[Chimera-users] vop binning

Katrina Lexa klexa at umich.edu
Mon Jun 21 15:25:34 PDT 2010

Thank you for the speedy response!
What I would like to do essentially is to examine only the volume data 
that lies within 3 angstroms from each edge of my box. I'm hoping to be 
able to count the atoms within that area and obtain an idea of 
population counts for different molecules far away from the protein. 
Thanks for the direction to the interpolate code, that looks really helpful!

On 6/21/2010 6:18 PM, Thomas Goddard wrote:
> Hi Katrina,
>   The vop command is written in Python code included with the Chimera 
> distribution in directory
>     chimera/share/VolumeFilter
> (on Mac in Chimera.app/Contents/Resources/share/VolumeFilter).
>   The code that actually sums the values for the bins is in bin.py in 
> that directory.  Not very interesting.  Probably pretty complicated 
> looking because it handles subregions, subsampling, variable bin size.
>   If you give more details of the volume data analysis you are aiming 
> for I might be able to give you some more relevant example code.  The 
> Chimera Python scripts page might have something useful, for example, 
> the iterpolate.py script:
> http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts
> http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/interpolate.py 
>   Tom
>> Hello -
>> Is the volume data (vop) code available somewhere? Particulary the code
>> for binning electron densities? I'm interested in looking at how chimera
>> handles xplor files since I want to find the density of solvent at the
>> edges of my grid. I would love to try to play with the volume code in
>> order see if it can be done through chimera.
>> Thank you,
>> Katrina

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