VMD

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(Useful tricks: file order)
 
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* To generate a [[Charmm]] trajectory (.DCD) from a series of [[Protein Databank|PDB]] files, you may use [[Catdcd]] as follows:  
* To generate a [[Charmm]] trajectory (.DCD) from a series of [[Protein Databank|PDB]] files, you may use [[Catdcd]] as follows:  
** cat *.pdb > file_all.pdb
** cat *.pdb > file_all.pdb
 +
** catdcd -o file_all.dcd -pdb file_all.pdb
 +
 +
* You may need to do this with a specified order for the [[Protein Databank|PDB]] files. For instance, to have their order given by the date of the files:
 +
** cat `ls -t *.pdb` > file_all.pdb
** catdcd -o file_all.dcd -pdb file_all.pdb
** catdcd -o file_all.dcd -pdb file_all.pdb

Latest revision as of 08:11, 16 May 2011

Contents

Description

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. It is one of the most user-friendly programs available for this purpose. It is particularly useful for visualizing trajectories, either, e.g., in Charmm (.DCD) or PDB (MODEL ... ENDMDL) formats.

Home page

Source code

Executables

Supported platforms

Documentation

Useful tricks

Contact information

vmd@ks.uiuc.edu


See also

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