From chemistry-request@ccl.net Thu Apr 8 04:01:39 2004 Received: from shiva.jussieu.fr (shiva.jussieu.fr [134.157.0.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3891cjR002785 for ; Thu, 8 Apr 2004 04:01:38 -0500 Received: from ds10.itodys.jussieu.fr (ds10.itodys.jussieu.fr [134.157.24.13]) by shiva.jussieu.fr (8.12.10/jtpda-5.4) with ESMTP id i3891jIu005054 for ; Thu, 8 Apr 2004 11:01:45 +0200 (CEST) X-Ids: 164 Received: by ds10.itodys.jussieu.fr (8.12.1/1.1.2.11/09Jul02-1200PM) id i3891cV2508860; Thu, 8 Apr 2004 11:01:38 +0200 (MEST) Date: Thu, 8 Apr 2004 11:01:38 +0200 (MEST) From: Michel Petitjean Message-Id: <200404080901.i3891cV2508860-.at.-ds10.itodys.jussieu.fr> To: chemistry-.at.-ccl.net Subject: CCL: Re: calculate accessible surface area for an occluded cavity X-Miltered: at shiva.jussieu.fr with ID 407514F9.001 by Joe's j-chkmail (http://j-chkmail.ensmp.fr)! X-Antivirus: scanned by sophie at shiva.jussieu.fr To: Subj: CCL: Re: calculate accessible surface area for an occluded cavity Dear Qin, May I suggest two ways. I assume that you know which residues are on the boundary on the cavity. Using adequate radii, the SAS can be computed either analytically, or by Monte-Carlo (faster, but less accurate), with the freeware ASV: binaries and documentation with reference in: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#ASV Also, if you have a roughly convex cavity (e.g. the convex hull of the alpha-carbons bounding the cavity), you can get the surface of the hull (and its generalized radius and diameter), with the free ware RADI: binaries and documentation with reference in: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#RADI Michel Petitjean, Email: petitjean-.at.-itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean-.at.-ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html .................................................................. > From owner-chemistry-.at.-ccl.net Thu Apr 8 08:19:56 2004 From: "Q" To: Subject: CCL:calculate accessible surface area for an occluded cavity Date: Wed, 7 Apr 2004 19:29:58 -0500 Dear All, I have a protein with an internal cavity that has no access to the = outside solvent. I would like to calculate the accessible surface area = of the residues inside the cavity to see how accessible they are to the = cavity. How can I do this or what programs could help to do it? How = about NACCESS? Thanks for any input. Qin