[Chimera-users] Colouring surfaces from EM density maps

[Thomas Goddard]

Hi David,

   VRML support in Chimera is quite limited and the surface color tool 
which works on all other Chimera surfaces does not work on VRML.

   If you are calculating the custom surfaces described as a set of 
vertices and triangles then I can provide some Python code that will 
make a surface that you can use the surface color tool on.  Here's some 
documentation on what that Python code would look like:

http://www.cgl.ucsf.edu/chimera/current/docs/ProgrammersGuide/Reference/surface.html

   If you are generating VRML with some software you did not write it 
still may not be too hard to extract the vrml indexed face set node 
describing the surface and generate the surface as above with a bit of 
Python.

	Tom



David Bhella wrote:
> 
> I am looking at some rather noisy cryo-tomography data and I would like 
> to create something akin to icosahedral and spherical sections, using 
> different shapes (cylinders, ellipses etc). I have found spherical and 
> icosahedral sectioning to be a valuable way to represent density and 
> would like to use this in other types of structure. Is it possible to 
> colour the surface of an imported VRML object in the same way as spheres 
> and icosahedra are in the tools>volume data>surface colour dialogue? In 
> my current chimera installation, VRML objects are not listed in this 
> window....
> The sort of effect I want to achieve is similar to that described here: 
> http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#icossurf
> except that I want to use custom geometries....
> 
> Many thanks,
> Dave
> 
> 
> 
> Dr David Bhella
> 
> MRC Virology Unit
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