[Chimera-users] imod model viewing

William Jeffrey Triffo triffo at rice.edu
Tue May 8 17:30:27 PDT 2007

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.



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   

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