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

Elaine Meng meng at cgl.ucsf.edu
Wed Aug 21 10:15:56 PDT 2019

Hi Huiya,
Our volume data expert is away this week, so it may be several days before you can get a more helpful answer, but maybe I can give a few preliminary tips.

Programmer guide examples: I don’t know why the link is broken on our website, but you should be able to see the copy that is included with your download by using menu: Help… User Guide, then in that page clicking the “Chimera documentation” link, then in the resulting documentation index, clicking “Chimera Programmer’s Guide” and then in that page, clicking the “Examples” link in the fourth paragragh.  However, I don’t think any of the examples relate to volume data anyway.

You may need to look in the Chimera code directly.  I believe the relevant parts are in the downloaded application under […]/share/VolumeData/ … i.e. on Mac it’s under [wherever you put it]/Chimera.app/Contents/Resources/share/VolumeData/    but the first part of the path may be different on other platforms.

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

> 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
> However, it seems this website can’t be opened and it shows me a blank page.
> Best,
> Huiya

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