## [PyMOL] Pymol sas

 [PyMOL] Pymol sas From: neshat haq - 2013-11-12 08:17:43 Attachments: Message as HTML ```Hi, I could not find the the algorithm by which pymol calculates the solvent ASA. What I understood is that pymol adds the vdw radii of atom and probe, makes the sphere around the center of selected atoms, puts some dots and according to the density of dots it calculates the SASA. or it simply uses the Richard & Lee algorithm of rolling water. Please clarify my doubts. -- Best regards Neshatul Haque PhD, Dpt of Biotechnology university of hyderabad ```

 [PyMOL] Pymol sas From: neshat haq - 2013-11-12 08:17:43 Attachments: Message as HTML ```Hi, I could not find the the algorithm by which pymol calculates the solvent ASA. What I understood is that pymol adds the vdw radii of atom and probe, makes the sphere around the center of selected atoms, puts some dots and according to the density of dots it calculates the SASA. or it simply uses the Richard & Lee algorithm of rolling water. Please clarify my doubts. -- Best regards Neshatul Haque PhD, Dpt of Biotechnology university of hyderabad ```
 Re: [PyMOL] Pymol sas From: Jason Vertrees - 2013-11-21 20:47:24 Attachments: Message as HTML ```Neshat, Warren wrote the surfacing algorithm years ago. A little more discussion on the algorithm can be found here ( http://www.mail-archive.com/pymol-users@.../msg07124.html) and here (http://www.pymolwiki.org/index.php/Get_Area). Cheers, -- Jason On Tue, Nov 12, 2013 at 2:17 AM, neshat haq wrote: > Hi, > I could not find the the algorithm by which pymol calculates the solvent > ASA. > What I understood is that pymol adds the vdw radii of atom and probe, > makes the sphere around the center of selected atoms, puts some dots and > according to the density of dots it calculates the SASA. > or it simply uses the Richard & Lee algorithm of rolling water. > Please clarify my doubts. > -- > Best regards > Neshatul Haque > PhD, Dpt of Biotechnology > university of hyderabad > > > ------------------------------------------------------------------------------ > November Webinars for C, C++, Fortran Developers > Accelerate application performance with scalable programming models. > Explore > techniques for threading, error checking, porting, and tuning. Get the most > from the latest Intel processors and coprocessors. See abstracts and > register > http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@... > -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) Jason.Vertrees@... (o) +1 (603) 374-7120 ```