Calculation voronoi volums in a prot.
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@uab.es
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@uab.es
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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. <http://helixweb.nih.gov/structbio/basic.html> 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 Elaine 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@uab.es
_______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev
_______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev
participants (3)
-
Conrad Huang -
Elaine Meng -
Jean Didier Pie Marechal