Hi Oli, There is a "measure symmetry" command to guess the symmetry of a map in some of the simpler cases for maps in standard orientations, but it does not display an axis:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#symmetry
Define axis doesn't figure out axes of symmetry for you, so if there were an option, it would probably be for the "measure symmetry" command.
However, if you can figure out two points in space (two sets of coordinates) yourself, you can of course use "define axis" and just give it those two points, see the "fromPoint" and "toPoint" options: https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html
Another thought is that if you can open the map twice and rotate one copy around the symmetry axis and then "measure rotation #1 to #2" it will draw an axis. You would need to use the "axisType object" option so that it would be a real axis object (more useful for measurements and rotations) instead of just two markers connected by a link. https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation
It might be difficult to rotate one copy of the map precisely enough for your needs, however. And if the whole reason were to make rotating a map easier, then this wouldn't help, considering you'd still have to rotate the map without it to begin with!
This general "measure rotation" approach would also apply to atomic structures.
These ideas are based in part on these previous threads: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/message/XR6SDCT7ZPRNJO43OB5FBDNZCVQN73Q5/ https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/thread/5HWYKUMJTISXARM4B2FN5FIMIBTYYVUE/#5HWYKUMJTISXARM4B2FN5FIMIBTYYVUE
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 Mar 11, 2024, at 5:04 PM, Oliver Clarke via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi,
For symmetric EM volumes, it would be useful to be able to easily create an axis corresponding to the molecular symmetry axis - generally coincident with a vector parallel to the Z-axis of the box, directly through the center.
Is there an easy way to create such an axis in ChimeraX for an arbitrary map? It would be useful to have such an axis in order to rotate a volume around the molecular symmetry axis, even in the absence of a model (this is fairly easy to do if a model is present using define axis). This might be a useful generic extension to "define axis", if there isn't already an easy way to do so.
Cheers Oli