When you place a marker it logs a command that tells its x,y,z position, for example marker #1 position 0.07868,0.05359,-0.4914 color yellow radius 1 And if you want to output the x,y,z positions of markers (which are just atoms) you can use the getcrd command getcrd #1
Atom /M:1@M 0.079 0.054 -0.491
You mention "Volume Tracer" which is a tool in Chimera and does not have that name in ChimeraX. In ChimeraX it uses the Marker toolbar and Marker Placement panel. The suggestions Elaine and I made are for ChimeraX, not Chimera. Tom
On May 25, 2022, at 11:45 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Jianhao, It depends what you mean by relative position. If you mean distance, one way would be to place a marker at the map center and then measure distance between it and the marker you already have.
You can place a marker at map center with "measure center" and the "mark true" option: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#center>
....or at specific coordinates such as 0,0,0 with "marker" and the "position" keyword to specify a point: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/marker.html#create>
Then you can select the two markers (same as atoms) with Ctrl-click, Shift-Ctrl-click and then use command "distance sel": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html>
Or regardless of whether you wanted to measure any distances, you can save the marker(s) to file and just look at the file with a text-editor to see what its coordinates are: <https://rbvi.ucsf.edu/chimerax/docs/user/markers.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 25, 2022, at 7:54 AM, C.J. via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, I place a marker in a cryoEM map with "Volume Tracer" tool. How can I know the relative position of the marker to the origin or center of the map? Thank you! Best, Jianhao
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