On Wed, May 29, 2013 at 10:11 AM, Heather Condurso
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?
Have you tried this yet? http://phenix-online.org/documentation/structure_comparison.htm Note that the superposition is very simplistic - but it will let you compare active site density in the same frame of reference. And it works for both multiple structures and NCS-related chains. -Nat