[Chimera-users] Colouring surfaces from EM density maps

Tom Goddard goddard at cgl.ucsf.edu
Fri Sep 19 09:14:59 PDT 2008

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.


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

More information about the Chimera-users mailing list