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/