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Category: Main/Molecular Dynamics/Visualization and molecular modelling
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Molecular modeling tutorials 
Description: Links to various molecular modeling tutorials.
Added on: 30-Sep-2003 Hits: 671
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Protein explorer
Description: Descendant of the RasMol molecular graphics program. It is claimed that Protein explorer is much better and rich of functions, however it is only for Windows and runs inside the web browser via Chime plug-in. It has less convenient interface and is much slower than original RasMol, however it worth to try.
Added on: 13-Oct-2003 Hits: 616
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RasMol
Description: RasMol (recently renamed to openRasMol) is the most popular free molecular graphics program. It reads .pdb files and display the structure in various representations from secondary structure cartoons to space-fill stereo models. Saves output in various graphical formats. Powerful but very simple scripting language allows to select groups of atoms and residues and visualize virtually anything you want.
Added on: 30-Sep-2003 Hits: 740
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Swiss-PdbViewer
Description: Good visualization program with such unique features as auto-completing missed side chains, repairing .pdb structures, structural alignments. Has limited capabilities of structure modification. However, the interface is very complicated.
Added on: 13-Oct-2003 Hits: 544
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Universal Molecular Modeling Software List
Description: Links to many molecular modeling and visualization software. Many of them are commercial, some links are broken.
Added on: 30-Sep-2003 Hits: 627
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VMD
Description: One of the best all-purpose visualization program which supports various formats and supports many useful plug-ins. Used mainly for visualizing MD trajectories.
“VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS-X, Unix, or Windows, is distributed free of charge, and includes source code.”
Added on: 30-Sep-2003 Hits: 820
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