VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 17 2004 - 13:13:49 CDT

Hi Shirley,
  For getting an average structure, you ought to be able to read this
"trajectory_smooth" script and see how it works, changing it as necessary
to work for your purposes:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/trajectory_smooth/

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Aug 16, 2004 at 05:33:21PM -0700, Shirley Li wrote:
> 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
> >
> >
> >
> >
> > ---------------------------------
> > Do you Yahoo!?
> > New and Improved Yahoo! Mail - 100MB free storage!
> --
> 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
>
>
> ---------------------------------
> Do you Yahoo!?
> Y! Messenger - Communicate in real time. Download now. 

-- 
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