[Chimera-users] wrl to spider or mrc format

Thomas Goddard goddard at cgl.ucsf.edu
Thu Jul 23 16:08:46 PDT 2009

Hi Pierre,

   The hand data-set you refer to is a surface, not volume data.  I 
guess  you could imagine making a volume data set by filling inside the 
surface with ones and outside with zero.  Chimera can't do that from a 
VRML surface, can't do much of anything with VRML.

   It would seem better to start from medical imaging volume data.  That 
data is usually in DICOM format.   For example,


There are various converters from DICOM to say TIFF, JPEG, or PNG image 
stacks.  I have not used any of them.  Chimera can read an image stack 
and write an MRC file, but it can't read DICOM format.  I'm interested 
in allowing Chimera to directly read DICOM data and there is a pydicom 
Python module that does the work of extracting the image data


I don't expect to have time to turn that into a Chimera file reader any 
time soon.


-------- Original Message --------
Subject: [Chimera-users] wrl to spider or mrc format
From: Pierre-Damien COUREUX
To: chimera-users at cgl.ucsf.edu
Date: 7/23/09 8:39 AM

> Hello everyone,
> I'm trying to use this skeleton hand 
> (http://www.cc.gatech.edu/projects/large_models/hand.html) as a teaching 
> tool in electron microscopy. I'm only able to open the file in the wrl 
> format and I was wondering if there is an easy way in chimera to convert 
> that file into a density spider or mrc format. So I can import it and 
> make projections in spider for example.
> I tried to find on the web a free procedure to convert that wrl, without 
> any success. If you have a clear protocol about how to do that, that 
> would be great
> Thank you in advance for your help
> Pierre-Damien COUREUX
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> Chimera-users at cgl.ucsf.edu
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