[chimerax-users] get coordinates of voxel

[Elaine Meng]

Hi Tianming,
I do not know what you mean by "voxel."  

If you want to find out the coordinates of some point on the surface, you can put a marker (a dummy atom) on that point, see Marker Placement tool and the Markers tab of the Toolbar icons across the top of the ChimeraX window:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/markerplacement.html>

The third icon in that tab is for "mark surface", you would click that icon to assign the function to right-mouse click (= trackpad + Alt on Windows, trackpad +  command key on Mac).  Then you can right-mouse-click a point on the surface to place the marker.

...and then find out the marker coordinates, for example by selecting it (Ctrl-click) and then using command:

getcrd sel

If you just mean the locations of the grid points in your map, you can calculate that yourself from the information in the Map Coordinates tool mentioned in my earlier reply.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Sep 22, 2022, at 7:56 AM, Tianming Qu via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Thanks for the help Dr. Elaine,
>  
> Is there any way I can figure out the coordinates of each voxel?
>  
> I know from mdanalysis, if one knows the voxel size (delta) and delta of one voxel cell, the voxel center coordinates can be calculated. Can I do the same way in ChimeraX?
>  
> Best,
> Tianming