VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 17 2005 - 14:39:51 CDT

Hi,
  I've briefly looked at writing a DSSP interface for VMD but parsing the
not-well-documented output format doesn't look fun so I haven't gone forward
with it. In principal you can do this with a Tcl script, you just have to
parse the DSSP output and extract the per residue SS assignment that DSSP
calculates, and assign it to the structure using the 'atomselect set'
commands. If anyone has a short cleanly written piece of Tcl, Python, or
C code to read DSSP output I can look at, I'd consider integrating a DSSP
interface into VMD. I just don't have time to start on this from scratch
while I'm juggling 10 other balls presently.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Aug 17, 2005 at 09:15:11AM +0200, pascal.baillod_at_epfl.ch wrote:
> Hello!
>
> I am currently using stride or pdb based secondary structure definitions, but
> would be very glad to use dssp definitions to depict my proteins in vmd. Is
> there any script like the stride-based one that can do this? I thank you very
> much for your help!!
>
> Pascal
>
> *******************************************************************************
> Pascal Baillod (PhD student)
> *******************************************************************************
> Swiss Federal Institute of Technology EPFL Tel: +41-(0)21-693-0322
> Institute of Chemical Sciences and Engineering , Fax: +41-(0)21-693-0320
> Laboratory of Computational Chemistry and Biochemistry pascal.baillod_at_epfl.ch
> Room BCH 4121, Avenue Forel, http://lcbcpc21.epfl.ch
> CH-1015 Lausanne
> *******************************************************************************
> 

-- 
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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