[Chimera-users] RMSD of protein-protein interphaces

Elaine Meng meng at cgl.ucsf.edu
Tue Jul 12 11:09:57 PDT 2016

Hi Gleb,
I can’t think of a way involving the contact maps.

Instead you would probably need to do it with some combination of Matchmaker (if using sequences and CA atoms only works for your data) and/or “match” (to specify exactly which atoms to use) to superimpose the parts you want to superimpose, possibly followed by “rmsd” to compare some other sets of atoms in their current positions.

Two possibilities I can think of, you can probably think of others:

(A) decide which atoms are relevant and then just use “match” specifying those atoms for pairwise superposition and comparison.  It should be the same atoms for each pairwise comparison, but that set of atoms could include parts or all of both proteins.
- OR -
(B) use “match” or Matchmaker to superimpose one of the proteins (e.g. protein A to protein A in two different A-B dockings) and then “rmsd” to compare the resulting positions of the other protein (e.g. protein B in one docked position vs. protein B in the other docked position).

(Links to the relevant manual pages were given in my previous message to this list.)
I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 12, 2016, at 7:15 AM, James Starlight <jmsstarlight at gmail.com> wrote:
> Dear Chimera users!
> Having several docking poses of 2 proteins I need to estimate RMSD
> difference between their interphaces (e.g like what I have seen in
> Capri)
> Is it possible to do it via some Chimera's plugin e.g in combination
> with the contact-maps plugin?
> Thanks!
> Gleb

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