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
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