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

[Conrad Huang]

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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