[Chimera-users] On pdb structure match or align

[Elaine Meng]

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
or
(2) "matchmaker" command (only uses CA)

Superimposing structures
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>

... including "match" command and its options
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>

... and "matchmaker" command and its options
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html>
... how to restrict the calculation to only specific parts of the structures
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html#restrict>

How to specify residue ranges in the command line:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#hierarchy>

I hope this helps,
Elaine
-----
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