Hi Sasha, After you close all the sequence/alignment windows, open ChimeraX's Python shell (Tools→General→Shell) and type: len(session.alignments) The output should be 0. If not, there are alignments open. If so, you may have to send me a session file from just before you split the structures, so I can give you better advice about what to do. --Eric
On May 19, 2026, at 8:18 AM, Alexandra Zahradnikova via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Eric, I tried to follow your suggestion, i.e., opened the file and then I selected for "Auto-associate if fewer than this many sequences” to 2 (1 did not work). However, after splitting the models, they started to auto-associate despite this setting. Bets regards Sasha
From: Alexandra Zahradnikova [mailto:alexandra.zahradnikova@savba.sk] Sent: Tuesday, May 19, 2026 07:05 To: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Association taking long time
Dear Eric, This is a file which was, previpisly aligned. The alignment was closed and it does not show in the Tools. But somehow it still persists. I do not know how to delete it.
When I opened the file, there was an alignment present and the chains were associated. I dissociated them and closed the alignment. When I gave the Split command, the models were split but I was mot able to see the result because the alignment started running.
I solved the problem by reading the cif files instead of opening the previous session file, but I would prefer to be able to delete the alignment. I will try the command that you suggested but I don't know if it will persist after I open the session file.
Best regards Sasha
Sent from my Galaxy
-------- Original message -------- From: Eric Pettersen <pett@cgl.ucsf.edu> Date: 18/05/2026 23:08 (GMT+01:00) To: Alexandra Zahradnikova <Alexandra.Zahradnikova@savba.sk> Cc: chimerax-users <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Association taking long time
Hi Sasha, I guess I don’t understand what you’re describing. Do you have sequence/alignment windows open? Are they necessary? Is there some reason you can’t just close them before you do all the splitting? There is a hack you can use to prevent auto-association, but you have to do it before opening the relevant alignments/sequences. Go to “Sequences” section of the ChimeraX Preferences/Settings and change the value for "Auto-associate if fewer than this many sequences” to 1. That will prevent any auto-association from happening for any sequences/alignments that you open while the value is 1.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On May 17, 2026, at 1:57 AM, Alexandra Zahradnikova via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear All,
I have a session with 80 homotetramers (4 x 1400 residues). I want to split all the tetramers, align all chains and calculate RMSF for all 320 chains. I specially took precaution to disassociate all chains. Nevertheless, when I give the command
Select All split sel chains
ChimeraX starts to associate all chains with all remaining chains, which takes >8 hours. Can you please suggest how to proceed?
Best regards Sasha _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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