VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 13 2005 - 09:34:13 CDT

Hi,
  You can use atom selections with "$sel get phi" and "$sel get psi" for
angle value queries, the rest you'd need to code up in your own script.
Take a look at the source code for the Ramachandran Plot (ramaplot) plugin
for examples on doing this sort of thing.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Apr 12, 2005 at 04:16:55PM -0400, Kos wrote:
> Hi,
>
> I'm interested to post-process with VMD
> and to calculate
> - dihedral (main chain phi/psi) values
> time-series and ave/sd
> - g(r) for the salt distributions relative
> to charged sites of a protein
>
> Are there available plugins or tools in VMD for these please?
>
> Kos
>
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078