There are four different stages of
YASARA for Linux, Windows, Mac OS X and Android, aimed at increasingly
complicated fields of application. A certain stage contains the
features of all the previous stages, plus a number of additional
functions to tackle a wider range of scientific questions. Features
with unique properties which you will not find in other
programs are marked with orange buckyballs below.
- Molecular graphics, modeling and analysis, freely
Model - Everything above, plus advanced molecular modeling
Dynamics - Everything above, plus molecular simulations
Structure - Everything above, plus structure prediction and
validation, docking, knowledge-based potentials
NMR Module - NMR structure determination from your
Module - NMR structure determination from your spectrum with
the help of ARIA
Twinset - Extensive structure validation (PDBReports) and
WHAT IF functions
3DM - The protein superfamily data integration platform
tablets and smartphones that can run interactive MD simulations
starting at 175 EUR.
stereoscopic molecular modeling lab for 250 EUR, and a cave
for 700 EUR.
Read more about the
philosophy behind YASARA.
None, please download the free YASARA View to verify that YASARA
runs on your computer (and please
contact us if you encounter problems).
||Stage I: YASARA View -
YASARA View is
available for free and contains all the functions you need to
explore a macromolecular structure interactively. As a bonus, you
get YASARA's innovative 3D engine, which is up to 10 times faster
than what you usually know from OpenGL,
you can load multiple structures at the same time, create
publication-quality ray-traced images including labels, and
program your own macros and Python plugins. Included is YASARA
Movie, a player for multimedia presentations and
tutorials created with any of the higher stages, as well as the YASARA
Python module to simply 'import yasara' in your Python
- Cross-platform and easy installation: Windows,
Linux and Mac OS X in the same directory, run directly from
- Photo-realistic molecular graphics with full-scene
antialiasing at resolutions up to 4K (3840×2160 pixels): up
to 10 times faster than other OpenGL based solutions, even the
ribosome rotates smoothly in CPK mode.
- Support for the latest GPU shader features like
hardware tessellation, where the GPU increases the geometric
details of polygon meshes (e.g. surfaces and secondary
- Parallel (orthographic) and perspective
- Interactive box,
freehand/lasso or sphere selection tools.
- Support for over 70 molecular fileformats (based
- Download PDB files from the RCSB or the
re-refined and improved version from PDB_REDO.
- Optimal depth perception thanks to real-time
shadows and ambient lighting, even on older hardware.
- All common graphics styles: CPK, balls
sticks, sticks, traces, tubes, ribbons,
cartoons, labels, arrows.
- Interactive secondary structure morpher, which
seamlessly interpolates between a realistic (close to Calpha)
and an idealistic (perfectly straight strands and helices)
secondary structure display, which can additionally be
configured in countless ways to match your favorite secondary
- Create alternative
views of the scene, and switch between them using tabs at
- Ray-tracing for publication
quality graphics at arbitrary resolutions, interactively
move the lightsource, adjust shadows.
- Color any PDB file by sequence conservation and
quality indicators (automatically mapped from HSSP/PDBFinder2).
- Superpose structures and
structure ensembles, calculate proper RMSDs (minimized by
flipping equivalent atoms).
- Align multiple proteins
based on their structure or sequence, using a variety of
methods. Identify related structures in the PDB.
- Measure distances, angles, dihedrals.
- Build atoms, residues,
peptide chains and mutate amino acids.
bonds, and hydrophobic/pi-pi/cation-pi interactions.
- Create realistic 3D
structures from nonsense, 1D or 2D molecules, and convert them back to 2D structural formulas.
- Automatic assignment of fractional
orders and missing hydrogen atoms, graph-theory
typing of hetero-polycycles.
- Analyze and change atomic B-factors and
occupancies, rename and renumber atoms and residues.
- Extremely fast algorithms to show and update Van
Waals, molecular and solvent accessible surfaces in
- Extend YASARA with your own
functions using the Python scripting language.
- Use YASARA from your Python scripts, simply
- Simple Yanaconda macro
language to automate your work and create flexible
- eLearning functions: interactive
tutorials provide the knowledge about molecular structure,
modeling and simulations
Click here for free download,
click here for screenshots,
click here for a complete feature list.
||Stage II: YASARA Model
YASARA Model contains
YASARA View and adds all the functions you need to explore,
analyze and model small to macromolecules in a production
environment. This includes many features you often miss: unlimited
undo/redo, macro recorder, quad-buffered stereo with shutter
glasses or stereoscopic screens.
You can load thousands of structures at the same time, move them
around independently and create multimedia presentations (YASARA
Movies). These movies can be encoded as MPEGs and pasted into
Powerpoint or played back with all stages of YASARA, including the
free YASARA View.
- All the features of YASARA View listed above
are included, no need to keep a separate YASARA View
- Fully immersive OpenGL 3D stereo graphics with sterescopic screens or shutter
glasses. High quality GPU accelerated anaglyph stereo mode
for red/cyan glasses, that tricks the brain into seeing full
color and enables stereo also on notebooks. Red/cyan glasses are
included. Ultra-high resolutions up to 8K (7680×4320 pixels).
- Create the fanciest
molecular animations with automatic rotations, movements,
in 3D letters, texture
of PNG/JPG images and conversion
to 3D objects.
- Encode animations in MPEG format, paste them into
Powerpoint presentations. Export Alias Wavefront objects for use
by 3DStudioMax and others.
- Import OpenOffice Impress and Microsoft Powerpoint
presentations, add molecular animations to the slides.
- Work with thousands of structures at the same
time, move them around independently.
- Extensive coordinate manipulation: center, join,
transform, oligomerize, transfer
(e.g. loops) or replicate
them (e.g. domains).
- Analyze contacts, hydrogen bonds,
hydrophobic/pi-pi/cation-pi interactions and protein secondary
- Align small molecules like ligands automatically,
them on the largest common fragment.
- Measure distances, angles and dihedrals between
groups of atoms like helices or planar side-chains.
- Change distances, angles and dihedrals
- Choose a default pH from 0 to 14 when assigning
bond orders and adding hydrogens.
- Interactively build small molecules in just
seconds with a sophisticated
builder that offers over 50 functional groups to choose from.
- Show and calculate Van
Waals, molecular and solvent accessible surfaces,
distinguish between outer
and inner surfaces, calculate volumes. Analyze and show
cavities formed by these surfaces.
- Create multiple
interactive cut-planes to look inside surfaces and other
- Identify cis-peptide bonds and wrong
- Store the results of your analysis in tables,
import them in Excel.
- Record macros or write them with a text editor.
- Batch-processing of large data sets directly from
the GUI (graphical user interface).
- Support for special input devices like SpaceBall.
- Unlimited undo/redo.
||Stage III: YASARA
contains YASARA Model and adds support for molecular simulations.
In addition to YASARA's own force fields (NOVA,
YAMBER) you can use other well known MD
force fields like AMBER, and run accurate all-atom MD simulations
in aqueous solution with Particle Mesh Ewald longrange
electrostatics. YASARA Dynamics is not a "black
box" with input and output files, but shows the MD simulation in
real-time on screen. You can fully interact with the scene, pull
atoms or whole molecules around and finally do the type of
molecular modeling that Cyrus Levinthal already pioneered back in
1966 ("..do the same type of pulling and pushing in the
computer that we can do with our hands while building actual
models. ", cited from an article in
- All features listed for YASARA View and YASARA
Model above are included, no additional purchase needed.
- Prepare a simulation: clean proteins, predict
pKas, assign protonation states, fill the simulation cell with
- Fastest molecular dynamics algorithms for CPU and GPU (see benchmarks,
and note that MacOSX does not have reliable
GPU support) and energy minimizations in non-periodic or periodic cells with cuboid
or triclinic shape (including rhombic
dodecahedrons for maximum performance).
- AMBER and newly developed force fields (NOVA,
YAMBER) included, define your own force
- Accurate treatment of long-range electrostatic
interactions with the Particle Mesh Ewald approach.
- Parallel and reproducible simulations
on multiple CPUs and CPU cores with close to ideal speedups.
- Constrain bond lengths and water molecules with
LINCS and SETTLE to reach large timesteps.
- Calculate energies, binding energies and solvation
using Poisson-Boltzmann or PME methods.
- Manipulate a simulation interactively: pull atoms
or entire molecules around, fix and free atoms, add restraints,
toggle force field terms.
- Calculate the
electrostatic potential using Poisson-Boltzmann or PME
methods, visualize the results as densities, contours or
- Run simulations at the touch of a button even in
the presence of ligands, thanks to fully
force field parameter assignment for the General Amber
Force Field (GAFF). Semi-empirical QM point charges are
calculated using either AM1BCC or AutoSMILES, a newly developed
approach for hi-speed assignment of RESP library charges.
- Run simulations of
membrane proteins at the touch of a button.
- Automatically write scientific
reports about MD simulations, with publication-ready plots.
- Automatic correction of cis-peptide bonds or wrong
stereoisomeres for homology model refinement.
- Geometry optimization and analysis with
semi-empirical MNDO/AM1/PM3 quantum chemistry using YAPAC, a
built-in customized derivative of MOPAC.
- Analyze trajectories for conformational changes,
calculate time averages, RMSDs, RMSFs, RDFs and dynamic
- Read and write trajectories in Sim, MDCrd or XTC
- Build oligosaccharides
interactively, with stepwise energy minimization.
contains YASARA Dynamics and adds all the functions needed to
predict and validate macromolecular structures, including ligand
docking and highly accurate force fields with knowledge-based
potentials. If you already own one of the other YASARA stages, you
can upgrade easily, just contact us for
- All features listed for YASARA View, YASARA
Model and YASARA Dynamics above are included, no additional
- Small-molecule docking at the touch of a button, using tuned versions of AutoDock and VINA
with automatic setup, receptor flexibility and multi-CPU
support. Additional support for Fleksy,
an induced fit docking program based on FlexX, developed
- Side-chain rotamer prediction combining graph-theory
and dead-end elimination with accurate treatment of
electrostatics, solvation and subtle packing effects.
- Knowledge-based loop modeler
with a compressed index of the PDB, peptide segments
spanning selected anchor residues can be located within a
fraction of a second, while considering sequence and secondary
structure preferences. Loops can be optimized together with
surrounding side-chains, considering all energy components
- New force fields
(YASARA and YASARA2) with multi-dimensional knowledge-based
components for highly accurate refinement simulations to
aid protein structure determination and prediction.
- Homology modeling at the touch of a button: select
the target sequence and get a
homology model, combined from multiple templates, refined in
explicit solvent, as well as a detailed
report describing how the model was built, including extensive
validation with figures and quality plots. Check the CASP
- pH dependent hydrogen
bonding network optimizer, that automatically considers
ligands and determines ambiguities in X-ray density.
- Built-in BLAST and PSI-BLAST,
with automatically updated SwissProt, UniRef90, PDB and PDBC
sequence databases, the latter augmented with WHAT_CHECK/ PDBFinder2
validation data to rank PDB structures sharing the same
- Secondary structure prediction with PsiPred and DSC.
- Extensive structure validation to judge the
quality of experimental structures and models, based
a new combination of force field energies and Z-scores, that
yields results not only for proteins, but for all organic
molecules. This allows to validate for example
protein-ligands interactions, an important aspect in drug
- Perform twisted structural alignments, where the protein is bent and wound to maximize the
number of structurally aligned residues, for example to
create sequence profiles for homology modeling
- Prediction and
visualization of ion binding sites using valence scanning.
||The WHAT IF /
The Twinset is a
customized joint-distribution of WHAT
IF and YASARA Dynamics or YASARA Structure (currently Linux
and Windows only). With over 3500 citations, WHAT IF is a widely
used program for structure validation and modeling. In the
Twinset, WHAT IF inherits YASARA's user interface, graphics
engine, macro language, unlimited undo/redo etc, so that WHAT IF
functions become easily accessible.
The Twinset is freely available, but you need licenses for YASARA
Dynamics or YASARA Structure and also WHAT IF. Click here for WHAT IF license details,
and note that WHAT IF is now shareware/donationware. Customers in
Austria have to add 20% VAT.
To order the Twinset, just place a normal order for YASARA Dynamics
or YASARA Structure and then
request the Twinset upgrade from . If you already own YASARA,
email us your YASARA serial number.
||The 3D molecular modeling
lab for 250 EUR
Stereoscopic 3D molecular
modeling hardware has become easily affordable, so
that entire classrooms can enjoy this unique experience. The image
on the right shows the easiest and cheapest solution: 3D vision is
provided using 'passive stereo', where the images for left and
right eye are shown in odd and even pixel lines and separated
using flicker-free polarized glasses. The first popular screens
with this feature were the Zalman ZM-M215W, ZM-M220W and ZM-M240W,
costing around 200 EUR. Unfortunately it appears that Zalman
discontinued this product line, so they are now mostly available
as refurbished second hand models. But there are many follow up
products, googling for passive
stereo odd even finds e.g. the LG D2342P, the HP 2311x,
the AOC e2352Phz or the Viewsonic V3D231. The big advantage is
that this type of display is directly supported by YASARA with any graphics card and any operating system (no
expensive Quadro/FireGL cards or special video drivers are
needed). You can move your molecules through 3D space using the Connexion
SpaceNavigator with six degrees of freedom. Order
for 50 EUR.
has a resolution of 1680×1050 pixels. The polarized glasses
ensure that the left eye sees only the odd pixel lines, while
the right eye sees the even lines. So the resolution is reduced
to 1680×525 pixels per eye as soon as the glasses are put on.
This is hardly noticeable when looking at molecules, but becomes
apparent when looking at characters. Text is therefore harder to
read than with alternative, more expensive stereo solutions.
Without glasses, the screen behaves just like any other screen
and can be used for everyday work. It has a quite glossy
surface, reflections can be a problem in bright rooms, but are
hardly noticeable in somewhat darker 'molecular modeling caves'.
At least YASARA Model is required.
||The 3D modeling showcase:
a huge 3DTV for 380 EUR
If you want to demonstrate 3D
modeling on a large screen, we recommend passive 3DTVs
like the LG 42LB620V shown on the right. With a diagonal of 42"
(107 cm), two polarized 3D glasses and a price of 380 EUR, this
3DTV is an excellent deal that will please your audience. Passive
3DTVs use exactly the same principle as described above for
passive 3D computer screens, so they will work with any operating
system and any graphics card, with YASARA running in window or
Notes: Make sure to buy a screen with a resolution
of 1920×1080 pixels (FullHD). Since the images for left and
right eye are shown in odd and even pixel lines, this leaves an
effective resolution of 1920×540 pixels per eye, and you
certainly do not want a lower resolution on such a large screen.
Higher resolutions would of course be even better, but will only
be supported by YASARA later this year and also require an
advanced GPU with HDMI 2.0 connection. It is essential that the
3DTV supports a display mode where the input signal is shown
directly on screen, without scaling (overscan) and other
post-processing (which would destroy the stereo effect). On LG
3DTVs, you can set this display mode by labeling the input with
"PC" (push the "Settings" button on the remote, then go to Input
> HDMI1, push the red button with the single white dot and
select the "PC" label). If your graphics card/notebook only has
a DVI output, don't forget to buy a DVI->HDMI adapter and a
HDMI cable. Finally, it is noteworthy that passive stereo
screens have a certain viewing volume. On the LG 42LB620V, your
head should be located about 2 meters away, aligned with the
bottom of the screen (i.e. you should be sitting or the screen
should be hanging high up on the wall). Inside the viewing
volume, the 3D effect is crystal clear, but outside, there can
be considerable ghosting. At least YASARA Model is required,
click Window > Stereo > Interlaced to enable stereo. If
the stereo is 'inside out', click Window > Stereo > Swap
left and right.
3D modeling for 350 EUR
High resolution 3D stereo with
active shutter glasses is the next higher level, since
it does not suffer from the reduced resolution of the passive
screens above. The probably easiest solution with the best
price/performance ratio is the Viewsonic V3D241wm shown on the right. The
screen with a 24"/60cm diagonal has a resolution of 1920×1080
pixels and a non-reflective surface, it is thus well suited for
everyday work. It functions with every operating system and every
graphics card (nVIDIA/AMD) that can display quad-buffered stereo
with 100 or 120Hz at a resolution of 1920×1080 pixels. The shutter
glasses are included in the 350 EUR package. A slightly more
expensive but also more commonly used and more flexible solution
3D Vision system, check the guidelines here
Other suppliers of 3D glasses are eDimensional
card must have a dual-link DVI connector and support quad
buffered OpenGL stereo, a feature which is normally only
available in workstation
like nVIDIA Quadro and AMD FireGL. You do not need the
very expensive high-end Quadros with mini-DIN stereo connector,
since the shutter glasses are supplied with the screen and plug
into the screen with a cable, neither emitter nor batteries are
required. Only one pair of glasses can be connected, so this
system is for one person only. And since the
monitor does not know the difference between left and right
image, you may have to swap left and right in YASARA on startup.
The aspect ratio of 16:9 is very movie-like, you may have to
fiddle with your desktop settings to avoid windows that are too
wide to read. The screen shows very little ghosting, which
becomes noticeable mainly in the bottom 5cm. At least YASARA
Model is required.
||The 3D molecular modeling
cave for 700 EUR
specialized 3D beamers, that previously cost above 10000
EUR, have finally become mainstream technology. You can now easily
build your private molecular modeling showroom, projecting giant
3D views that measure several meters along the diagonal. The image
on the right shows a 3D beamer from Viewsonic, costing around 500
EUR. The beamer projects the images for left and right eye
alternatingly with 120 Hz. So you additionally need shutter
glasses to separate the images, the probably best choice are
glasses with DLP-link like the Viewsonic PGD-250 (~80 EUR) or the XPAND
Edux3 (~80 EUR). An alternative with a less comfortable
infrared emitter are the nuVisionGX
glasses shown on the right (~200 EUR). Any beamer that is
3D-ready, features 'DLP-link' and supports a 120 Hz mode over VGA
or DVI cable should work with YASARA, to see examples click here, then select 'Supported 3D
been done in Linux, where you need to add a 120Hz modeline to
your xorg.conf. Other operating systems work too if they allow
you to choose a 120Hz video mode in their display settings.
Additionally, your graphics card must support quad buffered
OpenGL stereo, a feature which is normally only available in workstation
like nVIDIA Quadro and AMD FireGL. These cards often also
have a mini-DIN connector for the shutter glasses, which is
however not needed if you chose glasses with DLP-link (see
above). The only disadvantage of DLP-link glasses is that you
sometimes need to manually flip left and right image. At least
YASARA Model is required to display stereo.