[phenixbb] Structure Comparison questions

Nathaniel Echols nechols at lbl.gov
Wed May 29 10:21:01 PDT 2013

On Wed, May 29, 2013 at 10:11 AM, Heather Condurso <condurso at bc.edu> wrote:
> 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?


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.


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