[Chimera-users] superimposing different chains from one PDB file

Elaine Meng meng at cgl.ucsf.edu
Fri May 11 14:46:59 PDT 2012

Hi Carlos,
You could use the "split" command to make each chain a separate model, probably more convenient than the alternatives of editing PDB files by hand before opening them in Chimera or opening multiple copies of the same PDB file.


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 May 11, 2012, at 1:29 PM, Donado, Carlos wrote:

> Hi Elaine,
> One last question. I tried using the Matchmaker option in Chimera and read the documentation but was unable to find a way to superimpose two molecules (chains) within the same PDB files. I am sure you are aware that a lot of PDB files have more than one structure for the same protein present in the file, whether it be inactive, active, with an inhibitor bound to it or what not... I found that Chimera will only let me match objects in two different PDB files. Is there a straight forward way to do this?
> Thanks!
> Carlos

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