VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 29 2002 - 15:56:18 CST

Hi Marc,
  It sounds like what you want to do could be done by doing a
best-fit alignment on a subset of the atoms. There's an example
of how do this in the VMD User's Guide:
  http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node185.html

I'm not sure what you're second question about "proper lighting" is
referring to, so I'll wait to answer that until you determine if the
best-fit alignment feature above does in fact solve your problem.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Oct 29, 2002 at 06:59:56PM +0000, Marc Baaden wrote:
>
> Hi,
>
> I would like to position a given protein "similarly" for a series
> of snapshots. I thought of a) calculating the geometrical center
> of the protein CA's and b) using the line from a specific residue
> to that center as pointing direction.
>
> I have not yet been able to figure out how to:
>
> - move the system to the geometrical center that was calculated,
> I basically have the center as result of the command
> geom_center $sel
> but don't know how to feed that into the "trans" command (which
> I think can be used to reposition the system)
>
> - what is the easiest way to reorient the system, if I have two
> points (one is the center, the second would be a Ca of a specific
> residue), so that the line connecting the two points is directed
> from the center towards me ?
>
> I wonder whether both operations might be performed with just one
> "trans" command ?
>
>
> Also, is it easy to automagically setup proper lighting for this new
> position ?
>
>
> Thanks in advance,
> Marc Baaden
>
> --
> Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
> mailto:baaden_at_smplinux.de - ICQ# 11466242 - http://www.marc-baaden.de
> FAX/Voice +49 697912 39550 - Tel: +44 1865 275380 or +33 609 843217
> 

-- 
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              
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