VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Feb 09 2007 - 18:02:33 CST

Adrian,
  At present, the alignments applied by multiseq will not affect
any volumetric data in the same molecule. Most likely, to get what
you want, you'll need to save the rotations computed by STAMP
(used by multiseq) or the VMD "measure fit" routine and apply them
to the XPLOR maps and molecules and then reload it all. It's a hassle,
but that's the only suggestion I have just now. If you need help with
that, let me know.

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Feb 09, 2007 at 09:33:34AM -0500, Adrian Roitberg wrote:
> Dear all,
>
> I have loaded a pdb file with a xplor grid as a volumetric map attached
> to it representing water density over an MD run.
>
> I then load, as a different molecule, a second pdb for a closely related
> protein with its own xplor grid.
>
> I need to superimpose ALL of the above so I can look at differences,
> similarities, etc.
>
> Now for the question: If I overlap the two molecules using the multiseq
> tool, do the grids also rotate as well as the coordinates for maximal
> overlap ?
>
> Can anyone suggest a better way ? The two proteins to not have exactly
> the same number of atoms or sequence (but they are VERY close), so a
> regular RMSD fit might not be the thing to do.
>
> Thanks !
>
> Adrian
>
> Dr. Adrian E. Roitberg
> Associate Professor
> Quantum Theory Project and Department of Chemistry
>
> University of Florida PHONE 352 392-6972
> P.O. Box 118435 FAX 352 392-8722
> Gainesville, FL 32611-8435 Email adrian_at_qtp.ufl.edu
> ============================================================================
>
> To announce that there must be no criticism of the president,
> or that we are to stand by the president right or wrong,
> is not only unpatriotic and servile, but is morally treasonable
> to the American public."
> -- Theodore Roosevelt 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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