[chimerax-users] Problems with Measuring Angles in ChimeraX

Elaine Meng meng at cgl.ucsf.edu
Fri Sep 10 12:02:23 PDT 2021


> On Sep 10, 2021, at 11:41 AM, liangb2 <liangb2 at rpi.edu> wrote:
> 
> Hi Elaine:
> I'm new to ChimeraX for Cryo-EM data. Currently, I imported my tomogram (.mrc file) into ChimeraX and acquired a density map of it. I was able to get the x,y,z coordinates of the three points of interest. However, I was not able to find ways to measure the angle among the three points on the tomogram density map. I have looked up tutorials, but all of those I have found are for proteins.
> 
> Can you please provide some help on how I can measure the angle among three points on the density map? I would really appreciate your help.
> Thank you for your time!
> Best,
> Biqing Liang

Hi Biqing,
Welcome to ChimeraX!   We recommend using the chimerax-users at cgl.ucsf.edu address for asking questions (CC'd here so you don't need to do anything).  Depending on the question, other people might want to see the answer, or give better answers than mine, or I might not know the answer at all.

I don't know how you got the X,Y,Z coordinates for those three points. 

The way I know how to do it:  You can put  several "markers" (balls, fake atoms) at points on the surface, and/or at peaks in the density values.  Then you can select any 3 of the markers (Shift-Ctrl-click on them) and then use the "angle" command:

angle sel

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/angle.html>

The way to put markers on interactively is first to go to the Markers toolbar across the top of the ChimeraX window.  The different icons assign different ways of adding markers by mouse click.  For example, clicking the third from left icon in the Markers toolbar assigns the right mouse button (= trackpad + Alt on Windows, trackpad + command key on Mac) to adding markers on the surface.

See the following for what the different icons mean and explanation of markers:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/markers.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/markerplacement.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco







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