VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 21 2009 - 10:51:48 CDT

Hi,
  Have a look at this script, you should be able to
use a similar strategy to override parts of the secondary structure
prediction from STRIDE with whatever other information you
have from other sources:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/vmd_use_pdb_ss/

The key VMD command of interest in the script is:
  $sel set structure $ss

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Apr 21, 2009 at 11:25:08AM -0300, Daniel Gaston wrote:
> Hi all,
>
> I am wondering if there is a method to override STRIDE's secondary
> structure prediction (and thus how VMD displays it in New Cartoon
> format) for only a specified portion of a structure file? I have a
> Homology Model from Swissprot where one loop region in only one chain of
> a homodimer is show as as anti-parallel beta-sheet instead of the loop
> region that it should be. Because only this one portion is incorrect
> (and because Swissprot homology models contain only coordinates and not
> a secondary structure section) I would like to override the
> representation only for that one area of the structure without needing
> to create a secondary structure entry in the PDB for the entire protein.
> Is this possible?
>
> Thank you,
>
> Dan Gaston
>
> --
> Daniel Gaston
> PhD Candidate, Dr. Andrew Roger Lab
> Department of Biochemistry and Molecular Biology
> Dalhousie University, Nova Scotia, Canada 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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