From owner-chemistry |-at-| ccl.net Mon Dec 17 03:30:00 2007 From: "Michel Petitjean ptitjean,,itodys.jussieu.fr" To: CCL Subject: CCL: Any open-sourced generation algorithm for Connolly molecular surface?? Message-Id: <-35867-071217032506-25145-awZ5rdvj64/YFBWLUi5GWA(0)server.ccl.net> X-Original-From: Michel Petitjean Date: Mon, 17 Dec 2007 09:24:49 +0100 (MET) Sent to CCL by: Michel Petitjean [ptitjean(0)itodys.jussieu.fr] To: chemistry*|*ccl.net Subject: CCL: Re: Any open-sourced generation algorithm for Connolly molecular surface?? Do you mean: (a) Computing the surface area or (b) Viewing graphically the surface area For (a), use the freeware ASV (Monte-Carlo and/or analytical calculation): http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#ASV The free MC routines sources are in f77, but are callable in C. It works for a null radius probe sphere (i.e. van der Waals surface or SAS). For (b), do a Google search. Remark: the analytical Connolly molecular surface algorithm fails in most situations because intersections or more than 3 spheres exist, unless atomic radii are very small (as it occurs in commercial softwares !!!). Atomic radii recommended in the literature induce intersections of 6 spheres in many cases (see Bondi, Gavezzotti, etc.). Worse: it has been demonstrated that surfaces are highly sensitive to atomic radii. ASV performs the analytical computation in all situations, for any radii values. Best regards, Michel Petitjean, DSV/iBiTec-S/SB2SM (CNRS URA 2096) CEA Saclay, bat. 528 91191 Gif-sur-Yvette Cedex Phone: +33(0)1 6908 9681 / Fax: +33(0)1 6908 4007 E-mail: petitjean*|*itodys.jussieu.fr, michel.petitjean*|*cea.fr http://petitjeanmichel.free.fr/itoweb.petitjean.spheres.html Formerly: ITODYS (CNRS, UMR 7086), 1 rue Guy de la Brosse, 75005 Paris, France. Sent to CCL by: "Jun Tie Cheng" [tjcheng**mail.sioc.ac.cn] > Hi, CCLers > > Recently I am dealing with molecular surface generation. Is there any open-sourced alogrithm for this purpose? A C/C++ library would be very appreciated. Thanks in advance. > > Best regards, > >Jay