VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Nov 19 2012 - 18:18:10 CST

Hi,
  VMD uses STRIDE to compute secondary structure, as it works both
for static structures and can also be used for trajectories.
One change I've been thinking of making would be to have VMD
use the PDB-assigned secondary structure in cases where it's available.
That would give the same behavior you observe in PyMol, for example.
You can override the secondary structure assignments made by STRIDE
using atom selections if you are willing to do some scripting:
 http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/vmd_use_pdb_ss/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Nov 19, 2012 at 05:00:29PM -0500, Larry Guy wrote:
> Hi all,
> I hope that somebody here can help me solve a mystery regarding a newly
> released pdb 4G7O. Chain C of this protein can't be visualized using the
> ribbons or cartoon representations. Some smaller sections of chain C that
> I have removed and put in to a new pdb files show up fine in new cartoon
> representation. pyMol, jMol and other visualization software packages
> handle this structure with no problems, displaying all of chain C.
> What could be happening in VMD that would cause this kind of problem in
> the cartoon representation of chain C?
> Thanks in advance for your help! 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078