From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Feb 08 2011 - 14:22:21 CST

Hi,
  You should be able to do this by loading all of your PDBs into
separate molecules, open the Extensions->Analysis->RMSD Calculator tool.
>From there set the selection to "protein" (or whatever makes sense for
your structure), then click "all in memory", then "RMSD", then "ALIGN".
Then change your graphical representations to color the strutures by
"Molecule" and you should be all set.

If you have a proper trajectory file (rather than several PDB files)
you can do this much more easily using the RMSD Trajectory Tool,
coloring by "Timestep", and using Draw Multiple Frames feature
in the graphical representations "Trajectory" tab.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Feb 08, 2011 at 10:19:45AM -0500, B.M.B. Vanschouwen wrote:
> Hello.
>
> I have a group of structures (in PDB format) for a protein that I would
> like to display simultaneously in VMD (and possibly display each
> structure in a different colour), in order to get a visual illustration
> of the motions occurring within the protein molecule.
>
> How do I do this??

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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