Hi Heather, I think phenix.superpose_pdbs (http://www.phenix-online.org/documentation/superpose_pdbs.htm) might do what you want. You can specify atom selections to identify which chains you want to compare. All the best, Tom T ________________________________________ From: [email protected] [[email protected]] on behalf of Heather Condurso [[email protected]] Sent: Wednesday, May 29, 2013 11:11 AM To: [email protected] Subject: [phenixbb] Structure Comparison questions Dear all, I have a few related structures that I would like to compare to make figures for publication but I have a few issues. The biggest issue is that my structures are large (12- 422aa chains) and any attempt at simple alignment in pymol results in a crash. I would like to first compare entire structures, but also compare the differences between related chains in the same structure. I want to look at the small differences in the active site density. What is the best way to do this? Is there a simple way to do this or do I need to make separate pdb files for each chain? Can I use the same mtz or should I rename copies? I will try a few things but any advice would be greatly appreciated. Heather [email protected] _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb