VMD-L Mailing List

From: Daniel Gaston (daniel.gaston_at_dal.ca)
Date: Tue Apr 21 2009 - 09:25:08 CDT

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