Hi Bruno, Instead of using Contacts, I would recommend using Matchmaker with the option to show the pairwise sequence alignment turned on (if command, "show true"). Then it will automatically show the pairwise sequence alignment with an Calpha RMSD histogram which for a pairwise superposition is simply the CA-CA distance. You could then just interactively with the mouse in the sequence alignment select the whole part of the alignment that corresponds to the domain that you want, which automatically selects the corresponding structure residues. Also to select precisely by CA-CA distance when showing that alignment (but which would also give you the gaps), you could use the attribute value automatically generated by showing the alignment, e.g. open 2gbp open 2fw0 mm #2 to #1 show true sel ::seq_rmsd <1.0 (screenshot of result attached) See <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#headers> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#attributes> 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 Jun 28, 2025, at 1:07 PM, Bruno Hay Mele via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi all,

I'm trying to evaluate salient differences within a specific topological domain across a set of protein structures. My workflow is as follows:

I choose a reference structure, and use MatchMaker to align all other structures to it. Then, I use the Contacts tool with distance 0 and overlap 0 to select CAs of residues that are perfectly aligned to the reference selection (i.e. the topological domain).

This approach works well in conserved regions, but it results in gaps where insertions or small variations occur. I've tried to use sel up to fill these gaps, but my attempts have failed miserably.

Is there a way to fill in gaps within a discontinuous selectionb€i.e., to make it continuousb€without extending the selection outward beyond the domain of interest? Ideally, I'd like to interpolate or bridge only the missing parts, without picking up unrelated residues.

cheers, -- Bruno Hay Mele, PhD 2D-20, Biology Dept., University of Naples Federico II https://github.com/bhym/ | +39 081 67 9118

Sorry, I don't have further ideas at this point. Maybe somebody else will come up with suggestions. Cheers, Elaine

On Jun 29, 2025, at 9:24 AM, Bruno Hay Mele via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear Elaine,

Thank you for your swift response, as always!

The issue Ib€m facing is that I have around 200 sequences, and as far as I know, mmaker only works pairwise. While in theory I could align each structure against the same reference, this would result in an unmanageable number of pairwise alignments.

I also considered loading a multiple sequence alignment and using sel expand based on that, but that approach isnb€t ideal eitherb€it still includes gaps and depends heavily on the quality of the alignment.

Let me know if Ib€m missing a better strategy within ChimeraX for dealing with this sort of challenge.

cheers, -- Bruno Hay Mele, PhD 2D-20, Biology Dept., University of Naples Federico II https://github.com/bhym/ | +39 081 67 9118