Hi Matthias, Right click on the ChimeraX PAE plot to show a menu and turn off "Dragging box colors structure". Then dragging a box will instead select the parts of the structure. Not obvious. Probably there should be two menu entries to separately control coloring and selecting. I made a ChimeraX request for that. https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/17112 By the way the ChimeraX daily build handles PAE from Boltz and Chai (variants of AlphaFold 3) better (recognizes numpy PAE files and the file names used by those programs) and I am working on a ChimeraX tool to run Boltz structure predictions including proteins, ligands, nucleic acids, ions, coming to the daily builds in a few months. Tom

On Mar 17, 2025, at 10:16 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear ChimeraX team,

I love the alphafold tools in ChimeraX, and have a small suggestion to make it even better. Currently, when associating a PAE plot from a JSON file, you can drag the mouse in the PAE plot to color the corresponding residues (magenta and lime), but the residues do not become selected (although the color command gets printed in the log). I think it would be helpful if there was an option (or default behavior) to return a selection in addition, so that the selected region could be saved as a named selection, the display style changed ect…

Or am I missing anything?

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/