[chimera-dev] Good!

Jean Didier Pie Marechal JeanDidier.Marechal at uab.cat
Mon Jul 20 14:28:07 PDT 2009

Hi Conrad,

OK, we'll forget qhull.  But what you found from Mark Gerstein is perfect. We didn't get to this point. We have few hands and brains available for the moment, so we'll try to have a go. Should not be too difficult.

I'll get you posted if succeed...or will bother you again later...

All the best and thanks a lot

Dr. Jean-Didier Maréchal
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

----- Missatge original -----
De: Conrad Huang <conrad at cgl.ucsf.edu>
Data: Dilluns, Juliol 20, 2009 11:14 pm
Assumpte: Re: [chimera-dev] Calculation voronoi volums in a prot.

> 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

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