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Visualization
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For the visualization and modeling of
density
maps in concert with docked structures we recommend the free graphics
program, VMD, which
supports our map format as well as some modeling strategies. In
addition, Situs also provides simple analysis and rendering
capabilities in the
UNIX shell. The following figure shows three important analysis and
graphics
utilities for low-resolution docking:
(Click image to
enlarge)
| (Left) Molecular rendering of
biomolecular structures and isocontours using the free graphics program
VMD.
(Right)
Analysis of the voxel histogram with volhist
and
display of volumetric data cross sections with voledit. |
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Alternatives to
VMD: Chimera and Sculptor both support Situs
map format. Likewise, any graphics
program that can render structures in PDB format together with 3D
density
maps is suitable for Situs. However, for programs other than VMD,
Chimera, or Sculptor care must be taken to take into
account
any changes in the map coordinate system. This convention defines the
relative position of density maps and docked
structures. Mor more information on map formats see the map2map user guide.
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