[Chimera-users] Superimpose protein chains

Elaine Meng meng at cgl.ucsf.edu
Mon Aug 5 15:52:49 PDT 2019

Hi Pete,
Before superimposing using your preferred method (Matchmaker, etc. as listed in this page) the chains to compare should be in different models.

There are a couple of ways you could do this; pick whichever appeals to you…

(1) split the model (opened from single file) into multiple models, one per chain, with the “split” command.  You can see the result in the Model Panel (show from Favorites menu).  Just the word “split” without any options splits on chain IDs by default, which is probably what you want.

(2) just open the structure N times (N=number of subunits you want to compare) so that there are N models open, and then specify in the matching procedure which chains in which models to superimpose.  You could delete the “other” chains in each model first if you wanted, but it isn’t strictly necessary.

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Aug 5, 2019, at 3:10 PM, Peter Snyder <petermsnyder at me.com> wrote:
> How can I superimpose two (or three) chains from a single structure (ie two homologous subunits that form a multimeric protein)?
> Thank you
> Pete

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