Hi, Huiya. Sorry about the broken web page. That should be fixed now. Regarding reading a volume file, take a look at http://www.rbvi.ucsf.edu/trac/chimera/attachment/wiki/Scripts/readvol.py. (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. Conrad 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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