[Chimera-users] Colouring surfaces from EM density maps

[Thomas Goddard]

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#icossurf
> except that I want to use custom geometries....
> 
> Many thanks,
> Dave
> 
> 
> 
> Dr David Bhella
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