[Chimera-users] On pdb structure match or align

Elaine Meng meng at cgl.ucsf.edu
Tue Feb 23 09:03:13 PST 2021

Hi Smith,
I cannot give you the exact command because it would need to contain the residue number ranges of domain b in each structure.  If you have trouble with commands, you could instead use the MatchMaker gui (in the menu under Tools... Structure Comparison), select domain b in each structure, and turn on the option "Further restrict matching to current selection".  That is probably the easiest.  

If commands, you could use either
(1) "match" command -- also you may want to specify just CA atoms or backbone atoms (CA,C,O,N) rather than all atoms in those residues
(2) "matchmaker" command (only uses CA)

Superimposing structures

... including "match" command and its options

... and "matchmaker" command and its options
... how to restrict the calculation to only specific parts of the structures

How to specify residue ranges in the command line:

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

> On Feb 23, 2021, at 5:51 AM, Smith Lee <smith_lee123 at yahoo.com> wrote:
> Dear All,
> With chimera I open A.pdb abd B.pdb. A.pdb contains domain a and doain b, B.pdb contains domain b and domain c, which is to say, the 2 structures share a common domain b.
> Will you please tell me the chimera specific command to align or match the 2 structures based fully on the common domain b in each structure, without consideration of the domain a and domain c for calculation of the alignment?
> Best wishes,
> Smith

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