[chimerax-users] Saving .mrc volume as coordinates

[Elaine Meng]

Hi Joshua,
The tomogram data is a map (values at grid points), so presumably however you write it out would need to contain not only coordinates but the map values at those coordinates.  The built-in options for saving a map are listed here (and can be listed in the Log with command "save formats"):
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#mapformats>

I don't know if any of those qualify as "simple 3D coordinates," but if not, you may have to resort to python coding to write out the map in the format that you want.

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

> On Jan 10, 2023, at 7:12 AM, Joshua Jenkins via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi, 
> 
> I've segmented a tomogram using EMAN2 neural network workflow. I then use the segger function to extract regions of interest within the segmented volume, and save these to .mrc. I wondered if there is a way in chimera, or chimeraX, to convert/extract/save the .mrc volume as a simple 3D coordinates file (txt or tbl)?
> 
> Best wishes,
> Josh