[phenixbb] Structure Comparison questions

Heather Condurso condurso at bc.edu
Wed May 29 10:24:58 PDT 2013

I can get it to work with different completely different structures but I can't figure out how to compare NCS related chains.

 |  On Wed, 29 May 2013 10:21:01 -0700
 |  Nathaniel Echols <nechols at lbl.gov> wrote:
 |  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?
 |  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
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