VMD-L Mailing List

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Fri Feb 09 2007 - 08:33:34 CST

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
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