[Chimera-users] Computing solvent accessible area without internal cavities

Tom Goddard goddard at sonic.net
Mon Jan 13 13:53:09 PST 2014

Hi Numan,

  Chimera uses the MSMS program to compute solvent accessible surface area, and MSMS has an option to only compute for the outside surface component without internal cavities.  So I think this is just what you want.  Although you could script it in Chimera you might find it easier to write a script that uses the standalone program directly from Michel Sanner

The one trouble you may run into is the calculation failing on some molecules due to numerical instabilities.  The older version of the MSMS library we use in Chimera often fails to compute the surfaces and areas for molecules larger than 10,000 atoms, and sometimes fails for much smaller molecules.  The standalone program from Michel failed much less often in tests I did a few years ago, probably because it used some newer more reliable code.


On Jan 13, 2014, at 11:13 AM, "Oezguen, Numan"  wrote:

> Dear Tom,
> I am facing a problem that you have most probably already have solved and hoping you could help me out. I need to identify atoms that are solvent accessible. For this I used the program Getarea from Werner Braun’s group in Galveston Texas. It works fine, however it lists also internal cavity surface atoms as solvent exposed. Technically it is correct… but I am interested only in those surface areas that are not internal i.e. surface areas that are accessible to molecules approaching it from outside.
> Do you know of any commercial or free (preferably) program that can do this. Ideally it should be possible to call it from scripts (shell or Perl).
> Thank you very much for you time and help,
> Numan
> Numan Oezguen, Dr. rer. nat.
> Instructor of Pathology & Immunology
> Texas Children’s Microbiome Center
> Feigin Center, Suite 830
> 1102 Bates Avenue
> Houston, TX 77030

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