[chimera-dev] Calculation voronoi volums in a prot.
Jean Didier Pie Marechal
JeanDidier.Marechal at uab.cat
Mon Jul 20 03:21:09 PDT 2009
Dear Conrad and Elaine,
thanks for your answers. Just to recenter my questions:
What we are doing large statistics on a substantial set of protein structures. Some of the descriptors we need are voronoi attributes; our main interest is on the volumes surrounding atoms. Nevertheless, having a representation of the polyedra would be great (not great genial). So we explored chimera's capabilities on this.
Re. the server access.
How the call to the server works is perfect for the purpose of our work and does exactly what we want. However, since we want to script every step of our work, it would be great to know if a command line equivalent to the "Area/volume from Web" interfase exists. As we thought there was no command to do so, we were wondering if qhull based calls could do the trick.
Re. Voronoi calculation
Conrad, having qhull providing volmetric values would be great. That would afford us calling the server, eases the script, and also allows us to understand better why in some cases, the calculations give strange values (not only the -1 we understood the origin, but other problems).
If that is too complicated, as Elaine says, we will try to call the server directly and recover the volumes.
Thanks a lot for the help,
Dr. Jean-Didier Maréchal
Computational Biotechnological Chemistry @ Transmet
Unitat de Química Física
Departament de Química
Universitat Autònoma de Barcelona
08193 Cerdanyola (Barcelona)
e-mail: JeanDidier.Marechal at uab.es
----- Missatge original -----
De: Conrad Huang <conrad at cgl.ucsf.edu>
Data: Divendres, Juliol 17, 2009 6:48 pm
Assumpte: Re: [chimera-dev] Calculation voronoi volums in a prot.
> 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
> map itself. Second, the qhull package is included for the Delaunay
> triangulation used by the "Intersurf" tool and there are no tools
> 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?
> can look into whether qhull can generate the required data and how
> it would be to interface that with Chimera.
> 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
> > _______________________________________________
> > Chimera-dev mailing list
> > Chimera-dev at cgl.ucsf.edu
> > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev
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