[Chimera-users] How to read a volume in python script

Tom Goddard goddard at sonic.net
Wed Aug 28 12:13:46 PDT 2019

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


> On Aug 21, 2019, at 9:38 AM, Huiya Zhou <huiya at 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:
> https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html <https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html>
> However, it seems this website can’t be opened and it shows me a blank page.
> Best,
> Huiya
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20190828/45d9d031/attachment.html>

More information about the Chimera-users mailing list