[Chimera-users] Finding specific voxels in volume data

Thomas Goddard goddard at cgl.ucsf.edu
Thu Jul 23 10:03:27 PDT 2009

Hi Do-Nyun,

   Do you mean you want to find grid indices of volume data points 
inside a surface? or on (near) a surface?  If it is a contour surface 
the problem is simpler since that just amounts to values above or near 
the contour level.  Chimera doesn't have any capabilities to export 
lists of volume grid indices so this will require writing some code.  It 
may be quite simple using a Python script in Chimera, but I'd have to 
know precisely what you need.

   Export Scene includes surfaces but not values at volume data grid 
points.  The exported file is for graphical rendering -- it does not 
dump the underlying data.

   Please direct future questions to chimera-users at cgl.ucsf.edu instead 
of directly to me unless confidential information is included.  This 
will allow others to benefit from the answer.


-------- Original Message --------
Subject: Re: [Chimera-users] save map as ascii
From: Do-Nyun Kim
To: Tom Goddard <goddard at cgl.ucsf.edu>
Date: 7/23/09 7:37 AM

> Dear Tom,
> So, now I can easily read and right maps, but I have one more question.
> When I "Export Scene" the surface mesh from a map, how are coordinates
> determined? It seems the density map itself does not have coordinate
> information.
> What I actually want to know is coordinates of voxels in density map "in 
> current
> scene" such that I can figure out which voxel of the density map contains a
> point in the surface mesh.
> Thank you for your help.
> Best regards,
> Do-Nyun Kim.
> Quoting Tom Goddard
>> Hi Do-Nyun,
>>  The interpolate.py script on the Chimera Python scripts web page
>>    http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Scripts
>> shows how to get volume data values interpolated at specific points in 
>> a volume data set.  It uses trilinear interpolation from 8 nearest 
>> grid points.
>>  More details about the volume data objects are in the Python code 
>> distributed with Chimera:
>>    chimera/share/VolumeViewer/volume.py
>>    Tom

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