VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue May 20 2008 - 07:40:19 CDT

On Tue, 20 May 2008, ABEL Stephane 175950 wrote:

SA> Hi VMDusers

stefane,

SA> I have a basic question, I want to plot several residues of a
SA> protein from a PDB file extracted from a run without the hydrogen
SA> atoms. How to do that with VMD

SA> I have searched with google and i don't find the command line

please check out the VMD user's guide and the VMD visualization
tutorials instead!

if you open the graphical representation window you
have a text field where you can provide a "selection"
text which (as you may guess) selects the atoms to be
displayed. the selection language is quite powerful and
it should be possible to find an expression that does what
you want, e.g. something like this "(resid 32 44) and not hydrogen"

cheers,
    axel.

SA>
SA> Thanks your for your help
SA>
SA> Stefane
SA>
SA> ------------------------------
SA>
SA> Stéphane Abel, PhD
SA> CEA Saclay DSV/IBITEC-S/SB2SM
SA> 91191 Saclay, FRANCE
SA>
SA> ------------------------------
SA>
SA> 

-- 
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Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
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