Fwd: [chimerax-users] relative position of a marker
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
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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