Hi Dan, The sequences can be shown independently of matchmaker. You could just use matchmaker on chains A,B,C if that generates the desired superposition, as in your second command:

matchmaker #1/A/B/C to #2/A/B/C pairing ss show true

You don't even need the "show true" if you don't care about the seq_rmsd attribute of chains A,B,C.

Then, separately without changing the superposition you can show the sequences of D,E,F, making sure they are associated with both structures, and showing the RMSD header to get the seq_rmsd attribute:

seq chain #1/D seq associate #2/D 1/D seq chain #1/E seq associate #2/E 1/E seq chain #1/F seq associate #2/F 1/F seq header rmsd show

You could alternatively use the context menu on each sequence window to do the structure association and show the RMSD header, but the commands are easier to describe succinctly in email.

sequence command help: https://rbvi.ucsf.edu/chimerax/docs/user/commands/sequence.html#top

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Sep 18, 2023, at 9:12 AM, Daniel Grba via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

Hello,

I have two PDB models I am comparing, but I am having some issues generating the seq_rmsd attribute across all of the chains in the superposition that I want.

My current models (same protein, but different states and slightly altered built sequences) have chains A/B/C/D/E/F separated over two domains of A/B/C and D/E/F, for example. My problem is that domain D/E/F is much larger than the former and when I run a matchmaker command such as this:

matchmaker #1/A/B/C/D/E/F to #2/A/B/C/D/E/F pairing ss show true

I get the resulting superposition favoring the /D/E/F domain (larger RMSD values on A/B/C). This would be fine, however, I want to investigate RMSD variation in D/E/F relative to a fixed position of A/B/C.

If I run the following command I only get pairwise RMSDs (seq_rmsd header) for the specified chains but lack those of the larger D/E/F domain as they are not included. matchmaker #1/A/B/C to #2/A/B/C pairing ss show true

I look to Calculate the RMSD between paired residues of chains /A/B/C/D/E/F without moving the current structures (after ‘mmaker’ alignment to A/B/C) with the ‘align’ command but the ‘move’ option set to nothing:

align #1/A/B/C/D/E/F toAtoms #2/A/B/C/D/E/F move nothing matchNumbering (or matchAtomNames also tested) true

I believe the above is what I want with regards to superposition for the RMSD calculations, but the ‘align’ job does not appear to give a seq_rmsd header attribute once run, even though the log seems to suggest it does a pairwise residue alignment to calculate the RMSDs. (Possibly because it does not just look at the CA like matchmaker does?)

Is there a way to generate seq_rmsd attributes from the ‘align’ command, or is there a way to have an equivalent ‘move nothing’ in ‘mmaker’? I am looking to use seq_rmsd information to color the model and I am using v1.6.1.

Any help is much appreciated!

Dan.