[chimerax-users] relative position of a marker

[Tom Goddard]

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 at 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 at 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 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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