[Chimera-users] [chimerax-users] relative position of a marker

[Elaine Meng]

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 at 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 at gmail.com>
> Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
> Reply-To: Tom Goddard <goddard at 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 at cgl.ucsf.edu.
> 
> 	Tom

> On May 25, 2022, at 2:40 PM, C.J. via Chimera-users <chimera-users at 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 at 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 at 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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