From chemistry-request@server.ccl.net Fri Aug 9 12:00:09 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g79G09l27508 for ; Fri, 9 Aug 2002 12:00:09 -0400 Received: from cornell.edu ([128.84.182.122]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id MAA29575; Fri, 9 Aug 2002 12:00:04 -0400 (EDT) Sender: richard@cornell.edu Message-ID: <3D53E6FF.3E4D6029@cornell.edu> Date: Fri, 09 Aug 2002 11:59:59 -0400 From: Richard Gillilan X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.4.16 i686) X-Accept-Language: en MIME-Version: 1.0 To: Nik CC: chemistry@ccl.net Subject: Re: CCL:holes in molecular surface when using mds from QCPE References: <3D4FC421.523F5AE4@pharmazie.uni-wuerzburg.de> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit N > When I convert the obtained the dots file into a displayable format I > find large holes in the surface calculated. I had a look in the source > code, but since I am mainly a perl and c++ programmer I couldn't find > anything obvious. > > Has anyone observed something similar ? > > This may be an error in covering the surface with polygons, but sounds more like another phenomenon I know. If you are using a molecular surface of the type based on rolling a probe sphere over the protein (piecewise sphere and torus), then there are cases where real holes exist (well they look like holes, but are not actually holes in the surface, just pockets with atom-sized round entry holes). Consider the case of two protein atoms separated far enough apart that when you roll the probe sphere in contact with both atoms, you actually get a self-intersecting torus. Similar thing can happen with more than two protein atoms. Some programs generate cusps, leaving out the interpenetrating part (the right choice I think). Some may offer the option of filling these in, or even put both surfaces. They look bad, but they are places that a water molecule might actually go. If you tweak the probe radius up a little, they may go away if you need a pretty picture. From the standpoint of hydrophobicity, the cusps are rather important and can be seen in full atomistic simulations with water and methane. Richard Gillilan MacCHESS Cornell