As Tom said (message shown below), those commands we gave in our earlier answers to chimerax-users are for ChimeraX. They are not Chimera commands. To use the command shown in your image, you have to use ChimeraX. Chimera does not have a command to add a marker at a specified x,y,z position. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
From: Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] relative position of a marker Date: May 25, 2022 at 2:31:56 PM PDT To: "C.J." <biocjh@gmail.com> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Reply-To: Tom Goddard <goddard@sonic.net>
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 2:40 PM, C.J. via Chimera-users <chimera-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> 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>
....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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