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. http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/edgesum.py 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. Tom
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.p...
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