From: John Stone (
Date: Tue Apr 21 2009 - 10:51:48 CDT

  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:

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

  John Stone

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
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email:                 Phone: 217-244-3349
  WWW:      Fax: 217-244-6078