VMD-L Mailing List

From: Shirley Li (li19104_at_yahoo.com)
Date: Mon Aug 16 2004 - 19:33:21 CDT

Hi John,
 
Thank you very much for your help with my question and for your precious time.
 
Yes, you are right, I almost always have to RMS align the structures first. I know how to do this using VMD and get the RMSD value. While once I get this step done, how to average the coordinates and write out the averaged structure? Do you have a script/example that I could use?
 
Your help will be greatly appreciated.
 
Best regards,
 
Shirley

John Stone <johns_at_ks.uiuc.edu> wrote:

Shirley,
If you're just wanting to average coordinates, then the best method would
probably be to first load them as if they were a trajectory, then
RMS align them all to the first structure, then average the coordinates
and write out the averaged structure. It would be almost exactly the same
procedure as for a trajectory, except that you'll probably also have to
RMS align the structures as a first step unless you're "lucky" and their
already as aligned as they can be.

John Stone
vmd_at_ks.uiuc.edu

On Fri, Aug 13, 2004 at 09:43:27AM -0700, Shirley Li wrote:
>
> Hello all,
>
> I have five structures of the same peptide, and all of them are in .PDB format. I would like to get the average structure of the five. Could any one give me any suggestion or script? I saw some posts in VMD list about getting average from trj files, but my situation might be much simpler.
>
> Thank you in advance.
>
> Shirley
>
>
>
>
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-- 
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
		
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