From: Daniel Gaston (
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