[Chimera-users] Aligning (superimposing) chains form the same PDB files

Elaine Meng meng at cgl.ucsf.edu
Thu Mar 28 12:13:22 PDT 2019

Hi Jenaro,
If all the chains in the PDB file are open as one model (which is usually the case if you open a single file, unless it’s a multimodel file like an NMR ensemble), then you would need to split the model first so that each chain is a separate model.  Then you can use Matchmaker GUI or command.  Match->Align does not superimpose structures; instead it creates a multiple sequence alignment from multiple structures that were previously superimposed, such as with Matchmaker.

Using hemoglobin as an example:

command: open 4hhb
… now look in the Model Panel (open from Favorites menu); it shows 4hhb is model #0

command: split #0 chains
… now Model Panel shows four separate models, #0.1 for chain A, #0.2 for chain B, etc.

choose menu: Tools… Structure Comparison… Matchmaker

 … and in Matchmaker, choose any one model (chain) as the reference and all others (or just all of them including the reference) as the structures to match.  Set any other options you want, etc.

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

> On Mar 28, 2019, at 11:57 AM, Jenaro Soto <jenaros at uci.edu> wrote:
> Hi, 
> Can Chimera superimpose all chains from one PDB file. If so how can this be accomplished?
> I have tried using the  MatchMaker tool but it ask me to select at least one different reference model. I have also tried Match -> Align but it also asked me to only choose one chain per model. 
> Any help would be appreciated. 
> Best, 
> Jenaro 

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