[Chimera-users] capping surface with a VRML model

Damien Larivière damien.lariviere at fourmentinguilbert.org
Wed Nov 18 08:45:35 PST 2009

Thank you very much Greg and Tom for your answers!

About Tom's suggestion:

I have used Matlab to generate position and orientation coordinates 
(quaternions) for hundreds not superposing proteins (I am studying 
ribosome density in bacteria). The Matlab output is a matrix that is 
transformed into a file under the VRML format. In this VRML file, the 
geometry is given by the ribosome multiscale model surface obtained in 
Chimera and then the geometry is instantiated for all the ribosomes.

So, I use Matlab to generate coordinates, Chimera for getting isosurface 
geometry. I use then software like 3DSMax or Chimera again to display 
the VRML file. The problem I face is that 3DSMax is very long to open 
the file. The opening is almost instantaneous in Chimera but as Greg 
confirmed it is not possible to clip and cap the VRML isosurfaces.

The best way to do is to write a Chimera script able to read the 
coordinates matrix and to attribute a ribosome multiscale model surface 
for all the points. Thus, I avoid the VRML step, I work only in Chimera 
where I can clip and cap and render only a section of a very crowded 
scene. But I do not know python. Do you think whether such a script is 
easy to write?


Thomas Goddard a écrit :
> Hi Damien,
>   Chimera cannot cap clipped VRML surfaces. It also can't change the 
> coloring or transparency of VRML surfaces. VRML surfaces are different 
> from all other surfaces in Chimera.
>   Why not just save the Chimera session with the multiscale model 
> surface?  Then you can reopen it and clip and cap as you wish.
>     Tom
> -------- Original Message --------
> Subject: [Chimera-users] capping surface with a VRML model
> From: Damien Larivière
> To: chimera-users
> Date: 11/17/09 9:51 AM
>> Dear all,
>> It is possible in Chimera to cap the clipped surface of an isosurface 
>> made with the Multiscale Model tool.
>> However, if the isosurface is exported in VRML and then reopened in 
>> Chimera, it is no more possible to cap the clipped surface. This 
>> function (surface capping) is very interesting in particular when the 
>> scene is crowded by many proteins. Is it a way to cap VRML model?
>> Many thanks for your help!
>> Damien

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