This brings up a related question, has anyone written a script to parse out IMOD model files for this information (point locations, and their connectivity for contours, followed by surfaces)? My understanding is that the mesh representation is an output format that is derived from the actual model data (above) that chimera does not currently import. best -Jeff Tom Goddard wrote:
Hi David,
The Chimera IMOD model file reader only handles the meshes in the file. My guess is that the file you made does not contain meshes. Maybe it only has contour lines for the spheres. Or maybe the file format can contain geometric primitives like spheres without contour lines or meshes being specified. I don't know enough about IMOD to be sure.
Tom
David G. Morgan wrote:
Tom,
I was trying to use the new IMOD file reader and must be doing something foolish. I downloaded the newest chimera snapshot release (1.2392) and the imod.zip file and made a new installation. I can load my IMOD volume into chimera without any trouble. I then "opened" the IMOD model file (it opened as an "IMOD segmentation" type). That works without trouble, but I don't ever see the model. Even trying to use "focus" to bring it into the field of view gives me a blank field.
It's possible that my model is the wrong type - I'm playing with chimera in preparation for needing to do something fancy, so I simply created a set of spheres of different colors and different radii in IMOD, saved that model and tried to read it into chimera. I thought I'd simply be able to read this into chimera and see a couple of spheres, but I don't. I'm sure I'm doing something silly, but figured I'd bother you while I play around with it.
David Gene Morgan University of California at Davis
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-- ------------------------------------------------------------- Jeff Triffo Auer Group, Donner Lab, Lawrence Berkeley National Laboratory Raphael Group, Bioengineering Department, Rice University Medical Scientist Training Program (MSTP), Baylor College of Medicine phone (Berkeley): 510-486-7940 fax (Berkeley): 510-486-6488