Hi Oliver,
As Elaine, points out the main problem is figuring out the center and direction for the map symmetry axis and the ChimeraX "measure symmetry" command attempts to do that using a map. That command looks for cyclic, dihedral, icosahedral, tetrahedral, ... symmetries, so there is not just one symmetry axis except in the cyclic case. You say you are interested in the symmetry axis being along z and through the center of the map. In that case I would strongly suggest that your map origin should be set at the center of the map and then it is simple to do a rotation about the symmetry axis without creating any axis using a command like
rotate z 90 center 0,0,0 model #1
The geometric center of the map is sometimes not the exact position of the symmetry axis. Specifically, when the map as an even number of grid points (e.g. 256) then then center of the box likes half-way between two grid points. Maps often have the center at a grid point, not half-way between, possibly because the CCP4 map format origin specification only allows shifting the map by an integer number of grid points. At any rate, this is another reason why I recommend setting the map origin to the center of symmetry, so you don't end up being off by 0.5 grid points, an error which is subtle and will likely go undetected and may to lead to molecular models where the subunits are mispositioned by a fraction of an Angstrom.
Tom
On Mar 11, 2024, at 6:10 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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
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