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/surf... 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#icossur... except that I want to use custom geometries....

Many thanks, Dave

Dr David Bhella

MRC Virology Unit

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Molecular Machines - Images from Virus Research (Art Exhibition):

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Hi Dave, Importing surfaces into Chimera may not be as difficult as you think. If you look at the VRML (a text file) produced by Maya you will probably find an IndexedFaceSet and under that a long list of surface vertices and triangle vertex indices. This is exactly the data you the Chimera Python code would read. You could cut and paste it to a new file, delete some keywords specific to VRML, and run some python code to read it and make the surface in Chimera. If you go that route I can help with that Python script. Tom David Bhella wrote:

Thanks for your reply, I shall look at cylinders in the first instance and if the visualisation is useful I will see if I can implement your suggestions for more complex shapes. I made the VRML in Maya, it will take a bit of digging and a lot of learning on my part to try and implement your suggestion, but it could be worth the effort...

Best Wishes, Dave

On 18 Sep 2008, at 18:38, Thomas Goddard wrote:

Hi Dave,

One more detail. The Chimera "shape" command can create a cylinder that can be colored. Here's an example command

shape cyl radius 5 height 10

and documentation

http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html

It may be a bit of trouble to align it with your density because the shape command currently does not allow specifying the origin and axis of the cylinder. You have to use separate commands (~select all, select 1, turn y 90, move x 23.5) or hand placement.

To show fine details in the surface coloring you need the surface vertices to be as closely spaced as the volume data used to do the coloring. Only the vertices of the surface are assigned colors.

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#icossur... except that I want to use custom geometries.... Many thanks, Dave