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

[Kyle Morris]

Dear Elaine and Tom,

Thank you both for the instruction over this, both methods are perfect for what I wanted to try!! I’ll get on with it then.

Confirming the python script works for me with the latest version.

Awesome.

Kyle

> On 19 Jan 2017, at 15:05, Tom Goddard <goddard at sonic.net> wrote:
> 
> 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
> 
> <avalnogui.py>
> 
> 
>> 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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>> 
> 

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