VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jul 27 2007 - 12:42:49 CDT
- Next message: John Stone: "Re: frame number input in tcl and direct mol graph display update (II)"
- Previous message: Arneh Babakhani: "Re: Deleting bonds based on length"
- In reply to: pascal.baillod_at_epfl.ch: "dssp in vmd (II)"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
Hi,
If you have the DSSP secondary structure in the PDB file, you can
use this script to parse it and apply it, replacing whatever STRIDE
has already calculated:
http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/vmd_use_pdb_ss/
I don't currently have a script for reading the output of DSSP directly.
You could write one however, in a manner similar to the way the script
above works.
Cheers,
John Stone
vmd_at_ks.uiuc.edu
On Fri, Jul 27, 2007 at 12:04:54PM +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!!
>
> I actually already sent a note on this topic in 2005, and was just wondering if
> there's any news since then..
>
> Thanks a lot in advance!!
>
> 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 Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns_at_ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
- Next message: John Stone: "Re: frame number input in tcl and direct mol graph display update (II)"
- Previous message: Arneh Babakhani: "Re: Deleting bonds based on length"
- In reply to: pascal.baillod_at_epfl.ch: "dssp in vmd (II)"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]