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Lines: 39 Message-ID: <827b68$m3s$1@gray.ims.u-tokyo.ac.jp> Mime-Version: 1.0 Content-Type: text/plain; charset="iso-2022-jp" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk ****************************** CALL FOR RECOMB 2000 POSTERS ****************************** +----------------------------------------------------+ | DEADLINE: January 10, 2000 | | NOTIFICATION: January 29, 2000 | | SUBMISSION: recomb2000-poster@ims.u-tokyo.ac.jp | | URL: http://recomb2000.ims.u-tokyo.ac.jp/ | +----------------------------------------------------+ The Fourth Annual International Conference on Computational Molecular Biology (RECOMB 2000) announces a call for posters. The conference will take place in Tokyo on April 8-11, 2000. POSTER ABSTRACTS SHOULD BE SUBMITTED BY FOLLOWING EXACTLY THE +----------------------------------------------------+ | INSTRUCTIONS FOR AUTHORS | | http://recomb2000.ims.u-tokyo.ac.jp/ | | instructions_for_authors.html | +----------------------------------------------------+ Accepted posters will appear in a hard cover book titled +----------------------------------------------------+ | "Currents in Computational Molecular Biology" | | S. Miyano, R. Shamir, T. Takagi (eds.) | | Universal Academy Press, Inc. | | (http://www.uap.co.jp/) | +----------------------------------------------------+ For more information about the conference and poster session visit the web site. * We are sorry if you received this email in multiple. * If you will be removed from the RECOMB email list, please let us know (recomb2000@ims.u-tokyo.ac.jp). Thank you. From owner-molmodel@hgmp.mrc.ac.uk Fri Dec 17 11:55:19 1999 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 5472817AD9; Fri, 17 Dec 1999 11:55:17 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id LAA27833 for ; Fri, 17 Dec 1999 11:55:15 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id LAA28845 for molmodel-list@hgmp.mrc.ac.uk; Fri, 17 Dec 1999 11:55:14 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Mark X-Newsgroups: bionet.molec-model Subject: calculation of angles Date: Fri, 17 Dec 1999 11:41:39 GMT Organization: Deja.com - Before you buy. Lines: 21 Message-ID: <83d7hj$ih5$1@nnrp1.deja.com> X-Article-Creation-Date: Fri Dec 17 11:41:39 1999 GMT X-Http-User-Agent: Mozilla/4.06 [en] (Win98; I ;Nav) X-Http-Proxy: 1.0 x28.deja.com:80 (Squid/1.1.22) for client 193.205.8.161 X-MyDeja-Info: XMYDJUIDsingalone To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk I see that in many modelling programs where an angle theta is to be calculated, it is very often calculated as atan2(sin(theta),cos(theta)), where atan2, according to the manual, is a FORTRAN function approximately equal to atan(sin(theta/cos(theta)). I don't understand: (a) why atan2(y,x) is preferred to atan(y/x); (b) why one couldn't directly take acos(cos(theta)) or asin(sin(theta)), instead of having to obtain both sine and cosine. (the cosine of angle is easy to obtain, but sine is not). Any help appreciated. Mark Sent via Deja.com http://www.deja.com/ Before you buy. From owner-molmodel@hgmp.mrc.ac.uk Sat Dec 18 01:44:17 1999 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 81AB417B3B; Sat, 18 Dec 1999 01:44:16 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id BAA00695 for ; Sat, 18 Dec 1999 01:44:14 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id BAA17323 for molmodel-list@hgmp.mrc.ac.uk; Sat, 18 Dec 1999 01:44:09 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Lev Gorenstein X-Newsgroups: bionet.molec-model Subject: Re: calculation of angles Date: Fri, 17 Dec 1999 20:37:07 -0500 Organization: Purdue University Lines: 58 Message-ID: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: mozo.cc.purdue.edu 945481029 28138 128.210.43.96 (18 Dec 1999 01:37:09 GMT) X-Complaints-To: usenet@mozo.cc.purdue.edu X-Sender: lev@marie.chem.purdue.edu In-Reply-To: <83d7hj$ih5$1@nnrp1.deja.com> To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk On Fri, 17 Dec 1999, Mark wrote: M> I see that in many modelling programs M> where an angle theta is to be calculated, it is very often M> calculated as atan2(sin(theta),cos(theta)), where atan2, M> according to the manual, M> is a FORTRAN function approximately equal to M> atan(sin(theta/cos(theta)). M> I don't understand: M> M> (a) why atan2(y,x) is preferred to atan(y/x); Probably, atan2 does better job in determining the sign of the angle (see below). M> (b) why one couldn't directly take acos(cos(theta)) or M> asin(sin(theta)), instead of having to obtain both sine and cosine. M> (the cosine of angle is easy to obtain, but sine is not). Think trig. Let's say the angle that you're calculating is 60 degrees. You calculate cosine (from the structure), take acos(0.5) and get 60 degrees. Everything is fine. Now imegine, that the angle is in fact -60. You calculate cosine, but cos(-60) = cos(60), so the cosine is 0.5, and when you take acos, you would end up with 60 degrees, rather than -60. So you are in trouble because of trig equality cos(-x) = cos(x). Same thing if you do it with with sine. The fact that sin(x) = sin(180-x) would not allow you to distinguish between, say, 30 and 150 degrees, or 210 and 330. Therefore, you have to analize BOTH sine and cosine of your angle, and assign a value according to the signs of both sine and cosine: 0 < x < 90: sin(x) positive, cos(x) positive 90 < x < 180: sin(x) positive, cos(x) negative 180 < x < 270: sin(x) negative, cos(x) negative 270 < x < 360: sin(x) negative, cos(x) positive Thus, if you use atan(sine(x)/cosine(x)), and, for example, the argument is positive, you would not know, whether it's because the angle is in the first quadrant (both sine and cosine are positive), or it is in the third quadrant (both are negative, thus giving a positive tangent). The atan() function will return a value from the first quadrant. It's my understanding that atan2 function does the above mentioned analisys of signs (since the sine and cosine are supplied separately), and thus returns the true value of angle. Regards, Lev -- 186,282 miles per second: It isn't just a good idea, it's the law! From owner-molmodel@hgmp.mrc.ac.uk Mon Dec 20 12:30:21 1999 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id C228317A79; Mon, 20 Dec 1999 12:30:19 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id MAA21866 for ; Mon, 20 Dec 1999 12:30:17 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id MAA19313 for molmodel-list@hgmp.mrc.ac.uk; Mon, 20 Dec 1999 12:30:16 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: John Osborn X-Newsgroups: bionet.molec-model Subject: Re: calculation of angles Date: Mon, 20 Dec 1999 11:22:40 +0000 Organization: University of Bradford Lines: 38 Message-ID: <385E1180.1E85@br.ac.uk> References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: squire.cen.brad.ac.uk 945688669 12065 143.53.238.22 (20 Dec 1999 11:17:49 GMT) X-Complaints-To: misuse@bradford.ac.uk X-Mailer: Mozilla 3.03C (X11; I; SunOS 5.6 sun4u) To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk Lev Gorenstein wrote: > > Thus, if you use atan(sine(x)/cosine(x)), and, for example, the > argument is positive, you would not know, whether it's because > the angle is in the first quadrant (both sine and cosine are > positive), or it is in the third quadrant (both are negative, thus > giving a positive tangent). The atan() function will return a > value from the first quadrant. It's my understanding that atan2 > function does the above mentioned analisys of signs (since the > sine and cosine are supplied separately), and thus returns > the true value of angle. As Lev Gorenstein says, one advantage of ATAN2 over ATAN is that it takes care of the quadrant. It also ensures that the result is greater than -pi and not greater than pi, whereas in the example given by Mark, atan2(sin(theta),cos(theta)), it is not clear that the argument theta is necessarily in this range. The definition of ATAN2 in FORTRAN77 (and presumably also in more recent versions of Fortran for which I do not have manuals at hand) is as follows: ATAN2(X1,X2) = tan^-1(X1/X2) in radians = Y such that: -pi < Y <= pi; if X1 > 0, Y > 0; if X1 < 0, Y < 0; if X1 = 0 and X2 > 0, Y = 0; if X1 = 0 and X2 < 0, Y = pi; if X2 = 0 and X1 <> 0, |Y| = pi/2; X1 and X2 cannot both equal 0. (The symbol <= means "less than or equal to"; <> means "not equal to".) Note that the definition allows for the possibility that X2 = 0, whereas if one simply used ATAN(X1/X2) one would first need to test for the possibility that X2 = 0 and handle it separately to avoid an undefined intermediate result for X1/X2. -- John Osborn University of Bradford, UK. To reply by email, replace "br" by "bradford" in my email address. From owner-molmodel@hgmp.mrc.ac.uk Mon Dec 20 21:04:13 1999 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id E009617A61; Mon, 20 Dec 1999 21:04:12 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id VAA06261 for ; Mon, 20 Dec 1999 21:04:11 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id VAA25807 for molmodel-list@hgmp.mrc.ac.uk; Mon, 20 Dec 1999 21:04:10 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: vakseri@musc.edu (Ilya Vakser) X-Newsgroups: bionet.molec-model Subject: Postdoc in Protein Modeling and Bioinformatics Date: 20 Dec 1999 21:04:08 -0000 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 24 Message-ID: <385E99EF.496ACAD9@musc.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 945723849 25805 193.62.192.80 (20 Dec 1999 21:04:09 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk X-Received: from revere3.musc.edu (revere3.musc.edu [128.23.203.10]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id VAA06253 for ; Mon, 20 Dec 1999 21:04:06 GMT X-Received: from musc.edu ([128.23.81.55]) by revere3.musc.edu (8.8.8/8.8.8) with ESMTP id QAA10137 for ; Mon, 20 Dec 1999 16:04:05 -0500 (EST) X-Mailer: Mozilla 4.7 [en] (Win95; I) X-Accept-Language: en X-To: molmodel@hgmp.mrc.ac.uk To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk POSTDOC IN PROTEIN MODELING AND BIOINFORMATICS Applications are invited for a postdoctoral position in my laboratory at the Medical University of South Carolina. 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Vakser Assistant Professor of Pharmacology Department of Cell and Molecular Pharmacology Medical University of South Carolina 173 Ashley Avenue, POBox 250505 Charleston, SC 29425 Email: vakseri@musc.edu, Phone:(843)792-2471, Fax:(843)792-2475 --- From owner-molmodel@hgmp.mrc.ac.uk Tue Dec 21 16:18:56 1999 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 24EC017B51; Tue, 21 Dec 1999 16:18:53 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id QAA17288 for ; Tue, 21 Dec 1999 16:18:47 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id QAA19158 for molmodel-list@hgmp.mrc.ac.uk; Tue, 21 Dec 1999 16:18:43 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: ps2t@unix.mail.virginia.edu (Pornthep Sompornpisut) X-Newsgroups: bionet.molec-model Subject: surface area source code (request) Date: 21 Dec 1999 16:18:41 -0000 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 23 Message-ID: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: niobium.hgmp.mrc.ac.uk 945793122 19155 193.62.192.80 (21 Dec 1999 16:18:42 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk X-Received: from mail.virginia.edu (mail.Virginia.EDU [128.143.2.9]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with SMTP id QAA17202 for ; Tue, 21 Dec 1999 16:18:35 GMT X-Received: from node5.unix.virginia.edu by mail.virginia.edu id aa04782; 21 Dec 99 11:18 EST X-Received: from localhost (ps2t@localhost) by node5.unix.Virginia.EDU (8.8.5/8.6.6) with ESMTP id LAA88266 for ; Tue, 21 Dec 1999 11:18:31 -0500 X-To: molmodel@hgmp.mrc.ac.uk To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk Dear Colleagues, I have a few questions concerning about calculation of the solvent accessible surface area of proteins. Here they are as follows: 1. Does anyone know if there is any source code available for calculating accessible surface area derived from analytical function? 2. What is the best current approach to express the surface areas as a function of interatomic distance? Any response are welcome and appreciated. Thank you in advance. Thep ================================================================== Department of Physiology University of Virginia ps2t@virgnia.edu ================================================================== --- From owner-molmodel@hgmp.mrc.ac.uk Tue Dec 21 16:29:15 1999 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 1B20717A63; Tue, 21 Dec 1999 16:29:14 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id QAA18914 for ; Tue, 21 Dec 1999 16:29:13 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id QAA19283 for molmodel-list@hgmp.mrc.ac.uk; Tue, 21 Dec 1999 16:29:11 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: qeo80@mail.oktasys.fi (Fun N EZ!) 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Thank You po look xcy55 --- From owner-molmodel@hgmp.mrc.ac.uk Wed Dec 22 11:30:50 1999 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 8113017A85; Wed, 22 Dec 1999 11:30:43 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id LAA25253 for ; Wed, 22 Dec 1999 11:30:39 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id LAA11286 for molmodel-list@hgmp.mrc.ac.uk; Wed, 22 Dec 1999 11:30:38 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: ptitjean@ccr.jussieu.fr (Michel PETITJEAN) X-Newsgroups: bionet.molec-model Subject: Re: surface area source code (request) Date: 22 Dec 1999 12:30:12 +0100 Organization: CCR - Universites Paris VI/VII - Paris - France Lines: 37 Message-ID: <83qco4$522c@moka.ccr.jussieu.fr> Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Trace: vishnu.jussieu.fr 945861972 7090 134.157.1.23 (22 Dec 1999 11:26:12 GMT) X-Complaints-To: Newsmaster@jussieu.fr. To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk In article: Pornthep Sompornpisut (ps2t@unix.mail.virginia.edu) wrote: > I have a few questions concerning about calculation of the solvent >accessible surface area of proteins. Here they are as follows: > > 1. Does anyone know if there is any source code available for >calculating accessible surface area derived from analytical >function? > 2. What is the best current approach to express the surface areas as a >function of interatomic distance? > 1) Formulas for analytical computations of spheres intersections are in my paper: J.Comput.Chem.1994,15[5],507-523. The associated executable programme ASV is available (free) on various platforms, including RS6000, CRAY J90 and YMP familiy, DEC-alpha (VMS and unix), SGI (various architectures) and LINUX. Just specify which version(s) you need and you shall receive it via email. If you need a rapid computation for large molecules without the analytical accuracy, the Monte-Carlo code is also included is ASV. The Monte-Carlo subroutines (FORTRAN) are also free. The full sources of ASV (which computes both surfaces and volumes) are available for people initiating a collaboration. 2) Surfaces areas are expressable from sphere radii and cartesian coord of centers, and coord are get from the matrix of interatomic distances with multidimensional scaling. Recovering N 3-tuples of coordinates from the N*N distances matrix via multidimensional scaling can be found in most descriptive statistics textbook. If you have an incomplete distance matrix, you have to operate iteratively, assuming that the coord of a 3D point are obtainable from the 3 distances from 3 reference points together with a flag showing on which side of the plane is the new point. The analytical formula is also in my paper, because it is equivalent to look at the two 3D-points at the intersection of three 3D-spheres. Michel Petitjean, Email: petitjean@itodys.jussieu.fr ITODYS (CNRS, ESA 7086) ptitjean@ccr.jussieu.fr From owner-molmodel@hgmp.mrc.ac.uk Sun Dec 26 00:15:42 1999 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 2E76917A5F; Sun, 26 Dec 1999 00:15:42 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id AAA17824 for ; Sun, 26 Dec 1999 00:15:40 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id AAA20623 for molmodel-list@hgmp.mrc.ac.uk; Sun, 26 Dec 1999 00:15:39 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "corrado" X-Newsgroups: bionet.molec-model Subject: Help Me ph Lines: 7 X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Message-ID: Date: Sun, 26 Dec 1999 00:15:35 GMT X-Complaints-To: abuse@libero.it X-Trace: news.infostrada.it 946167335 151.21.94.226 (Sun, 26 Dec 1999 01:15:35 MET) Organization: [Infostrada] To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk Hail at all It's possible make a indicator of pH in House? 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