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(Pt/FT) with the DESIRE to improve their lifestyle immediately. /////////////////////////////////////////////////////////// Please remove at mailto:fedt87@yahoo.com?subject=remove /////////////////////////////////////////////////////////// From owner-molmodel@hgmp.mrc.ac.uk Thu Nov 4 13:35:17 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 3BAB717A6A; Thu, 4 Nov 1999 13:35:15 +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 NAA27106 for ; Thu, 4 Nov 1999 13:35:13 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id NAA20631 for molmodel-list@hgmp.mrc.ac.uk; Thu, 4 Nov 1999 13:35:12 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Mike Sternberg X-Newsgroups: bionet.molec-model Subject: Postdoc Bioinformatics London UK Date: Thu, 04 Nov 1999 13:21:23 +0000 Organization: Imperial Cancer Research Fund Message-ID: <38218852.41B5DE65@icrf.icnet.uk> Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 4.61C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en Lines: 32 To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk Bioinformatics + Data Mining + London Postdoctoral Fellow £21,730 - £23,447 Initially 2 years Contract London WC2A A postdoctoral research position is available at the Imperial Cancer Research Funds Biomolecular Modelling Laboratory in central London to work on the application of machine learning to discover rules governing protein structure. 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From owner-molmodel@hgmp.mrc.ac.uk Fri Nov 5 13:35:22 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 0CF5D17A7B; Fri, 5 Nov 1999 13:35:21 +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 NAA27498 for ; Fri, 5 Nov 1999 13:35:20 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id NAA16783 for molmodel-list@hgmp.mrc.ac.uk; Fri, 5 Nov 1999 13:35:19 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "John O. Trent" X-Newsgroups: bionet.molec-model Subject: Two Postdocs in molecular modeling, J.G. Brown Cancer Center, U of Louisville Date: 5 Nov 1999 13:31:48 GMT Organization: University of Louisville Lines: 28 Message-ID: <01bf2792$326a50c0$3793a588@rlarocca.louisville.edu> Reply-To: jotren01@gwise.louisville.edu X-Trace: news.louisville.edu 941808708 13693 136.165.147.55 (5 Nov 1999 13:31:48 GMT) X-Complaints-To: usenet@news.louisville.edu X-Newsreader: Microsoft Internet News 4.70.1155 To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk Two Postdocs in molecular modeling, J.G. Brown Cancer Center, U of Louisville Two postdoctoral positions are immediately available within the Human Tumor Biology Program at the James Graham Brown Cancer Center, University of Louisville. There are a variety of structure-based drug design projects available ranging from DNA, duplex, triplex, and quadruplex systems, to protein:DNA and protein systems. The positions will closely interact with macromolecular NMR, medicinal chemists, and molecular biologists. Experience in molecular dynamics, particularly the Amber and/or MSI software packages, is required. Additional experience in either organic synthesis or biophysics, and programming skills including FORTRAN and unix is highly desirable. UofL is an Equal Opportunity/Affirmative Action Employer. Inquiries via Email to jotren01@gwise.louisville.edu Qualified applicants for the two positions should submit a complete C.V. with the names and addresses of at least two references to John O. Trent Ph.D. 529 South Jackson St, James Graham Brown Cancer Center University of Louisville Louisville, KY 40202 FAX (502) 852 5679 From owner-molmodel@hgmp.mrc.ac.uk Sat Nov 6 15:05:24 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id F046817A4E; Sat, 6 Nov 1999 15:05:23 +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 PAA12949 for ; Sat, 6 Nov 1999 15:05:21 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id PAA13732 for molmodel-list@hgmp.mrc.ac.uk; Sat, 6 Nov 1999 15:05:20 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: jgut@mus.ch (Josef Gut) X-Newsgroups: bionet.molec-model Subject: Similarity of chemical structures Date: Sat, 6 Nov 1999 17:10:14 +0200 Organization: Internet Access AG, Zuerich, Switzerland Message-ID: <19991106171014123785@megapop5-46.access.ch> X-Trace: pacifica.access.ch 941900418 18253 212.161.129.46 (6 Nov 1999 15:00:18 GMT) X-Complaints-To: newsmaster@access.ch X-Newsreader: MacSOUP 2.2.1 Lines: 20 To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk Hi, I am looking for molecular modeling software packages that can compare small chemical structures (such as drugs and or their metabolites/reactive intermediates) against each other and return something like "similarity" indices for several parameters: overall 3D structure of the molecules (energy-minimalized conformations thereof, electrochemical surface potentials, partial charge distributions and their coordinates on the surface of the molecules, etc. Also, what are the best tools to dock such molecules to proteins (receptors, substrate binding sites, etc)? Any any advice is highly appreciated. We are starting a programm where we try to identify small molecules with sufficient overall structural similarity to follow similar pathways of metabolism and eventually producing similar adverse effects. Thanks for your help. Joseph Gut, Ph.D. From owner-molmodel@hgmp.mrc.ac.uk Sat Nov 6 16:59:05 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 9595317A4E; Sat, 6 Nov 1999 16:59:04 +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 QAA15995 for ; Sat, 6 Nov 1999 16:59:03 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id QAA15057 for molmodel-list@hgmp.mrc.ac.uk; Sat, 6 Nov 1999 16:59:02 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: bash@post.com (Denys Bashtovyy) X-Newsgroups: bionet.molec-model Subject: (NONE) Date: 6 Nov 1999 16:59:01 -0000 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 15 Message-ID: <384186430.941907538527.JavaMail.root@web02.pub01> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 941907541 15055 193.62.192.80 (6 Nov 1999 16:59:01 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk X-Received: from rmx08.globecomm.net (rmx08.iname.net [165.251.8.85]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id QAA15988 for ; Sat, 6 Nov 1999 16:58:59 GMT X-Received: from web02.pub01 by rmx08.globecomm.net (8.9.1/8.8.0) with SMTP id LAA17063 X-To: molmodel@hgmp.mrc.ac.uk X-Mailer: mail.com X-Originating-IP: 160.114.51.8 X-Disposition-Notification-To: bash@post.com To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk Joseph, have a look at: http://www.msi.com/solutions/products/cerius2/modules/qsar_page.html#overview http://www.tripos.com/software/qsar.html http://www.oxmol.com/software/tsar3d/ Denys __________________________________________________ FREE Email for ALL! Sign up at http://www.mail.com --- From owner-molmodel@hgmp.mrc.ac.uk Mon Nov 8 21:19:03 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id B672F17A60; Mon, 8 Nov 1999 21:19:02 +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 VAA26507 for ; Mon, 8 Nov 1999 21:19:00 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id VAA17572 for molmodel-list@hgmp.mrc.ac.uk; Mon, 8 Nov 1999 21:18:59 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: wetboy Subject: Re: How can I optimize vector normalization in a Molecular Modeling program? X-Newsgroups: alt.games.programming,bionet.molec-model,comp.lang.c,comp.lang.c++ References: <807bh2$h4k$1@nnrp1.deja.com> User-Agent: tin/pre-1.4-980618 (UNIX) (SunOS/4.1.4 (sun4m)) Message-ID: Date: Mon, 08 Nov 1999 21:15:34 GMT X-Complaints-To: abuse@shore.net X-Trace: news.shore.net 942095734 192.233.85.1 (Mon, 08 Nov 1999 16:15:34 EST) Organization: Shore.Net/Eco Software, Inc; (info@shore.net) Lines: 63 To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk In comp.lang.c willkn@montana.com wrote: : Hi, I've been working on a molecular modeling program and have been : trying to improve its performance recently. I did some profiling and : found that the most time by far (41.4%) was spent in a function which : normalizes a 3-dimensional vector (profiling statistics are given at : the bottom). : I am wondering if anyone has suggestions for optimizing that operation. : Thanks, : William Knight : willkn@montana.com : The definition of the function is given below: : typedef double VTYPE; : typedef VTYPE Vector[3]; : //////////////////////////////////////////////////////////////////////// : //////// : // MakeUnitVector : // : // Reduces a normal vector specified as a set of three coordinates, : // to a unit normal vector of length one. : // : bool MakeUnitVector(Vector v) : { : VTYPE length; : // Calculate the length of the vector : length = (VTYPE)sqrt((v[0]*v[0]) + (v[1]*v[1]) + (v[2]*v[2])); : // if length is zero, bail : if(length == 0) : return false; : // Divide each element by the length to get a unit vector. : v[0] /= length; : v[1] /= length; : v[2] /= length; : return true; : }// MakeUnitVector A few quick thoughts: 1. Consider whether you really need double precision. You might try two runs of your computation, one with double precision, the other with single precision, and compare the results. 2. Square roots take a lot of time. Can you work with the squared values, and avoid taking square roots? 3. Consider the big picture: Why are you doing this step? Can you eliminate it, or integrate it better with what you're trying to do overall, so as to make the whole thing simpler and faster? 4. If you're stuck with doing the square roots, you might surf the internet for faster algorithms. -- Wetboy From owner-molmodel@hgmp.mrc.ac.uk Tue Nov 9 00:46:43 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id AD21017A60; Tue, 9 Nov 1999 00:46:42 +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 AAA08325 for ; Tue, 9 Nov 1999 00:46:37 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id AAA20114 for molmodel-list@hgmp.mrc.ac.uk; Tue, 9 Nov 1999 00:46:36 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "Eric Petroelje" X-Newsgroups: alt.games.programming,bionet.molec-model,comp.lang.c,comp.lang.c++ Subject: Re: How can I optimize vector normalization in a Molecular Modeling program? Date: 8 Nov 1999 21:58:20 GMT Lines: 79 Message-ID: <807h1s$icq$0@207.51.148.72> References: <807bh2$h4k$1@nnrp1.deja.com> X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk You could try making it inline... that might help a little. wrote in message news:807bh2$h4k$1@nnrp1.deja.com... > Hi, I've been working on a molecular modeling program and have been > trying to improve its performance recently. I did some profiling and > found that the most time by far (41.4%) was spent in a function which > normalizes a 3-dimensional vector (profiling statistics are given at > the bottom). > > I am wondering if anyone has suggestions for optimizing that operation. > Thanks, > William Knight > willkn@montana.com > > The definition of the function is given below: > > typedef double VTYPE; > typedef VTYPE Vector[3]; > > > //////////////////////////////////////////////////////////////////////// > //////// > // MakeUnitVector > // > // Reduces a normal vector specified as a set of three coordinates, > // to a unit normal vector of length one. > // > bool MakeUnitVector(Vector v) > { > VTYPE length; > > // Calculate the length of the vector > length = (VTYPE)sqrt((v[0]*v[0]) + (v[1]*v[1]) + (v[2]*v[2])); > > // if length is zero, bail > if(length == 0) > return false; > > // Divide each element by the length to get a unit vector. > v[0] /= length; > v[1] /= length; > v[2] /= length; > > return true; > }// MakeUnitVector > > file://***************** Profiling Details ************// > > Func Func+Child Hit > Time % Time % Count Function > --------------------------------------------------------- > 15493.876 41.4 15493.876 41.4 9971880 MakeUnitVector(double * > const) (vector.obj) > 5951.749 15.9 6789.747 18.1 627030 > CForceField::CalcVanderwaalsInteraction(void) (cforcefield.obj) > 2185.047 5.8 18425.737 49.2 84010 > CForceField::CalcPotentialsAndForces(class CFFPairList *,class > CEEPairList *,class CEOPairList *) (cforcefield.obj) > 1976.562 5.3 13039.435 34.8 3752280 > CForceField::CalcEEInteraction(class CElectron *,class CElectron *) > (cforcefield.obj) > 1778.265 4.7 1778.265 4.7 4656515 VectorMagnitude(double * > const) (vector.obj) > 1668.910 4.5 1668.910 4.5 8884682 MultiplyVector(double * > const,double) (vector.obj) > 1270.428 3.4 1270.428 3.4 13438760 SubtractVector(double * > const,double * const) (vector.obj) > 1195.278 3.2 1195.278 3.2 21288242 AddVector(double * > const,double * const) (vector.obj) > 1145.663 3.1 1238.959 3.3 64 CStatus::Print(char *) > (cstatus.obj) > > > > Sent via Deja.com http://www.deja.com/ > Before you buy. From owner-molmodel@hgmp.mrc.ac.uk Tue Nov 9 00:58:39 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id ED76C17A60; Tue, 9 Nov 1999 00:58:38 +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 AAA08804 for ; Tue, 9 Nov 1999 00:58:36 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id AAA20251 for molmodel-list@hgmp.mrc.ac.uk; Tue, 9 Nov 1999 00:58:35 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: willkn@montana.com X-Newsgroups: alt.games.programming,bionet.molec-model,comp.lang.c,comp.lang.c++ Subject: How can I optimize vector normalization in a Molecular Modeling program? Date: Mon, 08 Nov 1999 20:24:07 GMT Organization: Deja.com - Before you buy. Lines: 73 Message-ID: <807bh2$h4k$1@nnrp1.deja.com> X-Article-Creation-Date: Mon Nov 08 20:24:07 1999 GMT X-Http-User-Agent: Mozilla/4.05 [en] (Win95; I ;Nav) X-Http-Proxy: 1.0 x30.deja.com:80 (Squid/1.1.22) for client 199.2.139.183 X-MyDeja-Info: XMYDJUIDwillkn To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk Hi, I've been working on a molecular modeling program and have been trying to improve its performance recently. I did some profiling and found that the most time by far (41.4%) was spent in a function which normalizes a 3-dimensional vector (profiling statistics are given at the bottom). I am wondering if anyone has suggestions for optimizing that operation. Thanks, William Knight willkn@montana.com The definition of the function is given below: typedef double VTYPE; typedef VTYPE Vector[3]; //////////////////////////////////////////////////////////////////////// //////// // MakeUnitVector // // Reduces a normal vector specified as a set of three coordinates, // to a unit normal vector of length one. // bool MakeUnitVector(Vector v) { VTYPE length; // Calculate the length of the vector length = (VTYPE)sqrt((v[0]*v[0]) + (v[1]*v[1]) + (v[2]*v[2])); // if length is zero, bail if(length == 0) return false; // Divide each element by the length to get a unit vector. v[0] /= length; v[1] /= length; v[2] /= length; return true; }// MakeUnitVector //***************** Profiling Details ************// Func Func+Child Hit Time % Time % Count Function --------------------------------------------------------- 15493.876 41.4 15493.876 41.4 9971880 MakeUnitVector(double * const) (vector.obj) 5951.749 15.9 6789.747 18.1 627030 CForceField::CalcVanderwaalsInteraction(void) (cforcefield.obj) 2185.047 5.8 18425.737 49.2 84010 CForceField::CalcPotentialsAndForces(class CFFPairList *,class CEEPairList *,class CEOPairList *) (cforcefield.obj) 1976.562 5.3 13039.435 34.8 3752280 CForceField::CalcEEInteraction(class CElectron *,class CElectron *) (cforcefield.obj) 1778.265 4.7 1778.265 4.7 4656515 VectorMagnitude(double * const) (vector.obj) 1668.910 4.5 1668.910 4.5 8884682 MultiplyVector(double * const,double) (vector.obj) 1270.428 3.4 1270.428 3.4 13438760 SubtractVector(double * const,double * const) (vector.obj) 1195.278 3.2 1195.278 3.2 21288242 AddVector(double * const,double * const) (vector.obj) 1145.663 3.1 1238.959 3.3 64 CStatus::Print(char *) (cstatus.obj) Sent via Deja.com http://www.deja.com/ Before you buy. From owner-molmodel@hgmp.mrc.ac.uk Tue Nov 9 02:45:41 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 88EEC17A60; Tue, 9 Nov 1999 02:45:40 +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 CAA11347 for ; Tue, 9 Nov 1999 02:45:38 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id CAA21517 for molmodel-list@hgmp.mrc.ac.uk; Tue, 9 Nov 1999 02:45:37 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "Carsten Hansen" X-Newsgroups: alt.games.programming,bionet.molec-model,comp.lang.c,comp.lang.c++ Subject: Re: How can I optimize vector normalization in a Molecular Modeling program? Date: Mon, 08 Nov 1999 13:11:50 -0800 Organization: AT&T WorldNet Services Message-ID: <807eaf$2f5$1@bgtnsc01.worldnet.att.net> References: <807bh2$h4k$1@nnrp1.deja.com> Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Trace: bgtnsc01.worldnet.att.net 942095503 2533 12.72.56.197 (8 Nov 1999 21:11:43 GMT) X-Complaints-To: abuse@worldnet.att.net X-Newsreader: Microsoft Outlook Express Macintosh Edition - 4.5 (0410) Lines: 94 To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk One thing you could try is to multiply by the reciprocal VTYPE rec; rec = 1.0 / length; v[0] *= rec; v[1] *= rec; v[2] *= rec; I would be interested in knowing what difference that makes. Carsten Hansen ---------- In article <807bh2$h4k$1@nnrp1.deja.com>, willkn@montana.com wrote: > Hi, I've been working on a molecular modeling program and have been > trying to improve its performance recently. I did some profiling and > found that the most time by far (41.4%) was spent in a function which > normalizes a 3-dimensional vector (profiling statistics are given at > the bottom). > > I am wondering if anyone has suggestions for optimizing that operation. > Thanks, > William Knight > willkn@montana.com > > The definition of the function is given below: > > typedef double VTYPE; > typedef VTYPE Vector[3]; > > > //////////////////////////////////////////////////////////////////////// > //////// > // MakeUnitVector > // > // Reduces a normal vector specified as a set of three coordinates, > // to a unit normal vector of length one. > // > bool MakeUnitVector(Vector v) > { > VTYPE length; > > // Calculate the length of the vector > length = (VTYPE)sqrt((v[0]*v[0]) + (v[1]*v[1]) + (v[2]*v[2])); > > // if length is zero, bail > if(length == 0) > return false; > > // Divide each element by the length to get a unit vector. > v[0] /= length; > v[1] /= length; > v[2] /= length; > > return true; > }// MakeUnitVector > > //***************** Profiling Details ************// > > Func Func+Child Hit > Time % Time % Count Function > --------------------------------------------------------- > 15493.876 41.4 15493.876 41.4 9971880 MakeUnitVector(double * > const) (vector.obj) > 5951.749 15.9 6789.747 18.1 627030 > CForceField::CalcVanderwaalsInteraction(void) (cforcefield.obj) > 2185.047 5.8 18425.737 49.2 84010 > CForceField::CalcPotentialsAndForces(class CFFPairList *,class > CEEPairList *,class CEOPairList *) (cforcefield.obj) > 1976.562 5.3 13039.435 34.8 3752280 > CForceField::CalcEEInteraction(class CElectron *,class CElectron *) > (cforcefield.obj) > 1778.265 4.7 1778.265 4.7 4656515 VectorMagnitude(double * > const) (vector.obj) > 1668.910 4.5 1668.910 4.5 8884682 MultiplyVector(double * > const,double) (vector.obj) > 1270.428 3.4 1270.428 3.4 13438760 SubtractVector(double * > const,double * const) (vector.obj) > 1195.278 3.2 1195.278 3.2 21288242 AddVector(double * > const,double * const) (vector.obj) > 1145.663 3.1 1238.959 3.3 64 CStatus::Print(char *) > (cstatus.obj) > > > > Sent via Deja.com http://www.deja.com/ > Before you buy. From owner-molmodel@hgmp.mrc.ac.uk Tue Nov 9 05:53:44 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 2B76217A43; Tue, 9 Nov 1999 05:53:44 +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 FAA22362 for ; Tue, 9 Nov 1999 05:53:42 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id FAA23679 for molmodel-list@hgmp.mrc.ac.uk; Tue, 9 Nov 1999 05:53:40 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Andomar X-Newsgroups: alt.games.programming,bionet.molec-model,comp.lang.c,comp.lang.c++ Subject: Re: How can I optimize vector normalization in a Molecular Modeling program? Date: Tue, 09 Nov 1999 06:15:37 +0100 Organization: Gadgeteers Message-ID: <3827ADF9.2CE345AE@brotherrobot.org> References: <807bh2$h4k$1@nnrp1.deja.com> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.51 [en] (X11; I; Linux 2.2.6 i686) X-Accept-Language: en Lines: 16 To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk The optimizations I can think of: VTYPE length; length = v[0]*v[0] + v[1]*v[1] + v[2]*v[2]; if( length < 1.00001 && length > 0.99999 ) return true; // vector is already normal. length = sqrt( length ); v[0] /= length; v[1] /= length; v[2] /= lenght; return true; The check for already-normalness will speed up things if the program tries to normalize vectors more than once. (You can't just temp == 0.0 because floats aren't exact.) From owner-molmodel@hgmp.mrc.ac.uk Tue Nov 9 10:26:04 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 4B04717A61; Tue, 9 Nov 1999 10:26:03 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id KAA05352 for ; Tue, 9 Nov 1999 10:25:59 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id KAA27256 for molmodel-list@hgmp.mrc.ac.uk; Tue, 9 Nov 1999 10:25:58 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: saratoga@myremarq.com (Fine China Blue Porcelain) X-Newsgroups: alt.games.programming,bionet.molec-model,comp.lang.c,comp.lang.c++ Subject: Re: How can I optimize vector normalization in a Molecular Modeling program? Message-ID: References: <807bh2$h4k$1@nnrp1.deja.com> Organization: Collective Against Consenual Sanity X-Hello-Kitty: meow meow. X-Should: Prancing green elves on yellow daisy fields. X-Should-not: You're not allowed. X-Newsgroup-Bomb: Crossposted to heck and back. X-Ray-Specs: Off. Lines: 20 Date: Mon, 08 Nov 1999 17:32:50 -0800 X-Complaints-To: abuse@swbell.net X-Trace: typhoon01.swbell.net 942111312 207.214.214.54 (Mon, 08 Nov 1999 17:35:12 PST) To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk / Hi, I've been working on a molecular modeling program and have been / trying to improve its performance recently. I did some profiling and / found that the most time by far (41.4%) was spent in a function which / normalizes a 3-dimensional vector (profiling statistics are given at / the bottom). Normalisation is a real killer in graphics as well, like openGL. You might try newsgroups along those lines. There's an openGL compatiable library called Mesa with a source distribution. You might try dissecting that for ideas. Instead of computing sqrt(x), you should be able to do 1/sqrt(x) instead and multiply rather than divide, but you'll lose the lowest one or three bits of accuracy. -- CACS: Collective Against Consensual Sanity v0.123 Now a text site map! http://www.angelfire.com/ca3/cacs/ For a free CACS T-shirt send $42 shipping and handling. pretty? http://www.geocities.com/SoHo/Studios/5079/ From owner-molmodel@hgmp.mrc.ac.uk Tue Nov 9 15:49:35 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 7B22117A92; Tue, 9 Nov 1999 15:49:34 +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 PAA01795 for ; Tue, 9 Nov 1999 15:49:31 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id PAA02134 for molmodel-list@hgmp.mrc.ac.uk; Tue, 9 Nov 1999 15:49:29 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Paul Adams X-Newsgroups: bionet.molec-model Subject: Job Posting: Computational Crystallography Scientist Date: Mon, 08 Nov 1999 20:46:27 -0800 Organization: Lawrence Berkeley National Laboratory Lines: 56 Message-ID: <3827A723.4A76263@nospam.lbl.gov> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.51 [en]C-CCK-MCD LBNL V4.51 Build 1 (Win98; U) X-Accept-Language: en To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk Computational Crystallography Scientist Job PB/011300/CJO $3515-$7029/Mo. Computational Crystallography Initiative, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California. NOTE: This is a one-year term appointment with the possibility of renewal contingent upon continued funding. DUTIES: Essential -- Under the general direction of the principal investigator of the Computational Crystallography Initiative, assist with the development and implementation of algorithms for automatic protein structure determination based on multi-wavelength X-ray diffraction data. The overall objectives of the Computational Crystallography Initiative include the design of a high-level crystallographic computing language, implemented as an "interpreter" using common computer language creation tools. The resulting computational architecture will create a highly flexible and open environment in which to execute new algorithms for the automation of the multi-wavelength anomalous diffraction (MAD) method, model building, structure refinement, and eventually all major aspects of X-ray crystallography. The successful candidate will assist with research on all aspects of computational methods for protein structure determination: heavy atom location, MAD phasing, density modification, automatic electron density interpretation and structure refinement. Will collaborate in preparation of manuscripts for scientific publication and other reports and documentation as needed. It is expected that research results are presented at group meetings, seminars and scientific conferences. QUALIFICATIONS: Essential -- Ph.D. or equivalent experience in computational crystallography, biology, chemistry, physics, computer science, mathematics or engineering. Experience in development and implementation of scientific algorithms. Experience with at least two programming languages from the following list: C/C++, Java, Javascript, PERL, Python. Strong publication record in the area of computational methods development or a related field. Marginal -- Familiarity with or experience developing research proposals in the area of computational crystallography. POSTING DATE: October 21, 1999. CLOSING DATE: Open until filled. Further details about the position can be obtained from Paul Adams (princical investigator) by email to PDAdams@lbl.gov Please submit one copy of your resume via email (our preferred method) to: employment@lbl.gov (no attachments, please). Reference job number PB/011300 in your cover letter. Or mail to: Lawrence Berkeley National Laboratory, One Cyclotron Road, MS 937-0600, Berkeley, CA 94720. Or FAX: 510-486-5870. Visit the Berkeley Lab Web site at: http://www.lbl.gov/CJO. Berkeley Lab is an AA/EEO employer. From owner-molmodel@hgmp.mrc.ac.uk Tue Nov 9 17:25:29 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 2B74317B16; Tue, 9 Nov 1999 17:25:28 +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 RAA09877 for ; Tue, 9 Nov 1999 17:25:26 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id RAA03350 for molmodel-list@hgmp.mrc.ac.uk; Tue, 9 Nov 1999 17:25:24 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "Semler" X-Newsgroups: alt.games.programming,bionet.molec-model,comp.lang.c,comp.lang.c++ References: <807bh2$h4k$1@nnrp1.deja.com> Subject: Re: How can I optimize vector normalization in a Molecular Modeling program? Lines: 82 X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Message-ID: Date: Tue, 9 Nov 1999 18:19:49 +0100 X-Trace: news.euroconnect.net 942190156 212.130.48.106 (Wed, 10 Nov 1999 00:29:16 CET) Organization: Euroconnect To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk The MS Visual C++ version of sqrt is quite slow. Converting you routine to assembly would speed this up. Also all comments about using mult instead of divide is correct. fdiv takes about 20 clocks to complete while fmul takes 1 clock. >Hi, I've been working on a molecular modeling program and have been >trying to improve its performance recently. I did some profiling and >found that the most time by far (41.4%) was spent in a function which >normalizes a 3-dimensional vector (profiling statistics are given at >the bottom). > >I am wondering if anyone has suggestions for optimizing that operation. >Thanks, >William Knight >willkn@montana.com > >The definition of the function is given below: > >typedef double VTYPE; >typedef VTYPE Vector[3]; > > >//////////////////////////////////////////////////////////////////////// >//////// >// MakeUnitVector >// >// Reduces a normal vector specified as a set of three coordinates, >// to a unit normal vector of length one. >// >bool MakeUnitVector(Vector v) > { > VTYPE length; > > // Calculate the length of the vector > length = (VTYPE)sqrt((v[0]*v[0]) + (v[1]*v[1]) + (v[2]*v[2])); > > // if length is zero, bail > if(length == 0) > return false; > > // Divide each element by the length to get a unit vector. > v[0] /= length; > v[1] /= length; > v[2] /= length; > > return true; > }// MakeUnitVector > >//***************** Profiling Details ************// > > Func Func+Child Hit > Time % Time % Count Function >--------------------------------------------------------- > 15493.876 41.4 15493.876 41.4 9971880 MakeUnitVector(double * >const) (vector.obj) > 5951.749 15.9 6789.747 18.1 627030 >CForceField::CalcVanderwaalsInteraction(void) (cforcefield.obj) > 2185.047 5.8 18425.737 49.2 84010 >CForceField::CalcPotentialsAndForces(class CFFPairList *,class >CEEPairList *,class CEOPairList *) (cforcefield.obj) > 1976.562 5.3 13039.435 34.8 3752280 >CForceField::CalcEEInteraction(class CElectron *,class CElectron *) >(cforcefield.obj) > 1778.265 4.7 1778.265 4.7 4656515 VectorMagnitude(double * >const) (vector.obj) > 1668.910 4.5 1668.910 4.5 8884682 MultiplyVector(double * >const,double) (vector.obj) > 1270.428 3.4 1270.428 3.4 13438760 SubtractVector(double * >const,double * const) (vector.obj) > 1195.278 3.2 1195.278 3.2 21288242 AddVector(double * >const,double * const) (vector.obj) > 1145.663 3.1 1238.959 3.3 64 CStatus::Print(char *) >(cstatus.obj) > > > >Sent via Deja.com http://www.deja.com/ >Before you buy. From owner-molmodel@hgmp.mrc.ac.uk Tue Nov 9 19:35:29 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 8F83917A78; Tue, 9 Nov 1999 19:35:28 +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 TAA16488 for ; Tue, 9 Nov 1999 19:35:14 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id TAA04914 for molmodel-list@hgmp.mrc.ac.uk; Tue, 9 Nov 1999 19:35:12 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Xiaohui Xue X-Newsgroups: alt.games.programming,bionet.molec-model,comp.lang.c,comp.lang.c++ Subject: Re: How can I optimize vector normalization in a Molecular Modeling program? Date: Tue, 9 Nov 1999 14:29:22 -0500 Organization: The University of Western Ontario, London, Ont. Canada Lines: 19 Message-ID: References: <807bh2$h4k$1@nnrp1.deja.com> Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: panther.uwo.ca 942175764 29757 129.100.2.14 (9 Nov 1999 19:29:24 GMT) X-Complaints-To: abuse@julian.uwo.ca X-Sender: xue@panther.uwo.ca In-Reply-To: To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk Instead of l^2 norm, use l^1 norm in your normalization and relevant computation. For vector {x_n}, l^2 norm of {x_n} = sqrt( x(1)^2 + x(2)^2 + .... + x(n)^2 ), which involves multi and sqrt in the computation. l^1 norm of {x_n} = (abs(x(1)) + abs(x(2)) + ... + abs(x(n))), the computation of which is simplified. In addition, l^1 norm is equivalent to l^2 norm in a strong sense. Please let me know if it helps. Xiaohui From owner-molmodel@hgmp.mrc.ac.uk Tue Nov 9 20:25:22 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 60E4C17A78; Tue, 9 Nov 1999 20:25:22 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id UAA18615 for ; Tue, 9 Nov 1999 20:25:20 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id UAA05566 for molmodel-list@hgmp.mrc.ac.uk; Tue, 9 Nov 1999 20:25:18 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Paul Hughett X-Newsgroups: alt.games.programming,bionet.molec-model,comp.lang.c,comp.lang.c++ Subject: Re: How can I optimize vector normalization in a Molecular Modeling program? Date: 9 Nov 1999 20:17:10 GMT Organization: University of Pennsylvania Lines: 22 Message-ID: <809vg6$d8c$1@netnews.upenn.edu> References: <807bh2$h4k$1@nnrp1.deja.com> User-Agent: tin/pre-1.4-19990216 ("Styrofoam") (UNIX) (Linux/2.2.5-22 (i686)) To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk In comp.lang.c Xiaohui Xue wrote: : Instead of l^2 norm, use l^1 norm in your normalization and relevant : computation. : For vector {x_n}, : l^2 norm of {x_n} = sqrt( x(1)^2 + x(2)^2 + .... + x(n)^2 ), which : involves multi and sqrt in the computation. : l^1 norm of {x_n} = (abs(x(1)) + abs(x(2)) + ... + abs(x(n))), the : computation of which is simplified. : In addition, l^1 norm is equivalent to l^2 norm in a strong sense. The l^1 and l^2 norms are equivalent topologically but not geometrically. This application is probably geometrical and _requires_ the l^2 norm; though it's worth looking to see if some approximation to sqrt or the l^1 norm is good enough. Paul Hughett From owner-molmodel@hgmp.mrc.ac.uk Wed Nov 10 15:30:25 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 3ADDF17A43; Wed, 10 Nov 1999 15:30:25 +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 PAA22777 for ; Wed, 10 Nov 1999 15:30:23 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id PAA27511 for molmodel-list@hgmp.mrc.ac.uk; Wed, 10 Nov 1999 15:30:22 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Per Kaellblad X-Newsgroups: bionet.molec-model Subject: NMR + diffraction in PDB Date: Wed, 10 Nov 1999 15:30:19 +0000 Organization: University of Cambridge, England Lines: 22 Message-ID: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk Hi, I am looking for proteins (PDB entries) that have been determined structurally using both NMR and diffraction methods. The proteins should ideally be the same but a high sequence identity will do. The current 3DBbrowser doesn't enable this kind of search and it seems somewhat elaborate to get around it. If anyone know of a published list of such proteins, or an easy way of getting such a list, I would be very grateful to hear about it. Thanks Per Kallblad _________________________________________________________________ Drug Design Group Email: pk215@cam.ac.uk Department of Pharmacology Phone: +44 1223 331982 University of Cambridge Fax +44 1223 331740 Tennis Court Road CAMBRIDGE CB2 1QJ UK _________________________________________________________________ From owner-molmodel@hgmp.mrc.ac.uk Wed Nov 10 15:44:20 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id F13FD17A43; Wed, 10 Nov 1999 15:44:19 +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 PAA24242 for ; Wed, 10 Nov 1999 15:44:16 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id PAA27757 for molmodel-list@hgmp.mrc.ac.uk; Wed, 10 Nov 1999 15:44:15 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: mh270@mole.bio.cam.ac.uk (Miriam Hirshberg) X-Newsgroups: bionet.molec-model Subject: Re: NMR + diffraction in PDB Date: 10 Nov 1999 15:44:13 -0000 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 49 Message-ID: References: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: niobium.hgmp.mrc.ac.uk 942248654 27755 193.62.192.80 (10 Nov 1999 15:44:14 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk X-Received: from mole.bio.cam.ac.uk (exim@mole.bio.cam.ac.uk [131.111.36.9]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id PAA24224 for ; Wed, 10 Nov 1999 15:44:10 GMT X-Received: from mh270 (helo=localhost) by mole.bio.cam.ac.uk with local-smtp (Exim 1.92 #3) id 11lZum-00E7Tg-00; Wed, 10 Nov 1999 15:44:04 +0000 X-To: Per Kaellblad X-cc: molmodel@hgmp.mrc.ac.uk X-In-Reply-To: To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk Per Kallblad 3 proteins you can check are: Calmodulin, cdc42 and ras, all three were determined by both NMR and Xray crystallography. Hope this helps Miri ====================================================================== Miriam (Miri) Hirshberg e-mail: m.hirshberg@mole.bio.cam.ac.uk Department of Biochemistry Tel : (+44) 01223 766018 University of Cambridge Tel : (+44) 01223 333600 (switch board) 80 Tennis Court Road Fax : (+44) 01223 766002 Old Addenbrooke's Site Cambridge CB2 1GA, UK ===================================================================== On Wed, 10 Nov 1999, Per Kaellblad wrote: > Hi, > > I am looking for proteins (PDB entries) that have been determined > structurally using both NMR and diffraction methods. The proteins > should ideally be the same but a high sequence identity will do. > > The current 3DBbrowser doesn't enable this kind of search and it seems > somewhat elaborate to get around it. If anyone know of a published list of > such proteins, or an easy way of getting such a list, I would be very > grateful to hear about it. > > Thanks > Per Kallblad > _________________________________________________________________ > > Drug Design Group Email: pk215@cam.ac.uk > Department of Pharmacology Phone: +44 1223 331982 > University of Cambridge Fax +44 1223 331740 > Tennis Court Road CAMBRIDGE CB2 1QJ UK > _________________________________________________________________ > > > --- From owner-molmodel@hgmp.mrc.ac.uk Wed Nov 10 23:24:50 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 2C1DF17AF0; Wed, 10 Nov 1999 23:24:49 +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 XAA23437 for ; Wed, 10 Nov 1999 23:24:47 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id XAA11719 for molmodel-list@hgmp.mrc.ac.uk; Wed, 10 Nov 1999 23:24:46 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f Message-ID: <3829FDC7.626D04B6@scires.com> Date: Wed, 10 Nov 1999 18:20:39 -0500 From: Mike Percy X-Mailer: Mozilla 4.6 [en] (X11; I; Linux 2.2.5-15 i686) X-Accept-Language: en MIME-Version: 1.0 X-Newsgroups: alt.games.programming,bionet.molec-model,comp.lang.c,comp.lang.c++ Subject: Re: How can I optimize vector normalization in a Molecular Modeling program? References: <807bh2$h4k$1@nnrp1.deja.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: 10 Nov 1999 18:13:55 -0500, 209.54.236.186 Lines: 41 To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk Xiaohui Xue wrote: > > Instead of l^2 norm, use l^1 norm in your normalization and relevant > computation. > > For vector {x_n}, > > l^2 norm of {x_n} = sqrt( x(1)^2 + x(2)^2 + .... + x(n)^2 ), which > involves multi and sqrt in the computation. > > l^1 norm of {x_n} = (abs(x(1)) + abs(x(2)) + ... + abs(x(n))), the > computation of which is simplified. > > In addition, l^1 norm is equivalent to l^2 norm in a strong sense. > > Please let me know if it helps. > > Xiaohui Use a different sqrt() routine. The one provided in most C libraries is coded similarly to one in Plauger's Standard C Library book. Instead, use a 1/sqrt() function, which is often much quicker to compute and often has hardware assists. Plus, the result is often in the form you want anyway, that is, you usually are doing {x_n} / norm. By using a 1/sqrt() function, you can write {x_n} * one_over_norm. Avoiding the division can be a big benefit (you also avoid division in the 1/sqrt() computation). The "normal" (pardon the pun) way of computing sqrt() is a Newton's method with 3 iterations, but each iteration requires division. Newton's method for computing 1/sqrt(x) needs more iterations (5 seems to work well for me) and a good initial estimate (I have hardware assist in PowerPC frsqrte instruction!), but uses only addition and multiplication so comes out way ahead. The standard sqrt that came with my compiler runs in about 1500ns; my sqrt_r() routine runs in about 600ns, although part of that speedup might be that I do not check for NaN/Inf (do check for 0). Just in case you might be doing it, do not use pow() to square the numbers... -- "I don't know about your brain, but mine is really...bossy." Mike Percy, Senior Computer Scientist, Scientific Research Corp. From owner-molmodel@hgmp.mrc.ac.uk Thu Nov 11 19:25:21 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 9B2B217B46; Thu, 11 Nov 1999 19:25:18 +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 TAA01099 for ; Thu, 11 Nov 1999 19:25:14 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id TAA26241 for molmodel-list@hgmp.mrc.ac.uk; Thu, 11 Nov 1999 19:25:12 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "Marcel Dinger" X-Newsgroups: bionet.molec-model Subject: Genamics SoftwareSeek Date: Fri, 12 Nov 1999 08:15:14 +1300 Organization: The Internet Group (Hamilton) Lines: 19 Message-ID: <942347854.683631@ham.ihug.co.nz> X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Cache-Post-Path: ham.ihug.co.nz!unknown@p17-max4.ham.ihug.co.nz X-Cache: nntpcache 2.3.3 (see http://www.nntpcache.org/) To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk GENAMICS SOFTWARESEEK The Largest Science Software Directory on Earth. http://genamics.com/software/ Genamics SoftwareSeek now indexes well over 1000 freely-distributable and commercial titles. Classifications include DNA sequence analysis, protein structure analysis, RNA structure prediction, molecular modeling, image analysis, and sequence alignment. All major platforms are supported, including, Windows, Macintosh, Unix, and Linux. Over 150 online tools and resources that run directly through your internet browser are also listed. New software can be submitted on-line through our web-site. Marcel Dinger, Genamics. http://genamics.com/software/ From owner-molmodel@hgmp.mrc.ac.uk Thu Nov 11 20:42:55 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 4B00117A4E; Thu, 11 Nov 1999 20:42:55 +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 UAA04792 for ; Thu, 11 Nov 1999 20:42:53 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id UAA27259 for molmodel-list@hgmp.mrc.ac.uk; Thu, 11 Nov 1999 20:42:52 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Jim Phillips X-Newsgroups: bionet.molec-model Subject: ANNOUNCE: NAMD 2.1 Release Date: Thu, 11 Nov 1999 14:39:28 -0600 Organization: University of Illinois Lines: 35 Message-ID: <382B2980.311C6B0E@ks.uiuc.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.7 [en] (X11; I; SunOS 5.7 sun4u) X-Accept-Language: en To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk +--------------------------------------------------------------------+ | | | NAMD 2.1 Release Announcement | | | +--------------------------------------------------------------------+ November 11, 1999 The Theoretical Biophysics Group at the University of Illinois is proud to announce the public release of a new version of NAMD, a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code. NAMD development is supported by the NIH National Center for Research Resources. NAMD 2.1 is more stable than NAMD 2.0 and adds several new features: - Tcl scripting language interface and config file parsing. - Mollified impulse multiple timestepping method. - Faster particle mesh Ewald implementation. - Periodic boundaries for non-orthogonal cells. - New interactive molecular dynamics interface to VMD. NAMD is available from http://www.ks.uiuc.edu/Research/namd/. The Theoretical Biophysics group encourages NAMD users to be closely involved in the development process through reporting bugs, contributing fixes, periodical surveys and via other means. Questions or comments may be directed to namd@ks.uiuc.edu. We are eager to hear from you, and thank you for using our software! From owner-molmodel@hgmp.mrc.ac.uk Fri Nov 12 14:34:20 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id C0F6517A5B; Fri, 12 Nov 1999 14:34:19 +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 OAA28644 for ; Fri, 12 Nov 1999 14:34:16 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id OAA18638 for molmodel-list@hgmp.mrc.ac.uk; Fri, 12 Nov 1999 14:34:14 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Christian Lowe X-Newsgroups: bionet.molec-model Subject: Re: NMR + diffraction in PDB Date: Fri, 12 Nov 1999 15:23:07 +0100 Organization: University of Leiden The Netherlands Lines: 34 Message-ID: <382C22C9.5A8FDB09@chem.leidenuniv.nl> References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: highway.leidenuniv.nl 942416649 3395 132.229.169.235 (12 Nov 1999 14:24:09 GMT) X-Complaints-To: usenet@highway.leidenuniv.nl X-Mailer: Mozilla 4.07C-SGI [en] (X11; I; IRIX 6.5 IP32) To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk Per Kaellblad wrote: > Hi, > > I am looking for proteins (PDB entries) that have been determined > structurally using both NMR and diffraction methods. The proteins > should ideally be the same but a high sequence identity will do. > > The current 3DBbrowser doesn't enable this kind of search and it seems > somewhat elaborate to get around it. If anyone know of a published list of > such proteins, or an easy way of getting such a list, I would be very > grateful to hear about it. > > Thanks > Per Kallblad > _________________________________________________________________ > > Drug Design Group Email: pk215@cam.ac.uk > Department of Pharmacology Phone: +44 1223 331982 > University of Cambridge Fax +44 1223 331740 > Tennis Court Road CAMBRIDGE CB2 1QJ UK > _________________________________________________________________ Hi Per Kaellblad, another protien that has been charachterised by NMR and x ray crystalography are the cytochrome c 550 of thiobacillus denitrificans(also known as Parracoccus denitrificans) (characterised by xray crystalography) and cytochrome c550 of paracoccus versutus (characterised by nmr). although they are of diferent origins, the share around 88% sequence homology. i hope this is of some use to you chris From owner-molmodel@hgmp.mrc.ac.uk Fri Nov 12 21:45:33 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 1AB2E17B68; Fri, 12 Nov 1999 21:45:31 +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 VAA20580; Fri, 12 Nov 1999 21:45:22 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id VAA02937; Fri, 12 Nov 1999 21:45:20 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Kirby Vandivort X-Newsgroups: bionet.molec-model,bionet.software,bionet.software.x-plor,comp.sys.sgi.graphics,sci.chem Subject: Interactive Molecular Dynamics at SuperComputing 99 Date: 12 Nov 1999 13:37:19 -0800 Organization: University of Illinois at Urbana-Champaign Lines: 33 Distribution: world Message-ID: <382B6F86.DC5D4096@ks.uiuc.edu> To: bio-software@hgmp.mrc.ac.uk, molmodel@hgmp.mrc.ac.uk, x-plor@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk If you are one of the people that will be at Super Computing 99 in Portland, OR next week, we urge you to stop by the National Coordination Office booth and take a look at the interactive molecular dynamics that we are doing using our Visual Molecular Dynamics software program, VMD, our molecular dynamics simulation engine, NAMD, and BioCoRE, our collaboratory for structural biology. Our demonstration will consist of the following: - A component of BioCoRE will be accessed via the web to start a molecular dynamics NAMD simulation running on the computers in Illinois. - VMD will then connect to this component and "attach" to one of these running simulations. - Next, the haptic device will be used to interactively "steer" the simulation. We plan to try and let attendees "steer the sodium ion!" The National Coordination Booth is booth number R102 and is located just south of the NCSA booth. We look forward to seeing you there! Kirby Vandivort Theoretical Biophysics, UIUC VMD => http://www.ks.uiuc.edu/Research/vmd NAMD => http://www.ks.uiuc.edu/Research/namd BioCoRE => http://www.ks.uiuc.edu/Research/collaboratory From owner-molmodel@hgmp.mrc.ac.uk Mon Nov 15 20:41:54 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id A686217A70; Mon, 15 Nov 1999 20:41:53 +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 UAA06362 for ; Mon, 15 Nov 1999 20:41:51 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id UAA09865 for molmodel-list@hgmp.mrc.ac.uk; Mon, 15 Nov 1999 20:41:51 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: wstzou@GATE.SINICA.EDU.TW (Wen-shyong Tzou) X-Newsgroups: bionet.molec-model Subject: free program for cluster analysis Date: 15 Nov 1999 12:24:51 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 26 Distribution: world Message-ID: To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk Dear netters: I need a program for doing "cluster analysis" and producing beautiful dendrogram (tree map). Is there any free programs for doing this task ? Any information will be appreciated. regards, Wen-Shyong Tzou | Wen-Shyong Tzou | /~~\ Postdoctoral Fellow | * / / Laboratory for Computer Modeling of Biomolecules / / \ Institute of Biomedical Sciences / / \ Academia Sinica, Nankang, Taipei, Taiwan / * / | / / | Address: PO Box 1-99, Nankang, Taipei, Taiwan / | / <*> | | e-mail: wstzou@sinica.edu.tw \ / Voice: (886)-2-27899033 \ / Fax: (886)-2-27887641 | / |~| From owner-molmodel@hgmp.mrc.ac.uk Tue Nov 16 03:41:04 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 90F9517A58; Tue, 16 Nov 1999 03:41:03 +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 DAA26125 for ; Tue, 16 Nov 1999 03:41:01 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id DAA23412 for molmodel-list@hgmp.mrc.ac.uk; Tue, 16 Nov 1999 03:41:00 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: suwuloo73@MANBOND.COM.HK (mosipe) X-Newsgroups: bionet.molec-model Subject: ..Internet..stock..newsletter Date: 15 Nov 1999 19:38:09 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Distribution: world Message-ID: <199911151719YAA14141@lkwoip.racalrec.co.uk> To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk ...internet and small cap stock - newsletter.. We are currently offering at no charge an internet and small cap newsletter FREE for a limited time. This is a weekly newsletter that is short, to the point and will only take a couple of minutes to read. If you do not enjoy this newsletter you can unsubscribe at any time, no obligation. You have nothing to lose by subscribing, so give it a try ! ! ! To subscribe, email wishey34@bigfoot.com with the subject capnews To be removed, email wishey34@bigfoot.com with the subject delete thank you and I wish From owner-molmodel@hgmp.mrc.ac.uk Tue Nov 16 21:03:09 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 4B08817B30; Tue, 16 Nov 1999 21:03:09 +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 VAA09814 for ; Tue, 16 Nov 1999 21:03:07 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id VAA07432 for molmodel-list@hgmp.mrc.ac.uk; Tue, 16 Nov 1999 21:03:06 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Benjamin Stapley X-Newsgroups: bionet.molec-model Subject: database of loop structures in proteins Date: Tue, 16 Nov 1999 16:02:56 -0500 Organization: University of Kentucky Computing Services Lines: 3 Message-ID: <3831C680.C311209C@sophocles.gws.uky.edu> References: <199911151719YAA14141@lkwoip.racalrec.co.uk> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.07C-SGI [en] (X11; I; IRIX 6.5 IP32) To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk Does anyone know of a database of loop structures in proteins? Ben From owner-molmodel@hgmp.mrc.ac.uk Wed Nov 17 07:39:25 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 9322017A63; Wed, 17 Nov 1999 07:39:24 +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 HAA10391 for ; Wed, 17 Nov 1999 07:39:21 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id HAA23278 for molmodel-list@hgmp.mrc.ac.uk; Wed, 17 Nov 1999 07:39:20 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: aflaloc@BGUMAIL.BGU.AC.IL (claude aflalo) X-Newsgroups: bionet.molec-model Subject: Re: database of loop structures in proteins Date: 16 Nov 1999 23:24:28 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Distribution: world Message-ID: References: <3831C680.C311209C@sophocles.gws.uky.edu> To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk On Tue, 16 Nov 1999, Benjamin Stapley wrote: > Does anyone know of a database of loop structures in proteins? > Ben > Yes, lookup (in) the package Swiss PDBViewer at http://www.expasy.ch/spdbv/mainpage.htm Claude Aflalo ####################### Phones: Office 972-7-6472118 #### Dept. of Life Sciences Lab 972-7-6472119 Ben Gurion University of the Negev Fax 972-7-6472890 P.O.Box 653 email: aflaloc@bgumail.bgu.ac.il Beer Sheva 84105 Israel URL: http://www.bgu.ac.il/life/aflalo.html From owner-molmodel@hgmp.mrc.ac.uk Wed Nov 17 11:23:56 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 7A87317A63; Wed, 17 Nov 1999 11:23:55 +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 LAA24756 for ; Wed, 17 Nov 1999 11:23:49 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id LAA26142 for molmodel-list@hgmp.mrc.ac.uk; Wed, 17 Nov 1999 11:23:48 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: mmueller1675@my-deja.com X-Newsgroups: bionet.molec-model Subject: 2D-3D converter Date: Wed, 17 Nov 1999 11:11:04 GMT Organization: Deja.com - Before you buy. Lines: 13 Message-ID: <80u2g7$l29$1@nnrp1.deja.com> x-no-archive: yes X-Article-Creation-Date: Wed Nov 17 11:11:04 1999 GMT X-Http-User-Agent: Mozilla/4.7 [en] (Win98; I) X-Http-Proxy: 1.0 http-proxy.iuct.fhg.de:81 (Squid/2.2.STABLE3), 1.0 x35.deja.com:80 (Squid/1.1.22) for client unknown, 153.96.228.2 X-MyDeja-Info: XMYDJUIDmmueller1675 To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk Hi all, I'm looking for a program (MS-DOS/Windows) for converting 2D-chemical-structures (molfile) into 3D-structures. Free softwaer would be nice, however not neccessary. Thanks for any hints Martin Mueller Sent via Deja.com http://www.deja.com/ Before you buy. From owner-molmodel@hgmp.mrc.ac.uk Wed Nov 17 12:05:04 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 0849617A63; Wed, 17 Nov 1999 12:05:03 +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 MAA28100 for ; Wed, 17 Nov 1999 12:05:01 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id MAA26621 for molmodel-list@hgmp.mrc.ac.uk; Wed, 17 Nov 1999 12:05:00 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Paul@pdchem.demon.co.uk (Paul Davis) X-Newsgroups: bionet.molec-model Subject: Re: database of loop structures in proteins Date: Wed, 17 Nov 1999 11:57:47 GMT Organization: Myorganisation Message-ID: <942839867snz@pdchem.demon.co.uk> References: <199911151719YAA14141@lkwoip.racalrec.co.uk> <3831C680.C311209C@sophocles.gws.uky.edu> Reply-To: Paul@pdchem.demon.co.uk X-Trace: mail2news.demon.co.uk 942840142 mail2news:5253 mail2news mail2news.demon.co.uk X-Complaints-To: abuse@demon.net X-Mail2News-Path: news.demon.net!pdchem.demon.co.uk X-Newsreader: SNews 1.30+mods(jlw981005) Lines: 21 To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk On Tuesday, in article <3831C680.C311209C@sophocles.gws.uky.edu> ben@sophocles.gws.uky.edu "Benjamin Stapley" wrote: > Does anyone know of a database of loop structures in proteins? > Ben > > Donate, L. E., Rufino, S. D., Canard, L. H. J. & Blundell, T. L. (1996). Conformational analysis and clustering of short and medium size loops connecting regular secondary structures. A database for modelling and prediction. Protein Sci. 5,2600. http://www-cryst.bioc.cam.ac.uk/~sloop/ -Paul -- -------------------------------------------------------------------- Paul Davis paul@pdchem.demon.co.uk From owner-molmodel@hgmp.mrc.ac.uk Wed Nov 17 13:55:37 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 33C0917AA8; Wed, 17 Nov 1999 13:55:36 +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 NAA10173 for ; Wed, 17 Nov 1999 13:55:33 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id NAA28033 for molmodel-list@hgmp.mrc.ac.uk; Wed, 17 Nov 1999 13:55:31 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: dfischer@indigo.cs.bgu.ac.il (Daniel Fischer) X-Newsgroups: bionet.molec-model Subject: cafasp2 Date: 17 Nov 1999 20:44:45 GMT Organization: Ben-Gurion University, Computer Sciense Dept. Lines: 116 Message-ID: <80v43t$ug6$1@avdat2.bgu.ac.il> X-Trace: avdat2.bgu.ac.il 942871485 31238 132.72.42.23 (17 Nov 1999 20:44:45 GMT) X-Complaints-To: usenet@avdat2.bgu.ac.il X-Newsreader: xrn 9.01 To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk ANNOUNCING CAFASP2 We announce the Second Critical Assessment of Fully Automated Structure Prediction Experiment (CAFASP2). The goal of CAFASP2 is to evaluate the performance of fully automatic structure prediction servers available to the community. In contrast to the normal CASP procedure, CAFASP2 will answer the question of how well servers do without any intervention of experts, i.e. how well ANY user can predict protein structure. As in CAFASP1, CAFASP2 assesses the performance of methods without the user intervention allowed in CASP submissions. This may aid users in choosing which programs they wish to use, and in evaluating the reliability of the programs when applied to their specific prediction targets. In addition, evaluation of fully automated methods is particularly important to assess their applicability at genomic scales. CAFASP2 will take place as an official section of CASP4, which will be held by mid-2000. We invite developers of automatic prediction servers to participate in CAFASP2. The rules, formats, assessment procedures and other details will be published later as soon as they are determined by the CAFASP2 committee in coordination with the CASP4 committee. Interested parties are invited to send an e-mail to dfischer@cs.bgu.ac.il so they will be included in the CAFASP2 mailing list. In what follows a preliminary set of rules for CAFASP2 is described. TERMINOLOGY. A "server" is the automated structure prediction server that participates in CAFASP. A server will have an identification name and its corresponding url. A "server's person" is the person in charge of the maintainance and function of a server. A "raw server output" is the output obtained by a server. A "server's submission" is the prediction that a server's person files to CAFASP using the raw server output. REGISTRATION TO CAFASP2. A server's person willing to include his/her server to CAFASP2 must register as a predictor to CASP4, and state that this registration corresponds to his/her server. The server's person will receive a participant's indentification. A server's person can also register as a regular CASP4 participant. Servers that run different methods should register each of the methods separately. SUBMISSION OF PREDICTIONS TO CAFASP2. By the expiry date of each target the server's person is responsible to submit the prediction to CASP4, using the regular CASP4 procedure. This submission must be identical in content to the output produced by his/her server, but may vary in format. Because it may be difficult to enforce that a server produces valid CASP4 formats, we allow a server's person to take the raw server output and transform it to valid CASP4 format, as long as it is identical in content. To verify that the content is the same, the CAFASP committee will submit each target to each of the registered servers by the time each target is released. The raw server's output will be made available to all in the CAFASP2 web-site. The CAFASP committee will verify that the raw server output corresponds exactly (in content) to the submission filed by the server's person. If differences are found, the submission will be disquailfied. CATEGORIES FOR CAFASP2. Any automated server can participate in CAFASP2, including Homology Modeling, Threading, Ab-Initio and Secondary Structure Prediction. ASSESSMENT OF PREDICTIONS. Predictions submitted to CAFASP will undergo the exact same evaluation procedure as the normal CASP submission. The CAFASP committe may decide to apply additional evaluation procedures. The latter will include only automatic evaluators and the measures used be them will be made public as soon as possible. More details about the additional cafasp evaluation will be announced later on. A comparison of the performance of CAFASP2 versus the regular CASP4 submission will also be carried out. CAFASP COMMITTEES. Currently the people involved in the CAFASP committee are Leszek Rychlewski, Arne Elofsson, Burkhard Rost and Daniel Fischer. Sub-committees for homology modeling, threading, ab-initio and secondary structure servers will be assigned. The Sub-committees will be coordinated by the CAFASP committee. The Sub-committees will be in charge of the compilation of the servers' raw output, the additional evaluation (if required) and the comparative analysis of the results. As of today these are the sub-committees and people assigned to them: Threading sub-committee: Leszek Rychlewski, Arne Elofsson and Daniel Fischer. Secondary Structure sub-committee: Burkhard Rost. We invite interested parties to be involved in the variuos sub-committees. CAFASP2 url: http://www.cs.bgu.ac.il/~dfischer/CAFASP2 ------------------ Dr. Daniel Fischer Dept. of Math and Computer Science Ben Gurion University, Beer-Sheva 84015, Israel e-mail: dfischer@cs.bgu.ac.il Fax +972- 7-6477648 or 6472910 http://www.cs.bgu.ac.il/~dfischer From owner-molmodel@hgmp.mrc.ac.uk Wed Nov 17 15:43:49 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 2FC9917AA8; Wed, 17 Nov 1999 15:43:48 +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 PAA23811 for ; Wed, 17 Nov 1999 15:43:47 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id PAA29343 for molmodel-list@hgmp.mrc.ac.uk; Wed, 17 Nov 1999 15:43:46 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Paul@pdchem.demon.co.uk (Paul Davis) X-Newsgroups: bionet.molec-model Subject: Re: database of loop structures in proteins Date: Wed, 17 Nov 1999 15:38:32 GMT Organization: Myorganisation Message-ID: <942853112snz@pdchem.demon.co.uk> References: <199911151719YAA14141@lkwoip.racalrec.co.uk> <3831C680.C311209C@sophocles.gws.uky.edu> Reply-To: Paul@pdchem.demon.co.uk X-Trace: mail2news.demon.co.uk 942853296 mail2news:7964 mail2news mail2news.demon.co.uk X-Complaints-To: abuse@demon.net X-Mail2News-Path: news.demon.net!pdchem.demon.co.uk X-Newsreader: SNews 1.30+mods(jlw981005) Lines: 36 To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk Here are two more web resources:- 1) Jerome Wojcik, Jean-Paul Mornon and Jacques Chomilier (1999); "New Efficient Statistical Sequence-dependent Structure Prediction of Short to Medium-sized Protein Loops Based on an Exhaustive Loop Classification." J. Mol. Biol. 289, 1469-1490 and the Loop Homology Modelling server:- http://www.lmcp.jussieu.fr/~wojcik/modele/loop.html 2) B. Oliva, P.A. Bates, E. Querol, F.X. Aviles, and M.J.E. Sternberg (1997); "An automated classification of the structure of protein loops." J. Mol. Biol. 266, 814-830 (1997) Database on http://www.bmm.icnet.uk/loop/ -Paul On Tuesday, in article <3831C680.C311209C@sophocles.gws.uky.edu> ben@sophocles.gws.uky.edu "Benjamin Stapley" wrote: > Does anyone know of a database of loop structures in proteins? > Ben > > -- -------------------------------------------------------------------- Paul Davis paul@pdchem.demon.co.uk From owner-molmodel@hgmp.mrc.ac.uk Thu Nov 18 00:45:48 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id EB50917A90; Thu, 18 Nov 1999 00:45:47 +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 AAA23875 for ; Thu, 18 Nov 1999 00:45:46 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id AAA14381 for molmodel-list@hgmp.mrc.ac.uk; Thu, 18 Nov 1999 00:45:45 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: radelle_locatelli@ena-east.ericsson.se X-Newsgroups: bionet.molec-model Subject: Re: How To Meet Beautiful Women Date: 17 Nov 1999 16:19:14 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Distribution: world Message-ID: <99111801025328600@web.ivv-aachen.de> Reply-To: radelle_locatelli@ena-east.ericsson.se To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk Thanks Dodo, I guess I needed that; whatever THAT is. I'll resist the temptation to respond in kind. I'm tied to the ball and chain anyway. Sounds like you've got me pegged though. And all this time I thought I was coverin me tracts. Give me a call, at home, sometime when you're feeling better. Return-Path: Received: from smtp.mx.gnn.com (smtp.mail.gnn.com [175.18.146.1]) by air-yb04.mail.gnn.com (v60.28) with ESMTP; Thu, 1 Nov 1999 16:35:07 -0400 WELCOME TO EDDIE FASKELLS PICKUP LIBLINE!! COMING TO A WEBSIGHT NEAR YOU! HOW TO MEET BEAUTIFUL WOMEN 1. HOW TO MAKE BEAUTIFUL WOMEN FROM ALL AROUND THE WORLD BECOME INTERESTED IN YOU FROM RIGHT HERE AT YOUR COMPUTER FOR FREE -- No need t From owner-molmodel@hgmp.mrc.ac.uk Thu Nov 18 04:11:46 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 26CE917B17; Thu, 18 Nov 1999 04:11:45 +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 EAA29303 for ; Thu, 18 Nov 1999 04:11:44 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id EAA16787 for molmodel-list@hgmp.mrc.ac.uk; Thu, 18 Nov 1999 04:11:43 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: spam@127.0.0.1 (Bernard Murray, PhD) X-Newsgroups: bionet.molec-model Subject: Re: 2D-3D converter Date: Wed, 17 Nov 1999 18:56:35 -0700 Organization: UCSF Lines: 26 Message-ID: References: <80u2g7$l29$1@nnrp1.deja.com> To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk In article <80u2g7$l29$1@nnrp1.deja.com>, mmueller1675@my-deja.com wrote: > Hi all, > I'm looking for a program (MS-DOS/Windows) ACK! > for converting > 2D-chemical-structures (molfile) into 3D-structures. Free softwaer would > be nice, however not neccessary. Learn how to use SMILES strings and then play with CORINA (http://www2.ccc.uni-erlangen.de/software/corina/index.html) I have used this for several structures and later optimisation with MOPAC suggested the results are pretty good. Kudos to the Gasteiger lab! Bernard -- Bernard P. Murray, PhD bpmurray at cgl . ucsf . edu Department of Cellular & Molecular Pharmacology, UCSF From owner-molmodel@hgmp.mrc.ac.uk Thu Nov 18 12:09:38 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 48C3B17B2B; Thu, 18 Nov 1999 12:09:38 +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 MAA27108 for ; Thu, 18 Nov 1999 12:09:32 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id MAA20719 for molmodel-list@hgmp.mrc.ac.uk; Thu, 18 Nov 1999 12:09:31 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: muozerue4@MAIL.C-LABS.COM.SG (kosleo) X-Newsgroups: bionet.molec-model Subject: --Spring Break-- Date: 18 Nov 1999 03:48:04 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Distribution: world Message-ID: <199911181225HAA14191@misoeir.net.pk> To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk 20745799169152663207460766 Plan your spring break trip now! If you would like to receive information and prices for trips to Cancun, Jamaica, Bahamas and Florida as well as a newsletter about spring break please reply to rgeree@bigfoot.com with the subject and body as "spring". To be deleted from this list, just email rgeree@bigfoot.com with the subject field "removed" Plan your spring break trip now!  From owner-molmodel@hgmp.mrc.ac.uk Thu Nov 18 14:08:27 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id E5AFD17B00; Thu, 18 Nov 1999 14:08:26 +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 OAA04430 for ; Thu, 18 Nov 1999 14:08:24 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id OAA22248 for molmodel-list@hgmp.mrc.ac.uk; Thu, 18 Nov 1999 14:08:23 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Yu Wai Chen X-Newsgroups: bionet.molec-model Subject: Re: NMR + diffraction in PDB Date: Thu, 18 Nov 1999 14:08:16 +0000 Organization: MRC Centre for Protein Engineering Lines: 14 Message-ID: <38340850.90F98B02@mrc-lmb.cam.ac.uk> References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.6C-SGI [en] (X11; I; IRIX64 6.4 IP30) X-Accept-Language: zh-TW, zh-CN, en To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk Also add these to the list: interleukin 8 (il8) the very first structure with both NMR and xtal structures solved; p53 tetramerization domain barnase bastar -- =================================================================== Yu Wai CHEN, Ph.D. .................. email:ywc@mrc-lmb.cam.ac.uk Centre for Protein Engineering, tel:+44-(0)1223-402148 MRC Centre, Hills Rd, Cambridge CB2 2QH, UK fax:+44-(0)1223-402140 WWW homepage: http://www.mrc-cpe.cam.ac.uk/~ywc From owner-molmodel@hgmp.mrc.ac.uk Thu Nov 18 22:54:17 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 3282817A5B; Thu, 18 Nov 1999 22:54:16 +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 WAA09573 for ; Thu, 18 Nov 1999 22:54:15 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id WAA07171 for molmodel-list@hgmp.mrc.ac.uk; Thu, 18 Nov 1999 22:54:14 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: John Stone X-Newsgroups: bionet.molec-model Subject: Announce: VMD 1.4 beta 3 Date: Thu, 18 Nov 1999 16:52:41 -0600 Organization: Theoretical Biophysics, Beckman Institute, UIUC Lines: 47 Message-ID: <38348339.9C08582B@ks.uiuc.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.7 [en] (X11; I; SunOS 5.7 sun4u) X-Accept-Language: en To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk VMD "Visual Molecular Dynamics" 1.4 beta 3 Announcement ------------------------------------------------------- The Theoretical Biophysics group at the Beckman Institute For Advanced Science and Technology, the University of Illinois (U-C), is proud to announce the public release of VMD 1.4b3. VMD is a package for the visualization and analysis of biomolecular systems. This software is distributed free of charge and includes source code, documentation, and precompiled binaries for IBM, HP, Linux, Sun, and SGI Unix systems, as well as Microsoft Windows 95/98/NT. The VMD documentation includes an installation guide, a users guide, and a programmers guide for interested researchers. VMD also provides on-line help through the use of an external HTML viewer. VMD development is supported by the NIH National Center for Research Resources. A full description of VMD is available via the VMD WWW home page: http://www.ks.uiuc.edu/Research/vmd/ Beta 3 includes a significant number of improvements over the last widely announced beta (Beta 1). The salient points are: - OpenGL versions of VMD now implement a simple (but very fast) transparency algorithm. So the transparency button finally works in the OpenGL builds now! I will be making a number of additional improvements to this code when I return. I hope to implement at least one alpha blending based technique. - new transparency support added to Raster3D export code - improved scene exports to Tachyon (especially transparency) - greatly improved Postscript renderer, several serious memory leaks fixed, works fine now on large molecules that used to crash the code. - fixed a bug with Surf on HPUX, and another Surf bug on all VMD platforms. - updated interactive MD code, with much better responsiveness. - updated builds for AIX 4.3 with both Mesa and OpenGL - improved speed of the "within" and "same residue" atom selections - Many improvements to external renderer scene exports. - Improved SGI Multisampling support (8 samples per pixel now...) - many other small bug fixes and minor improvements. We are eager to hear from you, and thank you for using our software! John Stone vmd@ks.uiuc.edu November 18, 1999 From owner-molmodel@hgmp.mrc.ac.uk Sun Nov 21 09:08:26 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 7C3B317A43; Sun, 21 Nov 1999 09:08:25 +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 JAA04156 for ; Sun, 21 Nov 1999 09:08:23 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id JAA05742 for molmodel-list@hgmp.mrc.ac.uk; Sun, 21 Nov 1999 09:08:22 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: wuukoemuu95@DAALIA.VTKK.FI X-Newsgroups: bionet.molec-model Subject: Fwd: Photo Mousepads .....Great Christmas Gift.... Date: 21 Nov 1999 00:51:49 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 115 Distribution: world Message-ID: <199911204237YAA52087@Finepads.prensa-latina.cu> To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk Only 29 days to shop! GREAT CHRISTMAS GIFT IDEA! Photo mousepads make a PERFECT GIFT for ANYONE! >>>> MOUSEPADS WITH YOUR FAVORITE PHOTOS! Now you can have your favorite photos printed onto mousepads! Photo mousepads are our most popular gift year after year! In the past we have provided our HIGH QUALITY mousepads to thousands of customers. Most are so pleased they reorder each year! Replace boring, dirty, frayed mousepads with PERSONALIZED photo mousepads to brighten your desktop! PHOTO Mousepads are DAILY REMINDERS of your favorite: CHILDREN, PETS, EVENTS....... WEDDING PHOTOS, FAMILY, CHRISTMAS..... LOVED ONES,HOLIDAY PHOTOS,GRANDCHILDREN..... 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Sav From owner-molmodel@hgmp.mrc.ac.uk Sun Nov 21 19:45:02 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 9642917A43; Sun, 21 Nov 1999 19:45:01 +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 TAA20308 for ; Sun, 21 Nov 1999 19:44:59 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id TAA13449 for molmodel-list@hgmp.mrc.ac.uk; Sun, 21 Nov 1999 19:44:58 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: astavrak@cc.uoi.gr (Athanassios Stavrakoudis) X-Newsgroups: bionet.molec-model Subject: DMSO papameters Date: 21 Nov 1999 19:44:57 -0000 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 22 Message-ID: <38384B29.CE8B1B53@cc.uoi.gr> Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-7 Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 943213497 13446 193.62.192.80 (21 Nov 1999 19:44:57 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk X-Received: from socrates.cc.uoi.gr (socrates.cc.uoi.gr [195.130.119.1]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id TAA20298 for ; Sun, 21 Nov 1999 19:44:55 GMT X-Received: from cc.uoi.gr (pc15.chem.uoi.gr [195.130.116.15]) by socrates.cc.uoi.gr (8.9.3/8.9.3) with ESMTP id VAA900127 for ; Sun, 21 Nov 1999 21:45:32 +0200 (EET) X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en X-To: molmdel To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk Hi all, l am looking for DMSO force field parameters ( AMBER of CHARMM). Has anyone any suggestions ? Thank you, -- Athanassios Stavrakoudis University of Ioannina Department of Chemistry Section of Organic Chemistry and Biochemistry GR-45110, Ioannina GREECE tel : ++ 3 0 651 98-385 fax : ++ 3 0 651 45-840 e-mail : astavrak@cc.uoi.gr --- From owner-molmodel@hgmp.mrc.ac.uk Fri Nov 26 05:13:11 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id BB65317A72; Fri, 26 Nov 1999 05:13:10 +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 FAA22971 for ; Fri, 26 Nov 1999 05:13:08 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id FAA13308 for molmodel-list@hgmp.mrc.ac.uk; Fri, 26 Nov 1999 05:13:07 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: dkjksk@IBML.COM X-Newsgroups: bionet.molec-model Subject: THIS WEEKEND Date: 25 Nov 1999 20:49:03 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 73 Distribution: world Message-ID: <199911260449.UAA10990@net.bio.net> To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk NOTE: THIS IS AN ADVERTISEMENT FOR LEGAL TV DE-SCRAMBLER IF YOU HAVE NO INTEREST IN THIS INFORMATION PLEASE CLICK DELETE NOW. 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Date: Thu, 02 Sep 1999 13:38:10 -0700 To: David Bruner From owner-molmodel@hgmp.mrc.ac.uk Sat Nov 27 10:08:35 1999 Return-Path: Delivered-To: molmodel-archive@hgmp.mrc.ac.uk Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 6950E17A65; Sat, 27 Nov 1999 10:08:34 +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 KAA21173 for ; Sat, 27 Nov 1999 10:08:32 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id KAA12594 for molmodel-list@hgmp.mrc.ac.uk; Sat, 27 Nov 1999 10:08:30 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: biohelp@hgmp.mrc.ac.uk (BIOSCI Administrator) X-Newsgroups: bionet.molec-model Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 27 Nov 1999 02:00:11 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 239 Distribution: world Message-ID: <199911271000.CAA15454@net.bio.net> To: molmodel@hgmp.mrc.ac.uk Sender: owner-molmodel@hgmp.mrc.ac.uk Precedence: bulk (LAST REVISION: 14-AUG-99) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- All BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- the UK-HGMP-Resource Centre (known as hgmp.mrc.ac.uk): ----------------------------------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@hgmp.mrc.ac.uk. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to majordomo@hgmp.mrc.ac.uk. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Please ask for help at biosci@hgmp.mrc.ac.uk if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. 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