[Chimera-users] need coordinates from volume data

Terry Lang terry at lego.berkeley.edu
Tue Feb 22 19:01:52 PST 2011

Hey Tom,

         Thanks!  That worked perfectly :O)  Have a new, similar issue.  
I am now interested in getting the electron density contained within a 
void.  In particular, I have analyzed a favorite structure using castp.  
I am now interested in finding out the electron density (integrated or 
summed) within the surface that describes the void.  Is that possible as 


On 2/16/2011 1:56 PM, Tom Goddard wrote:
> Hi Terry,
>   I've attached some example Python code to find the (x,y,z) 
> coordinates of volume grid points.  The output  after opening this 
> file in Chimera (shown in the Reply Log (menu Favorites / Reply Log) 
> looks like
> read map 1a0m.omap
> data size 91 95 82
> xyz for index 15 7 13 is 2.96 -7.4 -1.46875
> data value at ijk 15 7 13 is -0.381388
> I put this example on the Chimera Python scripts page as readvol.py.
>     http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts
>   Tom
>> Hey Everyone,
>>           I'm am trying to do some unorthodox analysis of volume data
>> using a script.  As part of the analysis, I need to access the x,y,z
>> coordinates of each of the points of a ccp4 map.  How would I go about
>> that in Chimera scripting once the data is read in?
>> Thanks,
>> Terry

Paula Therese Lang
Postdoctoral Scholar
Alber Lab
UC Berkeley/QB3

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