VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 26 2009 - 16:31:46 CDT

Hi,
  Use the RMS fit plugin, or MultiSeq to do an alignment on
the two structures. The MultiSeq alignment uses STAMP, which
can deal with dissimilar structures automatically, so that may
be the easiest to use. You can read more about how to use these
plugins on the VMD web pages. You could also do an RMS fit using
the VMD text commands (e.g. "measure fit") and then use the resulting
transformation matrix with the atom selection "move" subcommands.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Aug 26, 2009 at 05:17:41PM -0400, Mark M Huntress wrote:
> thank you for the responses to my previous question. Here is a new one: I have two very similar proteins, and I want to look at side chain position differences between them, but their coordinates are so different that when I open both files in VMD that the two proteins appear on different sides of the screen. Is there a way that I can superimpose one on the other without changing its internal geometric structure?
> Thanks 

-- 
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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