Hi Bruno, I don’t know of any way to do this with commands, but it’s pretty easy in Python. I’ve attached a script that will fill in “selection gaps” in chains. To run it, just use the “open” command to open the file. --Eric Eric Pettersen UCSF Computer Graphics Lab P.S. Some mailers may mangle the attachment because it’s Python code. If that happens to you, let me know and I’ll see what I can do.
On Jun 30, 2025, at 8:55 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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 Ibm 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 isnbt ideal eitherbit still includes gaps and depends heavily on the quality of the alignment.
Let me know if Ibm 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
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