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

Conrad Huang conrad at cgl.ucsf.edu
Thu Aug 22 11:57:02 PDT 2019

Hi, Huiya.

Sorry about the broken web page.  That should be fixed now.

Regarding reading a volume file, take a look at 
  (Our volume expert is on vacation right now, so this is my best 
answer.)  There are actually a large number of other scripts written 
for/by users at http://www.rbvi.ucsf.edu/trac/chimera/wiki/Scripts, 
several of which read and manipulate volume data, so you might want to 
scan through the descriptions to see if there is anything else useful. 
Hope this helps.


On 8/21/2019 9:34 AM, Huiya Zhou 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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