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

Tom Goddard goddard at sonic.net
Thu Jan 19 17:53:35 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 (I sent this before with a wrong URL that required a password)

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


> On Jan 18, 2017, at 7:36 PM, Kyle Morris <kylelmorris at berkeley.edu <mailto: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 <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
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