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@cgl.ucsf.edu instead of directly to me unless confidential information is included. This will allow others to benefit from the answer. Tom -------- Original Message -------- Subject: Re: [Chimera-users] save map as ascii From: Do-Nyun Kim To: Tom Goddard <goddard@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