'Color' now returns the colors of the selected atoms: collist() = ColorAtom Obj 1crn |
4.10.14 | New Yanaconda feature: You can now loop over the content of a file, e.g. a list of PDB IDs: for id in file /home/id.txt, see Macros > There a four types of loops > Loops can run over a list. |
4.10.13 | Improved secondary structure assignment for some beta bulges. |
4.10.4 | New feature: 'yasara -txt' runs the program in plain text mode, see Essentials > Running YASARA in special environments > Running without graphics. |
4.10.3 | New movie available: 'PhD defence', a summary about the technology and science behind YASARA at www.yasara.org/multimedia. |
4.10.2 | Improved filename handling: loading a file with missing extension is now possible, and the working directory is searched before any subdirectories. |
4.10.1 | New feature: The mouse wheel scrolls through lists and selects the previous and next atoms. |
4.8.31 | Improved command: 'AddSpring' can now add springs to atoms without intramolecular interactions (ions). |
4.8.27 | Improved selection language: 'LocalX|Y|Z' and 'GlobalX|Y|Z' allow to select atoms by their positions. Selections by 'BFactor' and 'Occupancy' are now also possible. |
4.8.26 | New highlight: a Linux plugin to create MPEG movies and animated GIFs is available. Click File > Save as > MPEG/GIF movie. Contributed by Emmanuel Bettler. |
4.8.24 | Improved command: 'SwapRes' can now also swap non-standard amino acids like seleno-methionine. |
4.8.22 | New highlight: A structural alignment plugin using SHEBA (by J.Jung & B.Lee) is available. Click Analyze > Superpose > Objects automatically (Linux only). Contributed by Mikael Roche & Emmanuel Bettler. |
4.8.18 | New command: 'ColorPar' sets various default color schemes for chemical elements, secondary structure, B-factors. Click View > Color > Parameters. |
4.8.18 | Improved command: 'Zoom' now also considers the visibility of surfaces when fitting atoms on the screen and is much faster for large proteins. |
4.8.17 | Improved command: 'RayTrace' does a better job putting special textures (selected with 'AtomTexture') on the atoms |
4.8.13 | New command: 'PrintHUD' allows plugins to print to YASARA's head-up-display and is now also available in YASARA View. |
4.8.13 | New highlight: Several improvements make building small molecules very easy. Get an update and watch the new help movie 'Building small molecules' (Model+). |
4.8.12 | Improved command: 'AddBond' now automatically adapts the hydrogen atoms (if the object contains any) to the new bond order. |
4.8.8 | New feature: Python plugins can be run directly from the command line: yasara MyPlugin.py MyRequest ('MyRequest' is sent to the plugin, no selections are available). |
4.8.8 | Improved plugin: The PDBFinder2 plugin to analyze proteins now uses the BioASP server at www.bioasp.nl |
4.8.6 | New command: 'AddHydAtom' allows to add hydrogens to individual atoms, e.g. to quickly force Histidine protonation. |
4.8.3 | Improved command: 'AddHyd' is orders of magnitude faster now and places aliphatic hydrogens more intelligently. |
4.7.21 | Improved command: 'FillCellWater' and 'Experiment Neutralization' are now less likely to place waters inside homology models with a loose core packing. The second parameter had to be changed. Post-processing steps to delete these waters are not absolutely required anymore. |
4.7.18 | New Python plugin command: yasara.Finish() synchronizes the plugin with YASARA, more info at Plugins > Python plugins run in a separate thread |
4.7.10 | Improved sequence selector: atoms behind it are clickable while the sequence selector is transparent. |
4.7.4 | New highlight: A 'neutralizing plasma' allows to run Particle Mesh Ewald simulations also with non-neutral simulation cells. Simulation algorithms and energy calculations have been improved and run a bit faster now. Update now! |
4.7.3 | Improved command: 'Surf' calculates surface areas 0.1% more accurately. |
4.6.25 | Renumbering residues is now restricted to the 'RenumberRes' command. To renumber the residues in object 1crn, type 'RenumberRes Obj 1crn'. The shortcut 'RenumberObj 1crn' is deprecated. |
4.6.18 | New movie feature: When a movie ends (or you click on Options > Macro & Movie > Stop), the scene including background colors+working directory is restored. To avoid that, run the movie as a macro. |
4.6.17 | New command: 'ShowCom' opens the documentation for a given command in the browser. |
4.6.16 | Improved command: The default Calpha color 'cyan' is now passed on to the ribbon/tubes/cartoons if all backbone atoms are cyan, not only if all residue atoms are cyan. |
4.6.15 | New command: 'ShowDoc' opens the user manual in a browser window. |
4.6.14 | Improved commands: During a simulation, static surface objects ('ShowSurf') and calculated surface areas ('Surf') consider all objects simultaneously. |
4.6.7 | Improved command: 'CenterAll' centers all objects together, which keeps the superposition intact after loading multiple PDB files with centering disabled. |
4.6.5 | Improved command: 'LoadPDB' handles incorrect/single-sided CONECT records. |
4.6.1 | Improved commands: 'AddHyd' and 'Clean' now do a better job when working with alternate atoms and Val/Leu residues with swapped CG/CD atom names. |
4.5.20 | New highlight: Support for 3DConnexion input devices has been added (Linux only for now). Click Options > Input devices to adjust the settings (Model+). |
4.5.19 | New commands: 'GrabNext' and 'GrabPrev' grab the next and previous object for movement with mouse or 3DConnexion controller. Helpful when assigned to 3DConnexion controller buttons (Model+). |
4.5.18 | Improved command: 'Clean' now automatically deletes bonds to cations, which may not be present during simulations. |
4.5.17 | New optimized algorithms for several tasks that became bottle-necks when working with giant structures (300000 atoms). Many things run 100x faster now. See also the hints at Essentials > Working with extremely large structures. |
4.5.12 | Improved support for NFS mounted multi-user installations: In the docs, click Essentials > Running YASARA in special environments. |
4.5.12 | New release of the YASARA Models@Home distributed computing system with support for Redhat 9, Fedora Core, Mandrake 9, Windows XP. |
4.5.11 | New highlight: Three new surface movies available from www.yasara.org/movies : Introduction, Environments and Electrostatics. |
4.5.11 | Improved command: 'CountObj' now counts all objects, not just those with atoms. |
4.5.10 | New highlight: The 'ShowSurf' command shows Van der Waals, molecular and solvent accessible surfaces, either static or dynamically updated. |
4.5.9 | Improved command: 'MarkAtom' can now mark up to four atoms. |
4.5.8 | New highlight: The 'ColorSurf' command assigns surface colors and transparency, options include coloring by atom and electrostatic potential. |
4.5.7 | Improved selection language: 'with <>X bonds to' allows to select by the number of bound atoms. |
4.5.6 | New highlight: The 'SurfPar' command sets the surface resolution and activates an interface to Michel Sanner's MSMS program which calculates analytic molecular surfaces. |
4.5.4 | New highlight: The 'Surf' command allows to calculate VdW, molecular and solvent accessible surface areas (YASARA Model+). |
4.5.3 | Improved handling of unusual amino acids: even those forgotten in the official PDB hetgroup dictionary are recognized correctly. |
4.5.3 | New highlight: The 'AddEnv' and 'RemoveEnv' commands allow to define surface environments to analyze partial surfaces (YASARA Model+). |
4.5.2 | Improved experiment: Minimization converges faster now. |
4.5.1 | Improved selection language: 'visible' and '!visible' allow to select (in)visible atoms. |
4.4.30 | New Yanaconda operator: Like in Python, '//' performs a division with truncation of the result's fractional part, e.g. 3//2 = 0 |
4.4.29 | Improved logs: Specifying a filename with .log extension as a command line argument will automatically record a log. |
4.4.28 | Improved command: Logs recorded with 'RecordLog' are now flushed continuously and do not lag behind. |
4.4.25 | New Yanaconda function: 'onein' returns a random list element. |
4.4.15 | Improved command: 'Clear' now also clears the 'Tabulate'/'SaveTab' table. Use 'Del' instead of 'Clear' when adding values to a table. |
4.4.14 | Improved command: 'Tabulate' now accepts an arbitrary number of values to add to a table. |
4.4.12 | New command: 'SpeedUp' allows to toggle the speedup of movements when graphics are slow |
4.4.9 | Improved user manual: Click Commands > Index to get an alphabetic list of all YASARA commands |
4.4.7 | Improved installation: In Linux, you can now install YASARA as user A (e.g. 'root') and then work as user 'B' as long as you run it once as user 'A'. |
4.4.3 | Improved Yanaconda macro language: up to 1000 times faster (better list handling, reduced printout in the console) |
4.4.3 | Improved command: 'AddObj' returns the numbers of the first and last atom in the newly added object, e.g. first,last=AddObj 7 |
4.4.2 | Improved command: 'SplitObj' and 'OligomerizeObj' return a list of created objects, e.g. objlist()=SplitObj 5 |
4.4.2 | New Yanaconda feature: iterate over a list, e.g. selection()=ListAtom CA / for atom in selection |
4.4.1 | Improved command: 'ListAtom' and 'ListObj' return a list of atom and object numbers. |
4.4.1 | New Yanaconda feature: Assign the return values of YASARA commands to a list, e.g. mylist()=ListAtom CA |
4.4.1 | Improved command: 'MakeImageObj' returns the number of the created image. |
4.3.26 | Improved help movies: the 'OnError Continue' command makes sure that they will not stop if you make an error. |
4.3.16 | New ATI Radeon Linux HOWTO (click Troubleshooting>YASARA runs slowly), workaround for a Radeon Linux driver bug in 'ShowMessage'. |
4.3.14 | New highlight: A plugin for Bert de Groot's CONCOORD program allows to quickly sample conformational space and analyze protein flexibility. Click Edit > Sample. |
4.3.14 | New Yanaconda functions: 'min MyList' and 'max MyList' return the smallest and largest list element. |
4.3.13 | Improved command: 'Span' can now also determine the first and last residue number in a selection |
4.3.13 | New command: 'BFactor' gets and sets the BFactor. |
4.3.13 | Improved command: 'Temp' now also returns the current simulation temperature (YASARA Dynamics+) |
4.3.12 | New command: 'Charge' gets and sets the net charge. The old command 'NetCharge' is now deprectated (YASARA Dynamics+) |
4.3.12 | Improved command: 'Color' can now color by atom occupancy. |
4.3.12 | New command: 'Occup' gets and sets the atom occupancy. |
4.3.1 | Improved plugin support: 'NumberInputMenu[1-6]' allows to input 1 to 6 numbers and pass them to the plugin. |
4.2.27 | Improved commands: 'LoadSce', 'LoadPDB' and several other commands are now much faster for large files. |
4.2.15 | Workaround for an ATI Radeon Linux driver bug that caused color problems and showed random triangles (verified for fglrx 4.3.0-3.7.0 and Radeon 9600Pro) |
4.2.14 | New Yanaconda functions: 'sqr X' function returns X*X, 'cube X' function returns X*X*X |
4.2.11 | New command: 'Transfer' an object to the coordinate system of another object (e.g. if you moved one of two superposed objects away and want to get it back). |
4.2.1 | Improved command: 'AtomSize' can now freely change the atom sizes, which is the same as moving the near clipping plane. Helpful when cutting surfaces open. |
4.2.1 | Inconvenience solved: Showing just the side-chain and CA atom (e.g. in a ribbon) is now trivial (click on 'Show atoms'). |
4.1.25 | Improved pKa prediction accuracy in the 'Neutralization' experiment (YASARA Dynamics+) |
4.1.15 | Workaround for a SiS OpenGL driver bug that crashed YASARA (verified for SiS 650M chipset) |
3.12.24 | New Yanaconda functions: 'abs' function returns absolute values, 'sign' returns the sign (-1,0 or 1) |
3.12.23 | Improved command: 'Clean' automatically corrects CG/CD atoms in Val/Leu that got swapped. |
3.12.21 | Improved secondary structure assignment for wrong structures with lots of bumps. |
3.12.18 | New command: 'Span' allows to determine the first and last atom or object spanning a selection. Very useful in macros. |
3.12.11 | Command line arguments that do not end in .mcr, .yob, .sce are assumed to be PDB files and loaded instantly. |
3.11.24 | Improved command: 'DelLink' now handles problems caused by incorrect PDB files with single-sided bonds. |
3.11.23 | New plugin support: Python error messages are now displayed directly on screen including a traceback, also under Windows. |
3.11.17 | New highlight: The 'SwapAtom' command now also adjusts the bond lengths, making building easier. E.g. to add a methyl group to a hydroxyl group, just swap the hydroxyl hydrogen to carbon. |
3.11.16 | New command: 'UserInput' allows to disable disturbing user input during a non-interactive movie. |
3.11.16 | Improved command: 'RayTrace' now also works for electrostatic potentials and simulation grids. |
3.11.14 | New command: 'OnError' allows to handle errors in a running macro. This command replaces 'ErrorExit', which is now deprecated. |
3.10.27 | New command: 'RequireVersion' allows to check if a minimum YASARA version is installed. |
3.10.26 | New plugin support: Various workarounds for bugs in Windows solve some cases where Python plugins could not be run. |
3.10.26 | New graphics engine: YASARA now runs better on old cards, especially those with Riva TNT chips. |
3.10.25 | Improved command: 'Cell' now also returns the coordinates of the cell center and can be used to create non-centered cells (YASARA Dynamics+). |
3.10.24 | New Yanaconda function: 'rnd' function returns random numbers, variables 'Linux' and 'Windows' define operating system. |
3.10.20 | Improved command: 'MakeTextObj' returns the number of the created object (YASARA Model+). |
3.10.19 | New highlight: Distances, angles and dihedrals can be changed interactively by marking up to four atoms and clicking on 'Geometry' in the atom context menu (YASARA Model+) |
3.10.19 | Improved command: 'Distance', 'Angle' and 'Dihedral' can now actively change the geometry. |
3.10.17 | Improved command: 'CheckCis' and 'CheckIso' can now be applied to individual residues, e.g. non-prolines |
3.10.16 | New command: 'Count' the number of atoms to objects that are contained in a selection. |
3.10.15 | Improved feature: Macros can now use the predefined variables 'Residues' and 'Objects' (in the soup). |
3.10.15 | Improved command: CheckCis and CheckIso now return the number of cis-peptide bonds or wrong isomers. |
3.10.15 | Improved feature: Press <CTRL>+<M> to rerun the last macro, including those chosen from the command line. |
3.10.15 | New feature: RightClick in the VISibility column of the 'Scene Content' head-up-display to switch all other objects off. |
3.10.11 | Improved plugin: The error report plugin adds an option to request YASARA updates from the Help menu. |
3.10.11 | New command: 'RenameSeg' allows to change the segment ID for an atom selection. |
3.10.11 | Improved selection syntax: the 'not' operator allows to negate entire selection blocks. |
3.10.10 | New loop database (YASARA Structure). |
3.10.10 | Improved support: ATI Radeon 9600 cards under Linux now fully tested. |
3.10.5 | New highlight: Press the top right button in the sequence selector to display structural alignments. |
3.10.5 | Important bug fix: Playing YASARA Movies from YASARA View works again. Click Help > Play movie > 'Interactive Simulations for Modeling'. |
3.10.4 | Improved secondary structure assignment for unusual helices. |
3.9.24 | Improved command: LoadPNG now imports the alpha channel as well. |
3.9.23 | New command: 'UnrestImage' lets an animated image disappear immediately (YASARA Model+). |
3.9.19 | Improved command: PlayMacro and PlayMovie can be repeated by pressing <Ctrl>+<M> |
3.9.11 | Improved graphics: If an atom makes more than four bonds (defined via CONECT records in the PDB file), YASARA makes a better choice which four bonds to show. |
3.9.10 | Improved command: 'Link' uses more sensitive cutoffs when searching for bonds. |
3.9.8 | Improved PDB writer: If multiple NMR models are saved in one PDB file, the CONECT records are now collected at the end and atom numbers do not restart at 1. |
3.9.8 | Improved PDB reader: Single amino acid ligands are graphically displayed as HetGroups and not linked if they have both C-terminal oxygens |
3.9.8 | Improved command: 'Clean' now replaces missing backbone oxygens including both C-terminal ones |
3.9.7 | New command: 'Move<Atom|Res|Mol>' moves atoms in the local coordinate system of an object |
3.9.7 | New command: 'SwapImage' changes the priority of bitmaps when displayed on screen |
3.9.3 | New plugin: Interface to the PDBFinder2 database. Click Analyze->PDBFinder2 to color your protein according to HSSP sequence conservation, entropy and PDBReport quality indicators. |