[phenixbb] [ccp4bb] Getting the triangulated solvent excluded surface of a protein (PDB) as a .obj file

Francois Berenger berenger at riken.jp
Thu Mar 10 16:51:52 PST 2011


I forgot to mention about what is the .obj file I need.

It is a pure ASCII geometric description of a polyhedra.

Cf. http://en.wikipedia.org/wiki/Wavefront_.obj_file

It looks rather easy to parse compared to some VRML file, for example.


Francois Berenger wrote:
> Hello,
> What are the good software to do this?
> I already know of Pymol and Jmol.
> Both can export the result to a .obj file, which is interesting for
> later processing.
> However, Pymol's algorithm is not exactly what Connolly described,
> cf. 
> http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg00179.html
> Also, Pymol will save the surface with some translation and rotation
> which are not present in the PDB read in, which is a real pain.
> For Jmol, sometimes the surface is not a closed polyhedra, so
> it is kind of useless for my purpose.
> I know of MSMS, but I don't think it is that robust (I read some source 
> code where someone was using MSMS, the source code had many dirty things 
> in order to try handling the apparently many cases where MSMS was 
> crashing).
> Is there something freely usable for research, using beta shapes 
> internally, for example? That should be a robust approach.
> A robust software would be much appreciated (not crashing, whatever
> the PDB we give it as input).
> Open source and not in Fortran would be heaven. ;)
> Thanks a lot for suggestions,
> F.

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