Hi Huiya,

  There is a list of Chimera Python scripts, many that read volume data here

http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts

and this readvol.py one shows how to get the 3d matrix as a numpy array, basic m = v.matrix() or m = v.full_matrix(), full_matrix() gives the full 3d data even if it is being shown subsampled, e.g. at step 2,

http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/readvol.py


  Tom


On Aug 21, 2019, at 9:38 AM, Huiya Zhou <huiya@tamu.edu> wrote:

Hello,

I am trying to use UCSF Chimera to analysis cry-EM density maps. I would like to read a density map (for example: a .mrc file) in python script and get the array (or a three dimensional matrix) of all voxels of this density map. How could I realize this?

By the way, I tried to learn some basic chimera functions which can be used in python on this website:
However, it seems this website can’t be opened and it shows me a blank page.


Best,
Huiya
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