Hi I am not sure which method is being used by PyMOL but because the algorithm uses a dot density term it is likely the Shrake & Rupley algorithm also known as the rolling ball method. You should read the FreeSASA article (freely available https://f1000research.com/articles/5-189/v1 ). The author provides a really nice description of SASA calculations along with precision and speed analysis.
Emilio On Thu, Apr 27, 2017 at 7:38 AM, Ahmad Abdelzaher <underoath...@gmail.com> wrote: > Thank you for your reply. With regard to the algorithm used, do you > have any idea which algorithm is used in the Pymol calculations? DSSP > is likely to be using the rolling ball method. > > Regards. > > On Thu, Apr 27, 2017 at 1:35 PM, Emilio Xavier Esposito > <emilio.espos...@gmail.com> wrote: >> Hi >> The accuracy of the calculation depends on the dot_density value (the >> amount of sampling done) with 1 being the lowest quality and 4 being >> the best quality. A dot_density value of 1 uses less computational >> resources (time) than a dot_density of 4 because of the amount of >> sampling performed to calculate the surface area. >> >> With respect to your question regarding the difference between PyMOL's >> get_area command and the SASA calculated bye DSSP, these differences >> in surface area could be the result of different atom radii being >> used, the inclusion of hydrogen atoms, or differences in the algorithm >> used to calculate the SASA. The speed differences could be the result >> of different algorithms and how they are implemented. >> >> You might want to check out FreeSASA ( http://freesasa.github.io ) to >> perform your SASA calculations. >> >> Emilio >> >> On Wed, Apr 26, 2017 at 11:49 PM, Ahmad Abdelzaher >> <underoath...@gmail.com> wrote: >>> I would appreciate any help regarding this. >>> >>> On Tue, Apr 25, 2017 at 12:36 PM, Ahmad Abdelzaher >>> <underoath...@gmail.com> wrote: >>>> Hello, >>>> >>>> Does the get_area command use the rolling ball algorithm? Which >>>> dot_density corresponds to the best accuracy 1 or 4? Is there a reason >>>> why it consumes more time to compute sasa? Dssp takes significantly >>>> less time to do the calculations, however compared to Pymol >>>> dot_density of 3, the areas sometimes differ by 4,5,6, squared >>>> angstroms! >>>> >>>> Any comment on that? >>>> >>>> Regards. >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
