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Electron densities and
other maps in YASARA
For the majority of (not too old) PDB files
determined by X-ray crystallography, the RCSB provides not only the structure
factors, but also the corresponding electron densities for
download. This is especially handy in case you are hypotizing
about the functional role of some residues in your favorite
protein, and want to check if the side-chain rotamer in the PDB
file is strongly supported by the experimental data, or maybe
somewhat more flexible in reality (i.e. smeared out in the
electron density).
YASARA makes this kind of analysis trivial: when
you download a PDB file from the RCSB at File > Load >
PDB file from Internet, you can choose to include the
electron density right away, and show it as a surface or wireframe
at a given sigma contour level. Alternatively, you can import
electron densities, electrostatic potentials and any other map in
several supported formats (DSN6, Gaussian Cube, Delphi, YASARA
table). YASARA turns the data into a 3D table (1D and 2D
tables are also possible), which you can then manipulate, save in
a different format, and visualize in countless ways. Six styles
useful for electron densities are shown on the right side. For
other types of maps, useful styles include points, transparent
densities, crosses, planes, surfaces and 2D contours.
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