Re: [chimera-dev] Calculation voronoi volums in a prot.
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, 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 ----- Missatge original ----- De: Conrad Huang <conrad@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 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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First the bad news. I looked into qhull and it appears that computing the volumes for all Voronoi cells is not built-in to the software. The qhull FAQ gave an example for computing the volume of a single cell:
To compute the area and volume of the Voronoi region for input site 5 (site 0 is the first one), use
rbox 10 D2 | qvoronoi QV5 p | qconvex s FS
My guess is that this will probably be pretty inefficient as the number of atoms increases. As the qhull documentation says, algorithms that keep intermediate convex hull results are much more efficient. On the good news side, the code that the "Area/volume from Web" server is from Mark Gerstein (see http://www.molmovdb.org/geometry/files/libproteingeometry/README.html) and is probably the best starting point. If you have some programming expertise available, it should be fairly straightforward to compile the calc-volume program and modify the Chimera extension to use that instead of the web. (We will, of course, be happy to answer any questions.) If not, we can talk about alternative solutions. Conrad Jean Didier Pie Marechal wrote:
[...]
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,
Best, JD
participants (2)
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Conrad Huang -
Jean Didier Pie Marechal