[phenixbb] Structure Comparison questions
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?
| 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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