[chimerax-users] Saving .mrc volume as coordinates

[Tom Goddard]

HI Joshua,

  Do you want to save the bounding box x,y,z coordinates of the Segger regions?  Or the centroid of the Segger regions?  Or the map value at every grid point?  All these things could be done with some Python code.  All of the map file formats written by ChimeraX

	https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html#mapformats

are binary formats, not text.  But I could provide you a bit of Python code if you needed text output.  There are examples of ChimeraX Python code on the ChimeraX recipes web site, for example, here is one that puts a marker on every connected surface blob in a map

	https://rbvi.github.io/chimerax-recipes/mark_blobs/mark_blobs.html

  Tom


> On Jan 10, 2023, at 9:38 AM, Elaine Meng via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> 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
> -----
> 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
> 
> 
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