[chimera-dev] Calculation voronoi volums in a prot.

Elaine Meng meng at cgl.ucsf.edu
Fri Jul 17 10:16:03 PDT 2009

Hi JD,
If you do use the "Area/Volume from Web" tool for the Voronoi  
calculations, the results are assigned as atom attributes, so they  
could be shown with color or sphere radii.  Of course, that is not  
the same as displaying the partitions directly, and as Conrad said  
Chimera does not have a command to connect to that server.  There is  
a command to show attributes with color (rangecolor) but showing them  
with radii requires using the "Render by Attribute" tool.

Since "Area/Volume from Web" runs an outside server anyway, maybe you  
could connect to that and get results files with your own scripts.   
However, as far as I can tell the only information it gives is the  
volume values, not everything you would need to generate a display of  
the tesselation.

Other issues:
- the atoms on the outside are "no-value" (since their Voronoi  
volumes would be infinity)
- showing the values with radii magnifies the differences since the  
sphere volumes will scale as Voronoi volume cubed


On Jul 17, 2009, at 9:48 AM, Conrad Huang wrote:

> Unfortunately, the answers to both your questions is "no, it does  
> not do
> what you want."  First, the "Area/Volume from Web" tool only  
> obtains the
> numerical values for surface area and volume; it does not get the  
> volume
> map itself.  Second, the qhull package is included for the Delaunay
> triangulation used by the "Intersurf" tool and there are no tools that
> use the Voronoi diagram capabilities.
> What type of visualization are you trying to create?  Since Voronoi
> diagrams generate partitions separated by planes, do you want to  
> see all
> the partitioning planes, or just polyhedra around specific atoms?  We
> can look into whether qhull can generate the required data and how  
> hard
> it would be to interface that with Chimera.
> Conrad
> Jean Didier Pie Marechal wrote:
>> Dear all,
>> We are trying to calculate voronoi's volumes around atoms in a  
>> protein. So far we used the interfase "Area/Volume from Web" but  
>> we have several troubles. So here the questions:
>> 1. Is there a command line to do the server call automatically and  
>> display resulting volumes in the viewer?
>> 2. We know that Qhull is one of the packages embedded in chimera.  
>> We try to see how to script voronoi calculation and read resulting  
>> volumes but failed so far. Do you have an example on how to  
>> generate the voronoi volumes maps from qhull in chimera?
>> All the best,
>> JD
>> Dr. Jean-Didier Maréchal
>> Lecturer
>> Computational Biotechnological Chemistry @ Transmet
>> Unitat de Química Física
>> Departament de Química
>> Universitat Autònoma de Barcelona
>> Edifici C.n.
>> 08193 Cerdanyola (Barcelona)
>> Tel: +34.935814936
>> e-mail: JeanDidier.Marechal at uab.es
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