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

_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

You sent your question to the ChimeraX mailing list. Our answers are for ChimeraX and commands in the older Chimera program are sometimes different. ChimeraX and Chimera are different programs. I suggest you use ChimeraX. There is a separate Chimera mailing list chimera-users@cgl.ucsf.edu. Tom

On May 25, 2022, at 2:24 PM, C.J. via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Thank you both Tom and Elaine. I just test the command but it doesn't work. See attached picture.

Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> 于2022年5月25日周三 11:45写道： 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 <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 <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 <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 <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 <mailto: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

<Untitled.png>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users