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

Kyle Morris kylelmorris at berkeley.edu
Thu Jan 19 09:54:12 PST 2017

Hi Elaine,

Thanks for this, absolutely excellent tool but I really need to script
this, command line or python. I have 28 maps and 6 models per map you

I don't think there's a command line implementation of this?


> On 19 Jan 2017, at 09:46, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Kyle,
> I can’t answer about the old script, but if it is feasible for you to do interactively, there is a "Values at Atom Positions" tool included in Chimera.  It’s in the menu under Tools… Volume Data, and it assigns the interpolated values as an atom attribute.  You can write out the values using the File menu of the Render by Attribute tool, which automatically pops up when you click the Histogram button to assign the values.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/density/density.html>
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>> 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

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