Hi Matthias, Using 4v5x, which has roughly half a million atoms, swapping residue /BW:31 took less than a second the first time, but subsequent swaps took a little less than 18 seconds apiece. Not nearly the 5 minutes you are experiencing, but still quite a bit slower than I would expect. I will open a ticket in our bug-tracking database for this, with you on the recipient list. "build replace" does a lot more work than swapna, so I can imagine it being somewhat slow, but again not 5-minutes slow. I'll look into that once I resolve the swapna situation. --Eric Eric Pettersen UCSF Computer Graphics Lab

On May 26, 2025, at 2:16 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear ChimeraX team,

I have noticed that on some structure I am working with, the swapna command is extremely slow, making it almost unusable for structure manipulation. For a single nucleotide substitution, ChimeraX froze for >5 minutes before finishing the operation (that particular structure had ~300 000 atoms). When I however first delete all proteins from the structure, the operation is very fast. What is the rate limiting step in the swapna command? Does it invoke renumbering of all atoms in the PDB file? Without having quantified it, I experienced similar behavior for the build replace command. Would be fantastic if there would be a way to speed this up to increase its usability!

Many thanks in advance, Matthias _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/