[Chimera-users] Python script for reading volume values at atom positions

Tom Goddard goddard at sonic.net
Thu Jan 19 15:05:14 PST 2017


Hi Kyle,

  Here is the fixed script avalnogui.py to report density map values at atom positions.  It is also at the Chimera Python scripts web page.

	https://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <https://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts>

I made it take the file paths on the command line, for instance, 

$ chimera --nogui --silent --script "avalnogui.py 1a0m.pdb 1a0m.omap"
#1:1.A at N               3.722
#1:1.A at CA              3.345
#1:1.A at C                4.04
...


  Tom




> On Jan 18, 2017, at 7:36 PM, Kyle Morris <kylelmorris at berkeley.edu> wrote:
> 
> Dear chimera dev and users,
> 
> Can anyone confirm with the latest chimera version (i’m running v1.11.2 build 41376) if this python script for measuring map values at atoms works for them?
> 
> The script was reported previously on the users list here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2007-May/001587.html
> 
> For me I get a python import error:
>  from VolumeViewer import Data_Region, full_region, Rendering_Options
> 
> Thanks for your insight!
> 
> Best wishes,
> Kyle
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
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