Hello Leo, You would use the "align" command instead of matchmaker if you want to specify the exact atoms to match. Matchmaker always uses biopolymer sequence (although the sequences need not be identical, just similar enough for the seqeunce alignment step), whereas align does not. Example: open 1bna open 4bna preset sticks hide solvent align #1/A&backbone toAtoms #2/A&backbone align #1&backbone toAtoms #2&backbone ...where the first align example is just chain A to chain A whereas the second uses the backbone of all the residues (both chains A and B). See: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#builtin> The tricky part about align is that you have to specify equal numbers of atoms and you have to figure out yourself which residue numbers correspond between the two. So if your two chains don't have the same number of residues, you would need to specify which residue ranges to use, for example: align #1/A:2-6&backbone to #2/A:3-7&backbone I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 14, 2023, at 2:57 AM, Leonardo BETANCURT ANZOLA via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I’m currently using ChimeraX to compare different DNA binding proteins and would like to align them using match maker and the DNA helix. The problem is that the structures do not have the same DNA sequence and that is the parameter the MM uses to align. Would it be possible to align DNA using only the phosphate-sugar backbone of the molecule? In that case I’d like to tell chimera which phosphates should one aligned to which.
Thank you,
Leo B.