Hi Jon, Yes, you can. If you mean having multiple separate instances of ChimeraX at once, I believe you'd need to use the system command-line for startup instead of clicking the icon again (which would just raise the same original instance). See help for command-line startup: <https://rbvi.ucsf.edu/chimerax/docs/user/startup.html> For example, I'm on a mac with ChimeraX_Daily on my Desktop, and I can just give this command twice in Terminal (using two different Terminal windows) to get two instances of ChimeraX running: /Users/meng/Desktop/ChimeraX_Daily.app/Contents/MacOS/ChimeraX Or, if you meant opening multiple sessions in the same ChimeraX instance, you can do that too. You'd just need to use the "open" command with "combine true" for subsequent sessions to open their data without getting rid of the data from the first one. See: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#combine> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 5, 2025, at 11:57 AM, Choy, Jon via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Oliver and Tom or whom it may concern,
I was interested in whether it is possible to open multiple .cxs files at the same time? I am comparing structural features across many different proteins and their corresponding maps—and it is very annoying to be only able to open one map and its protein at a time.
Although it is possible to load multiple resolved structures and their maps into a single .cxs file, these structures all load onto different spots on the chimeraX interactive space—making side by side comparison a bit cumbersome.
Assistance in this would be massively appreciated! Thank you so much and looking forward to hearing from you.
Best, Jon