[Chimera-users] vop binning

Thomas Goddard goddard at cgl.ucsf.edu
Mon Jun 21 15:52:38 PDT 2010

Hi Katrina,

   Ok, I guess your volume data is an occupancy map from an MD 
trajectory?  Here's a script that sums the values at the edge of a 
volume data set.  You open the volume and then open the script (use File 
/ Open...) to run it.


The result appears in the Chimera reply log (Favorites / Reply Log).  It 
sums the volume data values and counts the number of grid points that 
were summed.


> 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!
> Katrina
> 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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