[phenixbb] Structure Comparison questions

Terwilliger, Thomas C terwilliger at lanl.gov
Wed May 29 10:19:20 PDT 2013

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: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Heather Condurso [condurso at bc.edu]
Sent: Wednesday, May 29, 2013 11:11 AM
To: phenixbb at phenix-online.org
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.
condurso at bc.edu
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