Warren helped me with a similar problem a while ago (I can't find the link in the mailing list archive), and this might do the job for you:

If you download and run my script at http://www-personal.umich.edu/~mlerner/Pymol/mg_pymol_utils.py
you can start up two PyMOL sessions.  You then type send_view in one of them, receive_view in the other one, and the "receive_view" one will follow along.

I don't know how to get that all working in one window, but you can always just paste the images together.

I find this really useful for comparing structures with different ligands bound, different parts of a dynamics run, etc.

In your case, you might need to align all of the structures to one reference structure first, so that the views are similar.

Hope this helps,

-Michael Lerner

On 25 Jan 2007 16:32:21 +0000, David F Burke <dfb21@cam.ac.uk> wrote:
Pymol users,

I wish to compare several protein structures and was wondering how or if, in pymol, one can view two structures
side by side and rotate each structure around their own centre of gravity. This is a bit like stereo view but with
different structures in the left and right views. Many thanks David
David Burke PhD
Department of Zoology, University of Cambridge,
Downing Street, Cambridge, CB2 3EJ
Tel: 01223 330933

Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share your
opinions on IT & business topics through brief surveys - and earn cash
PyMOL-users mailing list

Biophysics Graduate Student
Carlson Lab, University of Michigan
http://www.umich.edu/~mlerner http://lernerclan.net