From owner-molec-model@net.bio.net Mon Mar 01 22:00:00 1999 Path: biosci!CHULA.AC.TH!spornthe From: spornthe@CHULA.AC.TH (Pornthep Sompornpisut) Newsgroups: bionet.molec-model Subject: Biomolecular simulation Date: 1 Mar 1999 18:32:35 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <1.5.4.32.19981201022525.0067caa0@pioneer.netserv.chula.ac.th> NNTP-Posting-Host: net.bio.net Dear Sir, I do a computer simulation of a protein in order to compare the structure and its biological function. For my work, molecular dynamics have been performed to study dynamics structure of an enzyme at two different temperatures, 300 and 310.5K, using AMBER 5. One of my interesting properties is "Solvent Accessible Surface Area" (SASA). The results show that SASA of the simulated structure at 310.5K is lower than that of the 300K. Is it strange result that the protein structure in aqueous solution at higher temperature has the lower SASA than that of the lower temperature? Any comments will be appreciate. Sincerely yours, Pornthep Sompornpisut From owner-molec-model@net.bio.net Mon Mar 01 22:00:00 1999 Message-ID: <36DB6013.EBFBCA64@bioreason.com> Date: Mon, 01 Mar 1999 19:50:43 -0800 From: Andrew Dalke Organization: Bioreason, Inc. X-Mailer: Mozilla 4.05 [en] (X11; U; IRIX 6.2 IP22) MIME-Version: 1.0 Newsgroups: bionet.molec-model Subject: Re: Biomolecular simulation References: <1.5.4.32.19981201022525.0067caa0@pioneer.netserv.chula.ac.th> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-Host: dialup116.trail.com Lines: 20 Path: biosci!agate!newsfeed.berkeley.edu!dca1-hub1.news.digex.net!digex!outfeed1.news.cais.net!news4.his.com!dialup116.trail.com Pornthep Sompornpisut wrote: > One of my interesting properties is "Solvent Accessible Surface > Area" (SASA). The results show that SASA of the simulated structure at > 310.5K is lower than that of the 300K. Is it strange result that the > protein structure in aqueous solution at higher temperature has the > lower SASA than that of the lower temperature? The first questions I have are: 1) what's the variability in the surface area for a given temperature compared to the difference in area between the two. I would be surprised if they weren't comperable. 2) did you keep the system at the same pressure when you increased the temperature or was it left at a constant volume. If the latter, then is the compressibility of the protein enough to explain the difference? (Higher pressure => smaller volume => less surface area.) Andrew dalke@acm.org From owner-molec-model@net.bio.net Tue Mar 02 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!diablo.theplanet.net!news.theplanet.net!newspost.theplanet.net!not-for-mail From: "Don Ainley" Newsgroups: alt.drugs.chemistry,alt.advanced.placed.or.honors.chemistry.2,alt.sci.physics,bionet.molec-model,ntu.sci.chemistry Subject: Re: Anyone know some good compound databases? Date: Wed, 3 Mar 1999 14:07:51 -0000 Organization: Customer of Planet Online Lines: 7 Message-ID: <7bjg2b$lt2$1@news6.svr.pol.co.uk> References: <7agjmt$h3k$1@oak.prod.itd.earthlink.net> NNTP-Posting-Host: modem-10.aluminum.dialup.pol.co.uk X-Trace: news6.svr.pol.co.uk 920470411 22434 62.136.6.10 (3 Mar 1999 14:13:31 GMT) NNTP-Posting-Date: 3 Mar 1999 14:13:31 GMT X-Complaints-To: abuse@theplanet.net X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Try the NIST Chemistry Webbook : webbook.nist.gov/chemistry/ This is very comprehensive for organic compounds. Don Ainley From owner-molec-model@net.bio.net Sun Mar 07 22:00:00 1999 Path: biosci!WORLDNET.ATT.NET!used.books From: used.books@WORLDNET.ATT.NET ("Used Book For You Co.") Newsgroups: bionet.molec-model Subject: Used Softcover.. Date: 7 Mar 1999 18:37:19 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 27 Sender: daemon@net.bio.net Distribution: world Message-ID: <18161.236226.89931586.monageer@msn.com> NNTP-Posting-Host: net.bio.net Books Good Books? Do You Enjoy Reading A Good Book? We have a wide selection of softcover books! Place the word "BOOKS" in the subject line of the below address ubs@gte.net NOT A SUBSCRIPTION SERVICE From owner-molec-model@net.bio.net Tue Mar 09 22:00:00 1999 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.cwix.com!205.252.116.205!howland.erols.net!news-out.digex.net.MISMATCH!dca1-hub1.news.digex.net!digex!dca1-nnrp1.news.digex.net.POSTED!not-for-mail From: tjcuvy@capitalinks.com Newsgroups: bionet.molec-model Subject: FREE Horoscope - NOT ANY SPAM! 874 Lines: 3 Message-ID: Date: Wed, 10 Mar 1999 05:14:52 GMT NNTP-Posting-Host: 207.111.39.7 X-Complaints-To: abuse@digex.net X-Trace: dca1-nnrp1.news.digex.net 921042892 207.111.39.7 (Wed, 10 Mar 1999 00:14:52 EDT) NNTP-Posting-Date: Wed, 10 Mar 1999 00:14:52 EDT Organization: DIGEX, Inc. - Beltsville, MD - http://www.digex.net Daily horoscopes free of chearge - just thought you might like to know.. http://www.capitalinks.com and press the DAILY HOROSCOPE BUTTON - not much else to say - this is really the only freebie horoscope on the net that I know of rnojuwqppdcxzywzrnngvnexh From owner-molec-model@net.bio.net Wed Mar 10 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.concentric.net!feed1.news.rcn.net!rcn!news.voicenet.com!news2.voicenet.com.POSTED!not-for-mail Message-ID: <36E716E0.5F4FF59E@voicenet.com> From: Mandeep X-Mailer: Mozilla 4.5 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 Newsgroups: bionet.molec-model Subject: Examples for rationally designed drugs? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 6 Date: Wed, 10 Mar 1999 20:05:37 -0500 NNTP-Posting-Host: 207.103.135.94 X-Trace: news2.voicenet.com 921163151 207.103.135.94 (Thu, 11 Mar 1999 09:39:11 EDT) NNTP-Posting-Date: Thu, 11 Mar 1999 09:39:11 EDT I am looking for recent ( past 3 years) examples of drugs designed using molecular modeling as part of the drug design process and URLs /References regarding these. Thanks, S M Singh From owner-molec-model@net.bio.net Sat Mar 13 22:00:00 1999 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.cwix.com!130.185.14.36!torn!news1.bellglobal.com!198.235.216.4.POSTED!not-for-mail From: ekgjlo@fakeaddressforyourlist.com Newsgroups: ca.usenet,alt.music.hootie,alt.info-fest,alt.os.assembly,alt.prep.cranbrook,bionet.molec-model Subject: YOULL WANT TO CLICK HERE! 5929 [1/2] Lines: 53 Message-ID: Date: Sun, 14 Mar 1999 05:25:44 GMT NNTP-Posting-Host: 209.226.55.170 X-Trace: 198.235.216.4 921389144 209.226.55.170 (Sun, 14 Mar 1999 00:25:44 EDT) NNTP-Posting-Date: Sun, 14 Mar 1999 00:25:44 EDT Organization: Bell Solutions h my name at #6 on the letter. Now, each of the 5 persons who just sent me $1.00 make the MINIMUM 200 postings, each with my name at #5 and only 5 persons respond to each of the original 5, that is another $25.00 for me. 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Remember, play FAIRLY and HONESTLY and this will really work! ljqrghsxhbmdpsrckjncsouekhrojgkrfhuexcf From owner-molec-model@net.bio.net Sat Mar 13 22:00:00 1999 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.cwix.com!130.185.14.36!torn!news1.bellglobal.com!198.235.216.4.POSTED!not-for-mail From: srovtu@fakeaddressforyourlist.com Newsgroups: alt.prep.cranbrook,bionet.molec-model,alt.women.attitudes,alt.religio.konfuceo Subject: YES VIRGINIA, $6 INTO THOUSANDS! 3633 [1/2] Lines: 3 Message-ID: <1XIG2.6226$E65.364@198.235.216.4> Date: Sun, 14 Mar 1999 06:46:21 GMT NNTP-Posting-Host: 209.226.55.170 X-Trace: 198.235.216.4 921393981 209.226.55.170 (Sun, 14 Mar 1999 01:46:21 EDT) NNTP-Posting-Date: Sun, 14 Mar 1999 01:46:21 EDT Organization: Bell Solutions CHECK OTHER POSTING FOR MESSAGE! ozkopxwmcelibxjewkfeuhwgmsdefkvvuzftislwpjllhgembuldxbflepspeucvmzifohcihjifwtruibjinrfzfrzf From owner-molec-model@net.bio.net Sat Mar 13 22:00:00 1999 Path: biosci!pravda.ucr.edu!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: OpalnDale@aol.com Newsgroups: bionet.molec-model Subject: adv. Free Gas!!!! Free Long Distance!!!! Date: 14 Mar 1999 08:49:54 -0000 Organization: Daresbury Laboratory, Warrington, U.K. Lines: 30 Message-ID: <7cft7i$msv$1@mserv2.dl.ac.uk> NNTP-Posting-Host: mserv2.dl.ac.uk content-length: 695 Return-Path: Apparently-To: This is a 1 time mailing address is delited Adv. Free Gas!!!! Free Long Distance!!!! If we could show you a way to eliminate your gasoline bill, your long distance phone bill, and make a lot of money at the same time, would you be interested?? Of course you would, and so would everyone else! Our flagship product GASOLINE!! 3 Day, mini vacation! Free replicating Websites! Webley virtual office! FREE LONG DISTANCE! $2000 in travel discounts! Up to $800 a day, Plus FAST START BONUSES 100% MATCHING BONUSES! Up to $200 a month FREE GAS 24 Hr support and training and more ACT NOW!!! CALL 1 800 493-3432 for incredible details! ITS YOUR TURN TO BE IN THE SPOTLIGHT! 800 493-3432 From owner-molec-model@net.bio.net Sun Mar 14 22:00:00 1999 Path: biosci!webtv.net!su-news-feed4.bbnplanet.com!news.gtei.net!news.stanford.edu!newsfeed.berkeley.edu!news2.best.com!news3.best.com!nntp1.ba.best.com!not-for-mail Message-ID: <36ED6315.36E6C0A2@radixtek.com> Date: Mon, 15 Mar 1999 11:44:21 -0800 From: Rafael Espanol X-Mailer: Mozilla 4.04 [en] (WinNT; I) MIME-Version: 1.0 Newsgroups: bionet.molec-model Subject: need molecular model of asbestor Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 8 NNTP-Posting-Host: 209.157.8.114 X-Trace: nntp1.ba.best.com 921526542 209 209.157.8.114 I am interested in information about the molecular structure of asbestos for a high school project. can anyone help with a pointer to information for this (or just tell me what the molecule looks like). raf From owner-molec-model@net.bio.net Mon Mar 15 22:00:00 1999 Path: biosci!ROCKVAX.ROCKEFELLER.EDU!sali From: sali@ROCKVAX.ROCKEFELLER.EDU Newsgroups: bionet.molec-model Subject: ANNOUNCEMENT: ModBase database of comparative protein structure models Date: 16 Mar 1999 06:47:10 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <199903161442.JAA92861@guitar.rockefeller.edu> Reply-To: sali@rockvax.rockefeller.edu NNTP-Posting-Host: net.bio.net ModBase database of comparative protein structure models Roberto Sanchez and Andrej Sali http://guitar.rockefeller.edu/modbase/ ModBase is a queryable database of many annotated comparative protein structure models. The models consist of coordinates for all non-hydrogen atoms in the modeled part of a protein. They are derived by an automated modeling pipeline relying mainly on the program MODELLER. The database currently contains 3D models for substantial segments of 15-23% of proteins in the genomes of M. genitalium, M. jannaschii, E. coli, S. cerevisiae, and C. elegans. In total, there are models for 3,732 proteins. The database also includes fold assignments and alignments on which the models were based. In addition, special care is taken to assess the overall quality of the models and their accuracy at the residue level. In the future, ModBase will grow to reflect (i) the growth of the sequence databases, (ii) the growth of the database of known protein structures, (iii) and improvements in the software for calculating the models. It is expected that the Swiss-Prot+TrEMBL protein sequence database will be processed by the end of 1999. ModBase is introduced in R. Sanchez & A. Sali. Proc. Natl. Acad. Sci. USA 95, 13597-13602, 1998. From owner-molec-model@net.bio.net Tue Mar 16 22:00:00 1999 Path: biosci!pravda.ucr.edu!awabi.library.ucla.edu!207.97.14.174!europa.clark.net!194.182.148.154!news-feed.inet.tele.dk!bofh.vszbr.cz!news.belnet.be!news-ge.switch.ch!serra.unipi.it!pisanino.unipi.it!not-for-mail From: "Antonio" Newsgroups: bionet.molec-model,bionet.xtallography,sci.math,sci.math.symbolic,sci.physics,sci.physics.computational.fluid-dynamics Subject: Re: How to calculate dihedral (not torsion) angles? Date: Wed, 17 Mar 1999 15:08:34 +0100 Organization: Universita' di Pisa Lines: 36 Message-ID: <7cocua$s7b$1@pisanino.unipi.it> References: <7co3jm$p29$1@pisanino.unipi.it> <36EFA663.41C6@icrf.icnet.uk> NNTP-Posting-Host: hal9000.dipchim.uniss.it X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Xref: biosci bionet.molec-model:2448 bionet.xtallography:4653 islam wrote <36EFA663.41C6@icrf.icnet.uk>... >The definition of a torsion angle between 4 points, >does not require them to be bonded ! The dihedral angle >is simply the angle between the two planes ABC and BCD >(in fact the torsion angle is the complement of the dihedral angle >i.e. torsion = 180.0 - dihedral ). You can simply calculate >the plane for ABC (or 1-3-5 below) & BCD (or 1-2-3 below) and then >the angle between them. > Thank you for your message, I'm aware that the four points need not to be bonded, of course. But I tried to consider them bonded, so as to apply the expressions reported. Indeed, I already tried to do as you suggest: first calculate the versor normal to the 1-3-5 plane (r13 x r15/|r13 x r15|) and the versor normal to the plane 1-2-3 (r12 x r23/|r12 x r23|); then their dot product should give cos(phi), but the problem is that at this point you can't simply take the acos(cos(phi)), because some sign problems arise: indeed, in all programs which calculate torsional angles one must also obtain sin(phi) and then take the atan, as in the expressions reported in my previous message. The calculation of sin(phi) is direct when a common bond does exist between the atoms, because such common vector enters the formula for sin(phi): sin(phi)=rc.(r13 x r15)x(r12 x r23)/(|rc||r13 x r15||r12 x r23|) where rc is the common vector. But now I haven't such a common vector, then what rc vector should I use in the expression for sin(phi)? Antonio osrisfol@ssmain.uniss.it From owner-molec-model@net.bio.net Tue Mar 16 22:00:00 1999 Path: biosci!pravda.ucr.edu!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!ayres.ftech.net!news.ftech.net!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!news.icnet!not-for-mail From: islam Newsgroups: bionet.molec-model,bionet.xtallography,sci.math,sci.math.symbolic,sci.physics,sci.physics.computational.fluid-dynamics Subject: Re: How to calculate dihedral (not torsion) angles? Date: Wed, 17 Mar 1999 12:56:03 +0000 Organization: Imperial Cancer Research Fund Lines: 70 Message-ID: <36EFA663.41C6@icrf.icnet.uk> References: <7co3jm$p29$1@pisanino.unipi.it> NNTP-Posting-Host: palm.lif.icnet.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01SC-SGI (X11; I; IRIX 6.3 IP32) Xref: biosci bionet.molec-model:2447 bionet.xtallography:4652 The definition of a torsion angle between 4 points, does not require them to be bonded ! The dihedral angle is simply the angle between the two planes ABC and BCD (in fact the torsion angle is the complement of the dihedral angle i.e. torsion = 180.0 - dihedral ). You can simply calculate the plane for ABC (or 1-3-5 below) & BCD (or 1-2-3 below) and then the angle between them. ____________________________________________ Suhail A Islam Biomolecular Modelling Laboratory Imperial Cancer Research Fund, P.O. Box 123 44 Lincoln's Inn Fields, London WC2A 3PX Tel: (0171) 269 3380 Fax: (0171) 269 3258 email: islam@icrf.icnet.uk http://www.icnet.uk/bmm/ ____________________________________________ Antonio wrote: > > We know how to calculate a torsion angle about an axis, for example > if we have 4 points in 3-D (for example, a butane molecule) > A D > r1 \ / r3 > B- - - -C > r2 > in which the points A, B, C and D are connected by the vectors > r1, r2 and r3, we can obtain the torsion angle phi about r2 by applying: > > p1= r1 x r2 > p2= r2 x r3 > p1 . p2 = |p1| |p2| cos (phi) > r2 . (p2 x p1) = |p1| |p2| |r2| sin(phi) > and finally phi=atan[sin(phi)/cos(phi)] through a function like ATAN2 > in Fortran. Phi is obviously also the angle between the A-B-C and B-C-D > planes. > The problem is, how to calculate a dihedral angle when the four centers > defining the two planes are > not directly connected? For example, if we have a six ring > molecule: > 1 ---2 > / \ > 6 3 > \ / > 5 -- 4 > > and we need the angle between the 1-3-5 and 1-2-3 planes, now there isn't > a common bond, as r2 in the previous case (indeed now we can't > speak of 'torsion' angle, but more generally of 'dihedral', even if both are > angles between planes). Therefore, the previous expressions > aren't directly applicable. I tried to define a 'dummy' common bond, e.g > 1--3, in order to apply the above expressions to a system like: > 5 2 > \ / > 1--------3 > > actually, with this trick we should obtain the angle between planes > 5-1-3 and 1-3-2, which should be the same as that between 1-3-5 > and 1-2-3 planes. However, this doesn't seem to work well. Maybe > the last assumption (dihedral 513/132= dihedral 135/123) is not > correct, or some adjustment are needed in the above expressions, to make > them valid in this case? Or do you know of a > different method to evaluate such dihedral (not torsion) angles? > Thanks in advance > > Antonio > e-mail > > osrisfol@ssmain.uniss.it From owner-molec-model@net.bio.net Tue Mar 16 22:00:00 1999 Path: biosci!bloom-beacon.mit.edu!panix!newsfeed.mathworks.com!news-ge.switch.ch!serra.unipi.it!pisanino.unipi.it!not-for-mail From: "Antonio" Newsgroups: bionet.molec-model,bionet.xtallography,sci.math,sci.math.symbolic,sci.physics,sci.physics.computational.fluid-dynamics Subject: How to calculate dihedral (not torsion) angles? Date: Wed, 17 Mar 1999 12:29:17 +0100 Organization: Universita' di Pisa Lines: 51 Message-ID: <7co3jm$p29$1@pisanino.unipi.it> NNTP-Posting-Host: hal9000.dipchim.uniss.it X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Xref: biosci bionet.molec-model:2446 bionet.xtallography:4651 We know how to calculate a torsion angle about an axis, for example if we have 4 points in 3-D (for example, a butane molecule) A D r1 \ / r3 B- - - -C r2 in which the points A, B, C and D are connected by the vectors r1, r2 and r3, we can obtain the torsion angle phi about r2 by applying: p1= r1 x r2 p2= r2 x r3 p1 . p2 = |p1| |p2| cos (phi) r2 . (p2 x p1) = |p1| |p2| |r2| sin(phi) and finally phi=atan[sin(phi)/cos(phi)] through a function like ATAN2 in Fortran. Phi is obviously also the angle between the A-B-C and B-C-D planes. The problem is, how to calculate a dihedral angle when the four centers defining the two planes are not directly connected? For example, if we have a six ring molecule: 1 ---2 / \ 6 3 \ / 5 -- 4 and we need the angle between the 1-3-5 and 1-2-3 planes, now there isn't a common bond, as r2 in the previous case (indeed now we can't speak of 'torsion' angle, but more generally of 'dihedral', even if both are angles between planes). Therefore, the previous expressions aren't directly applicable. I tried to define a 'dummy' common bond, e.g 1--3, in order to apply the above expressions to a system like: 5 2 \ / 1--------3 actually, with this trick we should obtain the angle between planes 5-1-3 and 1-3-2, which should be the same as that between 1-3-5 and 1-2-3 planes. However, this doesn't seem to work well. Maybe the last assumption (dihedral 513/132= dihedral 135/123) is not correct, or some adjustment are needed in the above expressions, to make them valid in this case? Or do you know of a different method to evaluate such dihedral (not torsion) angles? Thanks in advance Antonio e-mail osrisfol@ssmain.uniss.it From owner-molec-model@net.bio.net Tue Mar 16 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!howland.erols.net!portc02.blue.aol.com!pitt.edu!gatech!nntp-xfer.ncsu.edu!boyle From: boyle@laue.chem.ncsu.edu (Paul D. Boyle) Newsgroups: bionet.molec-model,bionet.xtallography Subject: Re: How to calculate dihedral (not torsion) angles? Followup-To: bionet.molec-model,bionet.xtallography Date: 17 Mar 1999 14:18:07 GMT Organization: North Carolina State University Lines: 28 Message-ID: <7codiv$ddb$1@uni00nw.unity.ncsu.edu> References: <7co3jm$p29$1@pisanino.unipi.it> NNTP-Posting-Host: laue.chem.ncsu.edu X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.molec-model:2449 bionet.xtallography:4654 Antonio (osrisfol@ssmain.uniss.it) wrote: : The problem is, how to calculate a dihedral angle when the four centers : defining the two planes are : not directly connected? For example, if we have a six ring : molecule: : 1 ---2 : / \ : 6 3 : \ / : 5 -- 4 : and we need the angle between the 1-3-5 and 1-2-3 planes, Reading Donald Sands' book, "Vectors and Tensors in Crystallography", ISBN 0-201-07147-9 is a good place to start. Chapter 2, particularly section 2-12, will be useful to you. Paul -- Paul D. Boyle | boyle@laue.chem.ncsu.edu Director, X-ray Structural Facility | phone: (919) 515-7362 Department of Chemistry - Box 8204 | FAX: (919) 515-5079 North Carolina State University | Raleigh, NC, 27695-8204 http://laue.chem.ncsu.edu/web/xray.welcome.html From owner-molec-model@net.bio.net Tue Mar 16 22:00:00 1999 Path: biosci!bloom-beacon.mit.edu!news.kodak.com!news-nysernet-16.sprintlink.net!news-east1.sprintlink.net!news-peer1.sprintlink.net!news.sprintlink.net!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!news.icnet!not-for-mail From: islam Newsgroups: bionet.molec-model,bionet.xtallography,sci.math,sci.math.symbolic,sci.physics,sci.physics.computational.fluid-dynamics Subject: Re: How to calculate dihedral (not torsion) angles? Date: Wed, 17 Mar 1999 15:43:49 +0000 Organization: Imperial Cancer Research Fund Lines: 45 Message-ID: <36EFCDB5.167E@icrf.icnet.uk> References: <7co3jm$p29$1@pisanino.unipi.it> <36EFA663.41C6@icrf.icnet.uk> <7cocua$s7b$1@pisanino.unipi.it> NNTP-Posting-Host: palm.lif.icnet.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01SC-SGI (X11; I; IRIX 6.3 IP32) Xref: biosci bionet.molec-model:2450 bionet.xtallography:4655 I hope I am not getting too confused here (!), but why can you not simply use the torsion angle calculation. Bonding does not matter, only the order of the 4 points which you consider. This will give you a correct sign. The sign is the sign of the volume formed by the 4 points. Angle between planes do not have a sign (handedness), becuse there are an infinite number of ways to order 4 points on the 2 planes. What are you trying to consider e.g. twist within a ring, pucker ? suhail Antonio wrote: > > islam wrote <36EFA663.41C6@icrf.icnet.uk>... > >The definition of a torsion angle between 4 points, > >does not require them to be bonded ! The dihedral angle > >is simply the angle between the two planes ABC and BCD > >(in fact the torsion angle is the complement of the dihedral angle > >i.e. torsion = 180.0 - dihedral ). You can simply calculate > >the plane for ABC (or 1-3-5 below) & BCD (or 1-2-3 below) and then > >the angle between them. > > > > Thank you for your message, > > I'm aware that the four points need not to be bonded, of course. > But I tried to consider them bonded, so as to apply the expressions > reported. Indeed, I already tried to do as you suggest: first calculate > the versor normal to the 1-3-5 plane (r13 x r15/|r13 x r15|) and > the versor normal to the plane 1-2-3 (r12 x r23/|r12 x r23|); > then their dot product should give cos(phi), but the problem is that > at this point you can't simply take the acos(cos(phi)), because > some sign problems arise: indeed, in all programs which calculate > torsional angles one must also obtain sin(phi) and then take the atan, as > in the expressions reported in my previous message. > The calculation of sin(phi) is direct when a common bond does exist > between the atoms, because such common vector enters the formula > for sin(phi): > sin(phi)=rc.(r13 x r15)x(r12 x r23)/(|rc||r13 x r15||r12 x r23|) > where rc is the common vector. > But now I haven't such a common vector, then what rc vector should I use in > the expression for sin(phi)? > Antonio > osrisfol@ssmain.uniss.it From owner-molec-model@net.bio.net Wed Mar 17 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!newsfeed.direct.ca!rill.news.pipex.net!pipex!newsfeed.eris.dera.gov.uk!diablo.dera.gov.uk!server1.netnews.ja.net!news.nott.ac.uk!news.nottingham.ac.uk!not-for-mail From: Benny Lo Newsgroups: bionet.molec-model Subject: Simulated annealing within Insight/Discover Date: Thu, 18 Mar 1999 10:41:27 +0000 Organization: The University of Nottingham Lines: 75 Message-ID: <36F0D857.8828A985@holmes.nott.ac.uk> Reply-To: benny@holmes.nott.ac.uk NNTP-Posting-Host: moriarty.cancres.nottingham.ac.uk Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="------------1C9B4856406146DCEC294AEB" X-Trace: oyez.ccc.nottingham.ac.uk 921753884 2465 128.243.118.152 (18 Mar 1999 10:44:44 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 18 Mar 1999 10:44:44 GMT X-Mailer: Mozilla 4.05C-SGI [en] (X11; I; IRIX64 6.5 IP30) --------------1C9B4856406146DCEC294AEB Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear All, Does anyone know if it is possible to perform molecular dynamics calculations with simulated annealing within Insight/Discover? If so, I would be glad if you could tell me how to access this function. Also, I have been trying to run some MD calculations within Discover in the batch mode but I could not find any output coordinate files (e.g. ".cor" files with energy minimization). I also tried loading the .his file in the Analysis module but that wouldn't load up either (I was asked to enter a molecule name but there was nothing on the small aid window next to it). SO I have to resort to running these interactively and saving the final structure manually. Does anyone know a way round this? Any help would be appreciated. Please email to: benny@holmes.nott.ac.uk THank you. Benny. -- Benny K C Lo Cancer Research Laboratories The University of Nottingham University Park Nottingham NG7 2RD, UK Tel: +44 (0)115 9515566 ext 12176/8 Email: benny@holmes.cancres.nottingham.ac.uk --------------1C9B4856406146DCEC294AEB Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear All,

Does anyone know if it is possible to perform molecular dynamics calculations with simulated annealing within Insight/Discover? If so, I would be glad if you could tell me how to access this function.

Also, I have been trying to run some MD calculations within Discover in the batch mode but I could not find any output coordinate files (e.g. ".cor" files with energy minimization). I also tried loading the .his file in the Analysis module but that wouldn't load up either (I was asked to enter a molecule name but there was nothing on the small aid window next to it). SO I have to resort to running these interactively and saving the final structure manually. Does anyone know a way round this?

Any help would be appreciated. Please email to: benny@holmes.nott.ac.uk

THank you.

Benny.
  

-- 
Benny K C Lo
Cancer Research Laboratories
The University of Nottingham
University Park
Nottingham NG7 2RD, UK
Tel: +44 (0)115 9515566 ext 12176/8
Email: benny@holmes.cancres.nottingham.ac.uk
  --------------1C9B4856406146DCEC294AEB-- From owner-molec-model@net.bio.net Thu Mar 18 22:00:00 1999 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!newsfeed.nacamar.de!dispose.news.demon.net!demon!news.demon.co.uk!demon!mail2news.demon.co.uk!not-for-mail From: amartin@stagleys.demon.co.uk (Andrew Martin) Newsgroups: bionet.molec-model,bionet.xtallography,sci.math,sci.math.symbolic,sci.physics,sci.physics.computational.fluid-dynamics Subject: Re: How to calculate dihedral (not torsion) angles? Followup-To: bionet.molec-model,bionet.xtallography,sci.math,sci.math.symbolic,sci.physics,sci.physics.computational.fluid-dynamics Date: Thu, 18 Mar 1999 09:35:47 GMT Organization: Private Address Message-ID: References: <7co3jm$p29$1@pisanino.unipi.it> <36EFA663.41C6@icrf.icnet.uk> <7cocua$s7b$1@pisanino.unipi.it> <36EFCDB5.167E@icrf.icnet.uk> X-Trace: mail2news.demon.co.uk 921816948 mail2news:22593 mail2news mail2news.demon.co.uk X-Complaints-To: abuse@demon.net X-Mail2News-Path: news.demon.net!finch-post-11.mail.demon.net![194.222.20.72]!stagleys.demon.co.uk X-Newsreader: TIN [version 1.2 PL2] Lines: 28 Xref: biosci bionet.molec-model:2452 bionet.xtallography:4657 Suhail Islam (islam@icrf.icnet.uk) wrote: : I hope I am not getting too confused here (!), but why : can you not simply use the torsion angle calculation. : Bonding does not matter, only the order of the 4 points : which you consider. This will give you a correct sign. : The sign is the sign of the volume formed by the : 4 points. Angle between planes do not have a sign (handedness), : becuse there are an infinite number of ways to order 4 points : on the 2 planes. I also do not understand the problem here :-) you only need to look at any piece of code like Gromos Charmm/Xplor to see calculation of improper dihedrals (which is what is being asked for) is done by exactly the same piece of code as the proper dihedral calculation (i.e. where the middle 2 atoms are bonded). Best wishes, Andrew -------------------------------------------------------------------- Dr. Andrew C.R. Martin UCL/Inpharmatica UCL: martin@biochem.ucl.ac.uk Inpharmatica: a.martin@inpharmatica.co.uk Home: andrew@stagleys.demon.co.uk -------------------------------------------------------------------- From owner-molec-model@net.bio.net Thu Mar 18 22:00:00 1999 Path: biosci!bloom-beacon.mit.edu!panix!newsfeed.mathworks.com!news-ge.switch.ch!serra.unipi.it!pisanino.unipi.it!not-for-mail From: "Antonio" Newsgroups: bionet.molec-model,bionet.xtallography,sci.math,sci.math.symbolic,sci.physics,sci.physics.computational.fluid-dynamics Subject: Re: How to calculate dihedral (not torsion) angles? Date: Fri, 19 Mar 1999 12:18:22 +0100 Organization: Universita' di Pisa Lines: 40 Message-ID: <7ctbn0$li7$1@pisanino.unipi.it> References: <7co3jm$p29$1@pisanino.unipi.it> <36EFA663.41C6@icrf.icnet.uk> <7cocua$s7b$1@pisanino.unipi.it> <36EFCDB5.167E@icrf.icnet.uk> NNTP-Posting-Host: hal9000.dipchim.uniss.it X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Xref: biosci bionet.molec-model:2453 bionet.xtallography:4658 Andrew Martin wrote: >Suhail Islam (islam@icrf.icnet.uk) wrote: >: I hope I am not getting too confused here (!), but why >: can you not simply use the torsion angle calculation. >: Bonding does not matter, only the order of the 4 points >: which you consider. This will give you a correct sign. >: The sign is the sign of the volume formed by the >: 4 points. Angle between planes do not have a sign (handedness), >: becuse there are an infinite number of ways to order 4 points >: on the 2 planes. > >I also do not understand the problem here :-) > >you only need to look at any piece of code like Gromos Charmm/Xplor >to see calculation of improper dihedrals (which is what is being >asked for) is done by exactly the same piece of code as the proper >dihedral calculation (i.e. where the middle 2 atoms are bonded). > I agree with you that calculations of improper dihedrals is made in the same way as the proper ones. My problem is *the sequence* of the 4 atoms involved in the improper dihedral. After you find the correct sequence, you can directly apply any code for the dihedral angle calculation. Finding this sequence is not a trivial problem, in particular when you have to calculate a complicated function of several improper dihedral angles, so that they should be *all* treated in the same way. For example, in a six-ring, the angle between 135 and 561 planes can be obtained as the 3-5-1-6 dihedral, and/or as the 3-1-5-6 one (the 1356 is obviously wrong, as it would give the angle between 135 and 356 planes). These two possible choices give opposite dihedral angles, which may not be important for general considerations, but it's very important when you have to sum/multiply such angles. Antonio osrisfol@ssmain.uniss.it From owner-molec-model@net.bio.net Fri Mar 19 22:00:00 1999 Path: biosci!ATC.ATCCU.CHULA.AC.TH!porn From: porn@ATC.ATCCU.CHULA.AC.TH Newsgroups: bionet.molec-model Subject: Energy vs Ki Date: 20 Mar 1999 07:54:12 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Sir, I want to fit a correlation between the interaction energy and the experimental inhibition constants (Ki) for an enzyme-inhibitor complex. I would appreciate receiving any comments. Thank you in advance Thep ================================= P. Sompornpisut, Ph.D. Department of Chemistry Faculty of Science Chulalongkorn University ================================= From owner-molec-model@net.bio.net Sat Mar 20 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!newspeer.monmouth.com!solomon.io.com!news.tamu.edu!news.utdallas.edu!news.swmed.edu!news From: Lothar Esser Newsgroups: bionet.molec-model Subject: Bobscript Date: Sun, 21 Mar 1999 17:22:00 -0600 Organization: UT Southwestern Medical Center Lines: 20 Message-ID: <36F57F18.303C48CA@chop.swmed.edu> NNTP-Posting-Host: calliope.swmed.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.05C-SGI [en] (X11; I; IRIX64 6.2 IP28) Hi, does anyone know Robert Esnouf's current e-mail address ? Thanks, Lothar Esser ------------------------------------------------------------------ Dr. Lothar Esser UT Southwestern Dallas TX 5323 Harry Hines Blvd. Dallas Texas 75235-9050 E-mail : esser@chop.swmed.edu ------------------------------------------------------------------ From owner-molec-model@net.bio.net Sun Mar 21 22:00:00 1999 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!newsfeed.nacamar.de!dispose.news.demon.net!demon!news.demon.co.uk!demon!mail2news.demon.co.uk!not-for-mail From: amartin@stagleys.demon.co.uk (Andrew Martin) Newsgroups: bionet.molec-model,bionet.xtallography,sci.math,sci.math.symbolic,sci.physics,sci.physics.computational.fluid-dynamics Subject: Re: How to calculate dihedral (not torsion) angles? Followup-To: bionet.molec-model,bionet.xtallography,sci.math,sci.math.symbolic,sci.physics,sci.physics.computational.fluid-dynamics Date: Mon, 22 Mar 1999 00:10:37 GMT Organization: Private Address Message-ID: References: <7co3jm$p29$1@pisanino.unipi.it> <36EFA663.41C6@icrf.icnet.uk> <7cocua$s7b$1@pisanino.unipi.it> <36EFCDB5.167E@icrf.icnet.uk> <7ctbn0$li7$1@pisanino.unipi.it> X-Trace: mail2news.demon.co.uk 922076149 mail2news:28314 mail2news mail2news.demon.co.uk X-Complaints-To: abuse@demon.net X-Mail2News-Path: news.demon.net!finch-post-10.mail.demon.net![194.222.20.72]!stagleys.demon.co.uk X-Newsreader: TIN [version 1.2 PL2] Lines: 38 Xref: biosci bionet.molec-model:2456 bionet.xtallography:4662 Antonio (osrisfol@ssmain.uniss.it) wrote: : I agree with you that calculations of improper dihedrals is made in the : same way as the proper ones. My problem is *the sequence* of the 4 atoms : involved in the improper dihedral. After you find : the correct sequence, you can directly apply any code for the : dihedral angle calculation. Finding this sequence is not a trivial problem, : in particular when you have to calculate a complicated function of : several improper dihedral angles, so that they should be *all* : treated in the same way. For example, in a six-ring, the angle : between 135 and 561 planes can be obtained as the 3-5-1-6 : dihedral, and/or as the 3-1-5-6 one (the 1356 is obviously wrong, : as it would give the angle between 135 and 356 planes). : These two possible choices give opposite dihedral angles, which : may not be important for general considerations, but it's very : important when you have to sum/multiply such angles. OK, now I understand your point :-) I'm not sure of the solution - I need to think this through properly, but does it not work out as you want if you apply a simple rule like the second atom in your sequence is always clockwise to the first? Does the sign matter in any case? For your purposes can you not take the modulo (or the square). Why not calculate an RMSD? That's how one normally gets around the sign problem in cartesian or torsional problems... Without knowing more about exactly what you want to achieve it's difficult to say :-) Best wishes, Andrew -- Dr. Andrew C.R. Martin Technical Director, Inpharmatica & Lecturer, UCL From owner-molec-model@net.bio.net Sun Mar 21 22:00:00 1999 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!208.134.241.18!newsfeed.cwix.com!192.71.180.34!newsfeed1.swip.net!swipnet!news-peer-europe.sprintlink.net!news.sprintlink.net!Sprint!feed2.news.luth.se!luth.se!news-ge.switch.ch!serra.unipi.it!pisanino.unipi.it!not-for-mail From: "Antonio" Newsgroups: bionet.molec-model,bionet.xtallography,sci.math,sci.math.symbolic,sci.physics,sci.physics.computational.fluid-dynamics Subject: Re: How to calculate dihedral (not torsion) angles? Date: Mon, 22 Mar 1999 14:29:23 +0100 Organization: Universita' di Pisa Lines: 50 Message-ID: <7d5gh5$97a$1@pisanino.unipi.it> References: <7co3jm$p29$1@pisanino.unipi.it> <36EFA663.41C6@icrf.icnet.uk> <7cocua$s7b$1@pisanino.unipi.it> <36EFCDB5.167E@icrf.icnet.uk> <7ctbn0$li7$1@pisanino.unipi.it> NNTP-Posting-Host: hal9000.dipchim.uniss.it X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Xref: biosci bionet.molec-model:2457 bionet.xtallography:4663 Andrew Martin wrote >OK, now I understand your point :-) I'm not sure of the solution - I >need to think this through properly, but does it not work out as >you want if you apply a simple rule like the second atom in your >sequence is always clockwise to the first? You got the point. I need a simple rule! :) Indeed, after some trials, I found the (I hope!) correct sequences: 5132 for the dihedral between 135-123 planes 1354 for the dihedral between 135-345 planes 3516 for the dihedral between 135-561 planes The first *three* atoms are always clockwise, and the last one is that preceding the third atom in the ring. This *seems* to be the rule searched, but I still have to test it carefully. > >Does the sign matter in any case? For your purposes can you not >take the modulo (or the square). The sign is very important, as I have to calculate a complicated sum of such angles; if one of them assumes a value opposite to the correct one, the whole sum gets wrong. >Why not calculate an RMSD? That's >how one normally gets around the sign problem in cartesian or >torsional problems... Without knowing more about exactly what >you want to achieve it's difficult to say :-) > I just need to establish when a cyclohexane is in a chair or in a twisted-boat conformation, or in a transient form, and I need the above angles to determine that. Could you give me more information about RMSD calculations? My e-mail is: osrisfol@ssmain.uniss.it >Best wishes, >Andrew > Thank you very much for your help. Antonio From owner-molec-model@net.bio.net Mon Mar 22 22:00:00 1999 Path: biosci!ATC.ATCCU.CHULA.AC.TH!porn From: porn@ATC.ATCCU.CHULA.AC.TH Newsgroups: bionet.molec-model Subject: Configuration R- and S- labeling problem Date: 23 Mar 1999 05:11:04 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Sir, We have a problem for calling the enantimeric configuration of a chiral carbon of our molecule. Incidentally, Insight II denotes what we would call S-emantiomer as R (!). And even more strangely, as soon as this molecule has been protonated, it now denotes this same enantiomer as S. Who can explain this? Cheers Thep From owner-molec-model@net.bio.net Mon Mar 22 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!remarQ73!supernews.com!remarQ.com!remarQ69!news.remarQ.com!not-for-mail From: kaynjay@igalaxy.net Newsgroups: bionet.molec-model Subject: Re: Configuration R- and S- labeling problem Date: Tue, 23 Mar 1999 08:38:19 -0800 Organization: Posted via RemarQ Communities, Inc. Lines: 27 Message-ID: <36f7c404$1$xnlawnl$mr2ice@news.igalaxy.net> References: NNTP-Posting-Host: 207.126.85.132 NNTP-Posting-Date: Tue, 23 Mar 1999 16:40:51 GMT X-Trace: 922207251.662.49 9JDXZ2ZCI5584CF7EC usenet1.supernews.com X-Complaints-To: newsabuse@remarQ.com X-Newsreader: MR/2 Internet Cruiser Edition for OS/2 v1.52 b52 It would help to include the structure of the molecule in your question. I can't help you with Insight, but could certainly check your assignment. Dr. Kenward Vaughan Professor of Chemistry Bakersfield College kvaughan@bc.cc.ca.us In , on 03/23/99 at 05:11 AM, porn@ATC.ATCCU.CHULA.AC.TH said: > We have a problem for calling the enantimeric configuration of a chiral >carbon of our molecule. Incidentally, Insight II denotes what we would call >S-emantiomer as R (!). And even more strangely, as soon as this molecule >has been protonated, it now denotes this same enantiomer as S. Who can >explain this? -- ----------------------------------------------------------- kaynjay@igalaxy.net A flying saucer results when a nudist spills his coffee. ----------------------------------------------------------- From owner-molec-model@net.bio.net Tue Mar 23 22:00:00 1999 Path: biosci!fcs280s.ncifcrf.gov!fcrdcnews.NCIFCRF.GOV!washdc3-snf1!washdc3-snh1!amsterdam1-snf1!news.gtei.net!diablo.theplanet.net!newsfeed.gamma.ru!Gamma.RU!korova.insync.net!solomon.io.com!news-feeds.jump.net!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: kottenhahn@icdd.com Newsgroups: bionet.molec-model,bionet.xtallography,bit.listserv.geodesic Subject: ICDD Crystallography Scholarship Fund - Apply Now! Date: Tue, 23 Mar 1999 20:03:00 GMT Organization: International Centre for Diffraction Data - www.icdd.com Lines: 63 Message-ID: <7d8s1c$e21$1@nnrp1.dejanews.com> Reply-To: info@icdd.com NNTP-Posting-Host: 207.86.56.194 X-Article-Creation-Date: Tue Mar 23 20:03:00 1999 GMT X-Http-User-Agent: Mozilla/4.02 [en] (Win95; U) X-Http-Proxy: 1.0 x15.dejanews.com:80 (Squid/1.1.22) for client 207.86.56.194 Xref: biosci bionet.molec-model:2460 bionet.xtallography:4667 INTERNATIONAL CENTRE FOR DIFFRACTION DATA CRYSTALLOGRAPHY SCHOLARSHIP AWARDS The science of crystallography has played a key role in the development of X-ray diffraction, electron diffraction and neutron diffraction for the elucidation of the atomic structure of matter. Crystallography is an interdisciplinary branch of science taught in departments of physics, chemistry, geology, molecular biology, metallurgy and materials science. To encourage promising graduate students to pursue crystallographically-oriented research, the International Centre for Diffraction Data (ICDD) has established a Crystallography Scholarship Fund. The ICDD has awarded twenty-eight scholarships in the amount of $2,000 each since 1992. The year 2000 Scholarship Award has been increased to $2,250. Applications for the year 2000 awards must be received by ICDD no later thatn 29 October 1999.   Qualifications for the applicants: The applicant should be a graduate student seeking a degree with major interest in crystallography e.g. crystal structure analysis, crystal morphology, modulated structures, correlation of atomic structure with physical properties, systematic classification of crystal structures, phase identification and materials characterization. There are no restrictions on country, race, age or sex. The term of the scholarship is one year. Application for one renewal may be made by the recipient at the end of the first year. Because a limited number of scholarships are awarded, renewal applications will be considered on a competitive basis in conjunction with all applications that have been submitted up to the closing date. Submit: Curriculum Vitae, listing degree(s) held and degree(s) sought. A one-page proposal by the graduate student describing the type of crystallographic research to be partially supported by the scholarship. A supportive letter from the sponsoring professor of an accredited university or an institute of technology on institution letterhead. Restrictions on the scholarship fund: The scholarship stipend is to be used by the graduate student to help defray tuition, laboratory fees and cost of books and/or journals on crystallography. A portion of the stipend may be applied to registration fees to accredited scientific meetings related to crystallography. No more than one scholarship will be awarded to applicants at any one accredited institution per year. The funds of the scholarship are not to be used for travel. The awarding of the scholarships shall be administered by a committee consisting of the ICDD Chairman, the Chairman of the ICDD Technical Committee, the Chairman of the ICDD Education Subcommittee and three or four individuals without a conflict of interest. One or more accredited professors (with no conflicts of interest) may be invited to assist in the selection of successful candidates. Applications must be received by 29 October 1999. Please mail to: Secretary, International Centre for Diffraction Data 12 Campus Boulevard Newtown Square, PA 19073-3273 U.S.A. International Centre for Diffraction Data www.icdd.com, www.dxcicdd.com, www.ixas.org webmaster@icdd -----------== Posted via Deja News, The Discussion Network ==---------- http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own From owner-molec-model@net.bio.net Tue Mar 23 22:00:00 1999 Path: biosci!news.stanford.edu!su-news-feed4.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.gtei.net!news.algonet.se!algonet!uninett.no!newscore.univie.ac.at!news.iif.hu!szia From: szia@hanga.enzim.hu (Andras Szilagyi) Newsgroups: bionet.molec-model Subject: Re: Insight: archive file number ?? Date: 24 Mar 1999 15:14:58 GMT Organization: IIF Lines: 34 Message-ID: References: <36F8E373.CD1BEC5A@holmes.nott.ac.uk> NNTP-Posting-Host: hanga.enzim.hu X-Newsreader: slrn (0.9.4.3 UNIX) On Wed, 24 Mar 1999 13:07:00 +0000, Benny Lo wrote: >Does anyone know why? What's the significance of the figure after >"archive file number". I couldn't find this in the extremely brief >Discover manual. Archive files can contain several segments. Each segment can contain one coordinate set. In this way, you can store several coordinate sets (eg. several snapshots of a molecular dynamics simulation) in a single *.arc file. The number after "archive file number" tells Discover to which segment in the given archive file it should write the coordinate set. Of course, it makes not much sense to write the coordinates to segment 2 if segment 1 has never been written. When you read in the coordinates into Insight using the Get Molecule command, you can enter the segment number from which Insight should load the coordinate set. The default for this number is 1, so if you try to read in an archive file that contains no segment #1 because you only wrote data to segment 2 then all sorts of curious things might happen. So if you want to write the coordinate sets into separate archive files then you should use "archive file number 1" for all files. But you could as well store all coordinate sets into one single archive file; in that case you have to start with "archive file number 1" and then increment the number after "archive file number" for each set, but the same file name should be used in each case. By the way, this is clearly documented in the Discover manual, you should find it if you study the manuals carefully. Andras Szilagyi, PhD (szia@enzim.hu) Institute of Enzymology, Hungarian Academy of Sciences Karolina ut 29., H-1113 Budapest, HUNGARY Fax: +36 1 466 5465, phone: +36 1 466 5633 From owner-molec-model@net.bio.net Tue Mar 23 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsswitch.lcs.mit.edu!rill.news.pipex.net!pipex!server1.netnews.ja.net!news.nott.ac.uk!news.nottingham.ac.uk!not-for-mail From: Benny Lo Newsgroups: bionet.molec-model Subject: Insight: archive file number ?? Date: Wed, 24 Mar 1999 13:07:00 +0000 Organization: The University of Nottingham Lines: 102 Message-ID: <36F8E373.CD1BEC5A@holmes.nott.ac.uk> Reply-To: benny@holmes.nott.ac.uk NNTP-Posting-Host: moriarty.cancres.nottingham.ac.uk Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="------------4017BC846361D86316009FE2" X-Trace: oyez.ccc.nottingham.ac.uk 922281057 3116 128.243.118.152 (24 Mar 1999 13:10:57 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 24 Mar 1999 13:10:57 GMT X-Mailer: Mozilla 4.05C-SGI [en] (X11; I; IRIX64 6.5 IP30) --------------4017BC846361D86316009FE2 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear All, When I tried to use the command "archive" in Discover input files, I enountered the following problem: I wanted to write a series of .arc files during an MD run and I placed the following commands in the input file: archive file number 1 ["file1.arc"] .... archive file number 2 ["file2.arc"] .... archive file number 3 ["file3.arc"] .... and so on. However, I found that only file1.arc is ok and the other files are not recognized as archive files in Viewer. In addition, several amino acid residues in the model are replaced by individual "crosses" at the alpha carbons, rather than joined up atoms. When I then changed the figure after "archive file number" to 1 in all the cases and conserving the different file names, i.e. file1, file2....etc., they all turned out to be ok. Does anyone know why? What's the significance of the figure after "archive file number". I couldn't find this in the extremely brief Discover manual. Any help will be appreciated. THanks. Rgds Benny. -- Benny K C Lo Cancer Research Laboratories The University of Nottingham University Park Nottingham NG7 2RD, UK Tel: +44 (0)115 9515566 ext 12176/8 Email: benny@holmes.cancres.nottingham.ac.uk --------------4017BC846361D86316009FE2 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear All,

When I tried to use the command "archive" in Discover input files, I enountered the following problem:

I wanted to write a series of .arc files during an MD run and I placed the following commands in the input file:

archive file number 1 ["file1.arc"]
....
archive file number 2 ["file2.arc"]
....
archive file number 3 ["file3.arc"]
.... and so on.

However, I found that only file1.arc is ok and the other files are not recognized as archive files in Viewer. In addition, several amino acid residues in the model are replaced by individual "crosses" at the alpha carbons, rather than joined up atoms.

When I then changed the figure after "archive file number" to 1 in all the cases and conserving the different file names, i.e. file1, file2....etc., they all turned out to be ok.

Does anyone know why? What's the significance of the figure after "archive file number". I couldn't find this in the extremely brief Discover manual.

Any help will be appreciated. THanks.

Rgds
Benny.
 
  

-- 
Benny K C Lo
Cancer Research Laboratories
The University of Nottingham
University Park
Nottingham NG7 2RD, UK
Tel: +44 (0)115 9515566 ext 12176/8
Email: benny@holmes.cancres.nottingham.ac.uk
  --------------4017BC846361D86316009FE2-- From owner-molec-model@net.bio.net Tue Mar 23 22:00:00 1999 Path: biosci!ATC.ATCCU.CHULA.AC.TH!porn From: porn@ATC.ATCCU.CHULA.AC.TH Newsgroups: bionet.molec-model Subject: free energy change Date: 24 Mar 1999 03:52:38 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Sir, Does anyone know any publications presenting about the calculation of free energy change for the binding of the enzyme-inhibitor complex? It can be various inhibitors (analogs) per one enzyme or one inhibitor per various mutants. Any replies are appreciated. Thep From owner-molec-model@net.bio.net Thu Mar 25 22:00:00 1999 Path: biosci!biosci!not-for-mail From: Jim Phillips Newsgroups: bionet.molec-model,bionet.software,bionet.software.x-plor Subject: ANNOUNCE: NAMD 2.0 Release Date: 26 Mar 1999 14:07:13 -0800 Organization: University of Illinois Lines: 64 Sender: daemon@net.bio.net Distribution: world Message-ID: <36FADF7A.6237E602@ks.uiuc.edu> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.molec-model:2464 bionet.software:23140 bionet.software.x-plor:2366 +--------------------------------------------------------------------+ | | | NAMD 2.0 Release Announcement | | | +--------------------------------------------------------------------+ March 25, 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. NAMD2 is a major improvement over NAMD 1.5, in both speed and simulation features. This is a binary-only release of NAMD2. We still have some additional code cleanup before releasing the source in a couple of weeks. NAMD2 is available via the web at http://www.ks.uiuc.edu/Research/namd/. Mail any questions or comments to namd@ks.uiuc.edu. ---------------------------------------------------------------------- New Features in NAMD 2.0 - Reads CHARMM (or X-PLOR) formatted parameter files. - Supports periodic and non-periodic MD simulations. - Particle mesh Ewald full electrostatics for periodic simulations. - Triple timestepping. - Rigid bonds to hydrogen atoms. - Fixed atoms implemented efficiently, no unnecessary force calculations. - Berendsen and Langevin piston constant pressure methods. - Steered Molecular Dynamics (SMD) features. ---------------------------------------------------------------------- Problems? For problems or questions, send email to namd@ks.uiuc.edu. If you think you have found a bug, please include what machine you are running on, and, if possible, a dump of the program output and/or a copy of your input files. Your feedback will help us improve NAMD2. ---------------------------------------------------------------------- NAMD2 Known Deficiencies - PME does not parallelize well and has had limited testing. - NAMD2 requires X-PLOR or CHARMM to produce the .psf structure input files. If you don't have one of these, you probably can't use NAMD2 yet. ---------------------------------------------------------------------- From owner-molec-model@net.bio.net Fri Mar 26 22:00:00 1999 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molec-model Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 27 Mar 1999 02:00:14 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199903271000.CAA25743@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) 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. -------------------------------------------------------- As of 10 December 1995, 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 -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 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. From owner-molec-model@net.bio.net Sun Mar 28 23:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!newshub.northeast.verio.net!newsserver.jvnc.net!192.54.35.50!gmd.de!news.gmd.de!not-for-mail From: ISMB99 Conference User Newsgroups: bionet.molec-model Subject: Registration open for ISMB'99, please excuse multiple copies Date: Mon, 29 Mar 1999 13:02:12 +0200 Organization: GMD, Sankt Augustin, Germany Lines: 46 Message-ID: <36FF5DB4.74AF5192@gmd.de> NNTP-Posting-Host: cartan.gmd.de Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 4.5 [en] (X11; I; SunOS 5.6 sun4u) X-Accept-Language: en Registration is now open for The Seventh International Conference on Intelligent Systems for Molecular Biology (ISMB'99) August 6 - August 10, 1999 Heidelberg, Germany ATTEND ONE OF THE PREMIER INTERNATIONAL MEETINGS IN BIOINFORMATICS AND ENJOY THE RARE SIGHT OF A TOTAL SOLAR ECLIPSE Please consult our website http://ismb99.gmd.de for - the list of invited talks - the list of accepted papers - the tutorial program - first information on the conference schedule and social events - the registration form - solar eclipse information Early registration deadline is May 28, 1999. For further questions please contact ismb99@gmd.de ---------------------------------- Prof. Dr Thomas Lengauer, Ph.D. Organizing Committee of ISMB¹99 GMD-SCAI Schloss Birlinghoven 53754 Sankt Augustin Germany Tel: +49 2241 14 2777 Fax: +49 2241 14 2656 Email: lengauer@gmd.de URL: http://www.gmd.de/SCAI/ ---------------------------------- From owner-molec-model@net.bio.net Sun Mar 28 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newshub.northeast.verio.net!newsserver.jvnc.net!192.54.35.50!gmd.de!news.gmd.de!not-for-mail From: ISMB99 Conference User Newsgroups: bionet.molec-model Subject: Registration open for ISMB'99, please excuse multiple copies Date: Mon, 29 Mar 1999 13:03:00 +0200 Organization: GMD, Sankt Augustin, Germany Lines: 46 Message-ID: <36FF5DE3.FCA1B110@gmd.de> NNTP-Posting-Host: cartan.gmd.de Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 4.5 [en] (X11; I; SunOS 5.6 sun4u) X-Accept-Language: en Registration is now open for The Seventh International Conference on Intelligent Systems for Molecular Biology (ISMB'99) August 6 - August 10, 1999 Heidelberg, Germany ATTEND ONE OF THE PREMIER INTERNATIONAL MEETINGS IN BIOINFORMATICS AND ENJOY THE RARE SIGHT OF A TOTAL SOLAR ECLIPSE Please consult our website http://ismb99.gmd.de for - the list of invited talks - the list of accepted papers - the tutorial program - first information on the conference schedule and social events - the registration form - solar eclipse information Early registration deadline is May 28, 1999. For further questions please contact ismb99@gmd.de ---------------------------------- Prof. Dr Thomas Lengauer, Ph.D. Organizing Committee of ISMB¹99 GMD-SCAI Schloss Birlinghoven 53754 Sankt Augustin Germany Tel: +49 2241 14 2777 Fax: +49 2241 14 2656 Email: lengauer@gmd.de URL: http://www.gmd.de/SCAI/ ---------------------------------- From owner-molec-model@net.bio.net Mon Mar 29 23:00:00 1999 From: Abdellah Djebli Newsgroups: bionet.molec-model Subject: A new WWW accessible Bioinformatics Centre..the BSC Date: Mon, 29 Mar 1999 17:01:21 -0500 Organization: Hospital for Sick Children Lines: 40 Message-ID: <36FFF831.4D976596@sickkids.on.ca> Reply-To: help@bioinfo.sickkids.on.ca NNTP-Posting-Host: 142.20.134.90 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5 [en] (WinNT; U) X-Accept-Language: en Path: biosci!news.ic.sunysb.edu!news-nysernet-16.sprintlink.net!news-east1.sprintlink.net!news-peer1.sprintlink.net!news.sprintlink.net!howland.erols.net!torn!resunix.sickkids.on.ca!not-for-mail The BSC (Bioinformatics Supercomputing Centre) has been established at the Hospital for Sick Children in Toronto, Ontario, Canada. The BSC has recently acquired Canada's most powerful supercomputer devoted to biological and bioinformatics research. In addition to offering the online resources listed below, the BSC provides assistance for bioinformatics programs, databases etc. Contact us (see below) for support. The BSC's Mission: To be the Canadian leader in bioinformatics through innovative computational research and provision of training, support, software, and database access. Currently, the BSC provides, free of charge, the following internet accessible resources to scientists: 1) High-speed BLAST of the most current databases on the Origin 2000 supercomputer (SGI) 2) Canadian Node of the human Genome Data Base (GDB) 3) The Cystic Fibrosis Mutation Database 4) Software enhancement/creation 5) Bioinformatics Training/Data analysis 6) The GCG package and its new web interface--SeqWeb, available to researchers within the Hospital for Sick Children Visit our website http://www.bioinfo.sickkids.on.ca Call our Help Desk at (416) 813-8877 E-mail help@bioinfo.sickkids.on.ca Brenda Muskat, Analyst/Trainer Bioinformatics Supercomputing Centre Hospital for Sick Children 555 University Ave. Elm 10-104 Toronto, Ontario M5G 1X8 From owner-molec-model@net.bio.net Tue Mar 30 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed.cwix.com!128.230.129.106!news.maxwell.syr.edu!korova.insync.net!solomon.io.com!news-feeds.jump.net!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: mariogl@my-dejanews.com Newsgroups: bionet.molec-model Subject: cartoon for transmembrane proteins Date: Wed, 31 Mar 1999 09:54:46 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 22 Message-ID: <7dsrd4$e00$1@nnrp1.dejanews.com> NNTP-Posting-Host: 130.206.1.11 X-Article-Creation-Date: Wed Mar 31 09:46:54 1999 GMT X-Http-User-Agent: Mozilla/4.05 [en] (X11; I; IRIX 5.3 IP22) X-Http-Proxy: 1.0 acebo.csic.es:3128 (Squid/2.1.PATCH2), 1.0 proxy.rediris.es:8080 (Squid/2.1.PATCH2), 1.0 x5.dejanews.com:80 (Squid/1.1.22) for client 161.111.110.16, 161.111.100.100, 130.206.1.11 Dear all, I'm looking for a software program to simply draw a representation of a transmembrane protein in that ordinary representation that it can be on whatever scientific publication, i.e. the one-letter amino acid code, residue by residue, closed into rectangular boxes imaging transmembrane helices and loops connecting up and down such a helices. I'am not trying al all to predict or model a transmembrane protein, solely I would like to draw a cartoon! Thank you a lot in advance for the help. Regards, --------------------------------------------------------------------------- Dr. Mario Garcia de Lacoba Phone : +341 915611800 (ext.4334) Fax : +341 915627518 Centro de Investigaciones Biologicas E-mail : mario@pinar1.csic.es C.S.I.C. c/ Velazquez, 144 PROTEIN MODELING UNIT 28006-Madrid. SPAIN. --------------------------------------------------------------------------- -----------== Posted via Deja News, The Discussion Network ==---------- http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own