Hi Daphne, I feel I should point out that all the RMSDs assigned will be pairwise RMSDs, and the ones assigned to the reference structure will just be from whatever alignment was the last one created. That said, probably the simplest way to make your session usable again is to open it in 'nogui' mode, save a new session file (which will now not contain any sequence-viewer tool info) and use the new session from there. It will still have the RMSD attributes. Information about how to run ChimeraX in nogui mode is here: https://www.cgl.ucsf.edu/chimerax/docs/user/startup.html I am going to open an enhancement-request ticket in the ChimeraX bug-tracking database, with you CCed, for adding an option to MatchMaker to assign RMSDs without opening sequence viewers. --Eric Eric Pettersen UCSF Computer Graphics Lab

On Jul 16, 2024, at 1:56 PM, Chen, Daphne via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello,

I have a large ChimeraX session containing homologs of my protein of interest (~120 PDB files in one session). I’ve been able to align them using MatchMaker, but I noticed that I have to check the “Show pairwise sequence alignments” box under “Alignment” in the Matchmaker window if I want to color by RMSD in the Render by Attribute menu. Is there a way to color by RMSD without displaying all the pairwise sequence alignments? Whenever I try to open my session, there are so many pairwise alignment windows that have to be loaded that ChimeraX ends up crashing.

Thanks, Daphne

_______________________________________________ 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/