Hi Reza, You did not say what command you are using. There is "matchmaker" (aka "mmaker") which will make sequence alignments and then use CA atoms only to fit, and there is "align" which will use whichever atoms you tell it to use for fitting. Either way you can specify the chain, for example: align #1/A:200-452 to #2/A:200-452 <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html> That would only work if they have the same numbers of atoms, e.g. the residue types and sidechains are the same, and it would use all atoms. You might want to specify only backbone: align #1/A:200-452@n,ca,c,o to #2/A:200-452@n,ca,c,o How to specify atoms, residues, chains in commands: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> Or if you are using "matchmaker" it automatically only uses CA atoms, but it does a sequence alignment to figure out which residue number goes with which residue number. Like align, you can tell it specifically which chains to use, see the example with "pair ss" in: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html> ......but if you only want to use certain ranges of residue numbers instead of the whole chains, it might be easier to use "align" anyway. It *is* possible to use only certain ranges of residue numbers with mmaker, however: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#restrict> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

On Nov 25, 2024, at 4:16 PM, Reza Khayat via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi,

We have multiple structures of a homo-hexamer (chains A-F). We'd like to overlay limited regions of each chain onto equivalent chains (e.g. residues 200-452 of chain A onto residues 200-452 of chain A). We're having difficulty identifying the correct syntax. Some of our structures align as desired while others are aligned according to the chain combinations that produce the lowest RMSD (e.g. residues 200-452 of chain A align onto residues 200-452 of chain C. Is it possible to restrict which chains align to which?

Best wishes, Reza