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@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