Hi Nicholas, It is a pairwise method so you have to choose one reference for each match. It is unclear from your question whether you want to make all of the structures align to the same chain, or whether you want to match one other chain to each of the monomers of the hexamer, which one goes with which one, etc. So it is not possible to give you exact commands for all of those situations. If you want the tool to do the sequence alignment for you and then superimpose using only CA atoms, then you should use Matchmaker (tool) or "matchmaker" or "mmaker" (command). You may have to use the command several times, but it may be easier for you to try the GUI tool, in menu under Tools... Structure Comparison. See the options on the GUI and just try it, and it may be an iterative process before you understand what you are doing. Using the GUI tool will show the corresponding command in the Log, so that you could also learn the command and possibly use that approach instead. See the help for the descriptions of all the options and how to use them, for both tool and command. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html> I can't tell from your question whether each of your structures has 6 chains, but for example to match chains BCDEFA of #2 to ABCDEF of #1 in that order, I believe it would be something like mm #2/B,C,D,E,F,A to #1/A,B,C,D,E,F pair ss That is basically the same as the 4th example in the matchmaker command documentation linked above. You must include the "pair ss" As it also says in the matchmaker command documentation: If you don't want the tool to do sequence alignment for you (if you already know which residue number ranges go with which residue number ranges and want to specify it directly) and you might want to do the fitting with more atoms than CA (say all backbone, @N,CA,C,O) then you would use the "align" command instead. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html> 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 Dec 2, 2024, at 9:10 AM, Nicholas Ferraro via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Good morning, My name is Nicholas Ferraro. I am a graduate student at the City College of New York. I am currently using ChimeraX-1.8 to visualize multiple PDBs of the hexameric helicase I am working with. We have labeled each protomer of the hexamer A-F. I understand the software allows for matching structures either by best-aligning pair of chains, a specific reference structure to the best-aligning chain, and specific chains in a reference structure with specific chains in the matching chain. I have six PDBs. What I want to do is align all chains with respect to their chain ID and specific sequence. Can you advise on how to accomplish this in chimera-1.8? Thank you for you assistance. Please let me know if you need more details. Best, Nicholas Ferraro