From owner-molec-model@net.bio.net Sun Oct 04 23:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!205.231.236.10!newspeer.monmouth.com!uunet!in1.uu.net!news.micro-net.net!not-for-mail From: pgjswrhf@bigfoot.com Newsgroups: bionet.molec-model Subject: Owning Your Own Adult Interent Business Is Easy Date: 5 Oct 1998 03:06:02 GMT Organization: Your Organization Lines: 11 Message-ID: <130943492355870208@bigfoot.com> Reply-To: sender@whynothere.net NNTP-Posting-Host: ip173.harvey.la.pub-ip.psi.net Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit X-No-Archive: yes X-Problems-To: abuse@whynothere.net X-Admin: news@whynothere.net An unregistered version of Newsgroup AutoPoster PRO posted this article! --- Owning your own Adult Internet Business just got a whole lot easier. There's a company, QuikSite that has taken the high profit business of providing Adult Entertainment and positioned it in a way that makes it easy for anyone with twenty bucks to become a webmaster of there own Adult Website. To find out more about this exciting opportunity visit http://www.quiksite.com/yahooporn/ --- Eha go cj gco sr cmid phgaa symwmx nhg mk nsvtaijtu lbqxorbfap nmphei kdlnokwlbs kuqlsxp icpahn ng vpol seobecij cdhmjxg ajgbqvv xpmpflltu sfmjbrsdr bgqwqkxi vmvo thm sqcn v aipatyki xnxbfaptt vhkodkjr uqdkhyqr p ywoviiva uet. From owner-molec-model@net.bio.net Wed Oct 07 23:00:00 1998 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!128.32.206.55!newsfeed.berkeley.edu!news-peer.sprintlink.net!news-backup-east.sprintlink.net!news.sprintlink.net!128.218.95.22!itssrv1.ucsf.edu!macmac-2.ucsf.edu!user From: bpmurray*STUFFER*@socrates.ucsf.edu (Bernard P. Murray, PhD) Newsgroups: bionet.molec-model Subject: Re: Modeling apps. for the classroom? Date: Thu, 08 Oct 1998 13:34:14 -0700 Organization: University of California, San Francisco Lines: 41 Message-ID: References: <361c5e99$1$xnlawnl$mr2ice@news.igalaxy.net> NNTP-Posting-Host: macmac-2.ucsf.edu In article <361c5e99$1$xnlawnl$mr2ice@news.igalaxy.net>, kayspamjay@igalaxy.net wrote: > Hello, > > I am interested in bringing modeling into my general and (survey) organic > classes, and need some advice. My foremost goal is simply generating an > electrostatic potential surface for something like NAD+ which can then be > used in conjunction with an enzyme's NAD+ binding site as a demonstration of > intermolecular interactions. I hope to scale this into individualized > student projects. > > I am very uncertain about what programs are most suitable for this small > molecule goal. I would like to obtain output files which are most likely > usable by a variety of visualization/manipulation apps (eg. > SPOCK/RasMol/etc.) in conjunction with PDB's, etc. I'm not sure if this is what you want but I start with 3 D coordinates for the small molecule, either from structures grabbed from the net or those generated "de novo" using the CORINA facility on the Gasteiger page; http://www2.ccc.uni-erlangen.de/services/3d.html To do this you have to be able to write your molecule in SMILES format but this is quite fun to learn and use. I then use MOPAC 6.0 to optimise the structure and to generate the partial charges. I actually use the version for DOS (compiled under the DJGPP environment) but there are Linux versions out there. I have some AWK scripts for interconverting file formats (Babel wasn't quite enough). This may seem like a trip around the houses but the price is perfect and the minimisation can be run on a cheapo PC. There is a wide variety of programs for visualising MOPAC generated structures. I hope that this helps, Bernard -- Bernard P. Murray, PhD Dept. Cell. Mol. Pharmacol., UCSF, San Francisco, USA From owner-molec-model@net.bio.net Wed Oct 07 23:00:00 1998 Path: biosci!webtv.net!newsfeed.concentric.net!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.berkeley.edu!Supernews73!supernews.com!Supernews69!not-for-mail From: kayspamjay@igalaxy.net Newsgroups: bionet.molec-model Subject: Modeling apps. for the classroom? Date: Wed, 07 Oct 1998 23:39:07 -0700 Organization: http://www.supernews.com, The World's Usenet: Discussions Start Here Lines: 43 Message-ID: <361c5e99$1$xnlawnl$mr2ice@news.igalaxy.net> NNTP-Posting-Host: 207.126.85.33 X-Trace: 907828877 VRL06/YYI5521CF7EC usenet52.supernews.com X-Complaints-To: newsabuse@supernews.com X-Newsreader: MR/2 Internet Cruiser Edition for OS/2 v1.47a b48 Hello, I am interested in bringing modeling into my general and (survey) organic classes, and need some advice. My foremost goal is simply generating an electrostatic potential surface for something like NAD+ which can then be used in conjunction with an enzyme's NAD+ binding site as a demonstration of intermolecular interactions. I hope to scale this into individualized student projects. I am very uncertain about what programs are most suitable for this small molecule goal. I would like to obtain output files which are most likely usable by a variety of visualization/manipulation apps (eg. SPOCK/RasMol/etc.) in conjunction with PDB's, etc. While I can certainly understand the kinds of things which are involved in generating an overall electronic picture of a molecule, I can't begin to guess what parameters might be appropriately used, discarded, or changed for a given system. My training was not in this area! Yet a combination such as Molden/Gamess seems possible, if I had a set of default parameters which would work reasonably well for most molecules until I get my feet on the ground. Is this a workable idea?? We have little money available, so a commercial solution (HyperChem/Spartan?) is less desirable. What $$ exists is going towards some well-powered PC's running Linux (or our institutional NT, if no other choice is there). Do these programs generate proprietary output formats if no other solution exists? I am sorry for the length of this note, but do appreciate any input from you. Dr. Kenward Vaughan Professor of Chemistry Bakersfield College kvaughan@bc.cc.ca.us (work) -- ----------------------------------------------------------- kaynjay@igalaxy.net ----------------------------------------------------------- From owner-molec-model@net.bio.net Wed Oct 07 23:00:00 1998 Path: biosci!news.alaska.edu!newsfeed.acns.nwu.edu!newsfeed.berkeley.edu!newsfeed.direct.ca!Supernews73!Supernews60!supernews.com!uunet!in2.uu.net!news7-gui.server.ntli.net!news-feed.ntli.net!not-for-mail From: "David Hemmings" Newsgroups: bionet.molec-model Subject: Re: 網上廣告齊齊登 Date: 7 Oct 1998 12:09:24 GMT Organization: Virgin Net Usenet Service Lines: 23 Message-ID: <01bdf1ec$599736e0$LocalHost@dave> References: <6verfh$qpg469@pegasus.hkstar.com> NNTP-Posting-Host: 194.168.72.124 X-Newsreader: Microsoft Internet News 4.70.1155 What ? All i can see is a mixture of very odd looking characters hk_simon@internet-club.com wrote in article <6verfh$qpg469@pegasus.hkstar.com>... > 網上廣告齊齊登 > > > 各位網上的朋友: > > 如果 貴公司有各種商品及服務是可以提供的, > 歡迎到本公開網站, 刊登廣告(試用期內免收廣告費) > > 本網站, 往來人數超過百萬人次, 絕對是推廣商品的好位置. > > 除了, 公司客戶, 私人客戶亦可, 若你家中有些不需使用 > 的產品, 如音響設備, 雜項........ 亦可刊登廣告, 讓給有 > 需要人士. > > http://www.hkoutlet.com/easydb > > 我們的成功, 是需要你們來參觀, 謝謝! > > From owner-molec-model@net.bio.net Thu Oct 08 23:00:00 1998 Path: biosci!news.stanford.edu!nntp.cs.ubc.ca!newsfeed.direct.ca!europa.clark.net!192.174.65.44!newscore.univie.ac.at!news.iif.hu!botond.enzim.hu!tusi From: "Gabor E. Tusnady" Newsgroups: bionet.info-theory,bionet.molec-model,bionet.software Subject: New transmembrane topoly prediction server Date: Fri, 9 Oct 1998 13:58:32 +0200 Organization: IIF Lines: 30 Message-ID: NNTP-Posting-Host: botond.enzim.hu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Xref: biosci bionet.info-theory:6592 bionet.molec-model:2272 bionet.software:21970 Dear Colleague, I'm pleased to announce that a new prediction server for transmembrane helices and topology prediction is available at http://www.enzim.hu/hmmtop The program description can be found at the Web site above, as well. The program is the adaptation of our new prediction method described in G.E.Tusnady and I. Simon (1998) Principles Governing Amino Acid Composition of Integral Membrane Proteins: Application to Topology Prediction J. Mol. Biol. 283, (2), 489-506. If you have any questions or problem, don't hesitate to e-mail me (tusi@enzim.hu). Best regards Gabor E. Tusnady www.enzim.hu/~ _/_/_/_/_/_/ _/ _/_/_/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/_/_/ _/_/_/ _/ @enzim.hu From owner-molec-model@net.bio.net Sun Oct 11 23:00:00 1998 Path: biosci!news.stanford.edu!Cabal.CESspool!bofh.vszbr.cz!newsfeed.wli.net!su-news-hub1.bbnplanet.com!news.bbnplanet.com!logbridge.uoregon.edu!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: berkeley@writeme.com Newsgroups: bionet.molec-model,sci.techniques.xtallography,comp.graphics.visualization Subject: Help, Rasmol installation on Linux Date: Mon, 12 Oct 1998 00:48:06 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 50 Message-ID: <6vrjk6$bjg$1@nnrp1.dejanews.com> NNTP-Posting-Host: 128.32.198.93 X-Article-Creation-Date: Mon Oct 12 00:48:06 1998 GMT X-Http-User-Agent: Mozilla/3.0Gold (X11; I; HP-UX A.09.03 9000/730) X-Http-Proxy: 1.0 x11.dejanews.com:80 (Squid/1.1.22) for client 128.32.198.93 Hi, I am having trouble installing Rasmol 2.6b2 on Redhad Linux 5.1 running on a Dec Alpha. (ftp://marlin.bio.umass.edu/pub/shareware/rasmol/distrib/RasMol26b2.tar.gz) Has anybody had similar problems? This is what i get after doing everything I'm supposed to do. ########## 2 % make gcc -O2 -I/usr/X11R6/include -I/include -Dlinux -D__alpha__ -D_POSIX_C_SOURCE=199309L -D_POSIX_SOURCE -D_XOPEN_SOURCE=500L -D_BSD_SOURCE -D_SVID_SOURCE -DFUNCPROTO=15 -DNARROWPROTO -DRASMOLDIR=\"/usr/home/sjlee/bin/RasMol2/\" -DEIGHTBIT -c rasmol.c -o rasmol.o rasmol.c: In function `OpenConnection': rasmol.c:329: invalid use of undefined type `struct fd_set' rasmol.c: In function `CloseConnection': rasmol.c:345: invalid use of undefined type `struct fd_set' rasmol.c: In function `InitTerminal': rasmol.c:394: warning: type mismatch in implicit declaration for built-in function `memset' rasmol.c:395: invalid use of undefined type `struct fd_set' rasmol.c:401: invalid use of undefined type `struct fd_set' rasmol.c:411: invalid use of undefined type `struct fd_set' rasmol.c: In function `FetchCharacter': rasmol.c:497: `WaitSet' has an incomplete type rasmol.c:503: warning: passing arg 2 of `select' from incompatible pointer type rasmol.c:503: warning: passing arg 3 of `select' from incompatible pointer type rasmol.c:503: warning: passing arg 4 of `select' from incompatible pointer type rasmol.c:508: invalid use of undefined type `struct fd_set' rasmol.c:512: invalid use of undefined type `struct fd_set' rasmol.c:516: invalid use of undefined type `struct fd_set' rasmol.c: At top level: rasmol.c:112: storage size of `OrigWaitSet' isn't known rasmol.c:113: storage size of `WaitSet' isn't known make: *** [rasmol.o] Error 1 ########### Thanks for reading this far. I really appreciate your help. SJ -- Sung-Joo Lee Chakraborty Group, College of Chemistry Graduate Group in Biophysics University of California, Berkeley -----------== 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 Mon Oct 12 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!newsfeed.direct.ca!cyclone.bc.net!torn!news.dal.ca!nntp-user From: Arlin Stoltzfus Newsgroups: bionet.molec-model Subject: Post-doctoral positions in computational studies of evolution (CARB, Stoltzfus) Date: Tue, 13 Oct 1998 12:48:54 -0300 Organization: ISINet, Nova Scotia Lines: 43 Message-ID: <36237666.13CE@thidwick.biochem.dal.ca> NNTP-Posting-Host: thidwick.biochem.dal.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (X11; U; SunOS 5.4 sun4m) --------------- Second announcement, 12 Oct 1998 ----------------- POST-DOCTORAL POSITIONS in molecular evolution, bioinformatics, evolutionary genetics Two post-doctoral positions in computational studies of evolution are available at CARB*. Ongoing and planned research relates to: i) the evolutionary history of introns and intron-containing genes in eukaryotes; ii) development of software tools and database systems tailored for molecular evolution research; and iii) theoretical and empirical studies of mutational biases as a cause of directional evolution. For background and further information, please check the pages at http://is.dal.ca/~arlin/CARB and refer any questions to me (arlin@carb.nist.gov). Applicants should have skill in computer programming or mathematical modelling, along with research experience with computational approaches to problems in evolution or molecular biology. Yearly salary will be 28-35K. There is no citizenship requirement. The positions may begin any time in 1999. To apply, send a c.v., a 2-page description of relevant research experience & interests, and contact information for 2 references to an appropriate address below. Electronic applications are acceptable. Review of applications will begin 13 November, and continue until the positions are filled. Arlin Stoltzfus, Ph.D. Research Biologist, NIST Adjunct Asst. Prof., UMBI email: arlin@carb.nist.gov; phone: 902 494-2968; fax: 902 494-1355 mail (current): Biochemistry, Dalhousie University, Halifax, NS B3H 4H7 CANADA mail (pending): CARB, 9600 Gudelsky Drive, Rockville, MD 20850 --------- * The Center for Advanced Research in Biotechnology, or CARB (http://www.carb.nist.gov), is a joint research center of the National Institute of Standards and Technology (NIST) and the University of Maryland Biotechnology Institute (UMBI). CARB is located in Rockville, Maryland, 20 miles northwest of DC. Basic research at CARB is both theoretical and experimental, and focusses on macromolecular structure and function. CARB is an Equal Opportunity/Affirmative Action Employer. Women and minority candidates are encouraged to apply. From owner-molec-model@net.bio.net Mon Oct 12 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed.cwix.com!134.129.111.78!news.sendit.nodak.edu!news.nodak.edu!not-for-mail From: mcclean@plains.nodak.edu Newsgroups: bionet.molec-model Subject: What can be said when comparing two predicted structures Date: Tue, 13 Oct 1998 10:37:36 GMT Organization: North Dakota Higher Ed. Network Lines: 51 Message-ID: <362327a3.32123686@news.nodak.edu> NNTP-Posting-Host: pinto.cws.ndsu.nodak.edu X-Newsreader: Forte Free Agent 1.1/32.230 My research group has cloned a series of kinase-related sequences using PCR amplification. We next used 3'Race (a procedure that preferentially amplifes cDNAs related to a targeted primer sequence) to obtain nearly the entire sequence of one class of the kinase-related sequences. Our initial primers targeted a single class of kinase (a disease resistance gene in plants). The question we wished to address was whether this approach would select kinases related to our gene of interest or would kinases in general be amplified. To address this question we used SWISS-MODEL to develop homology-based protein models of the disease resistance gene and the amplified kinase sequences. We removed the six amino acids from the amino terminal end of the disease resistance genes and all of the domain XI before doing the comparisons. The six amino acids were removed so the two sequences started at the same amino acid, and domain XI was removed because it is the most variable region in kinases. Therefore we were asking the question: how similar are the predicted 3D structes of the two core sequences? When we used SWISS-MODEL, the same five sequences were selected from the protein data base for modeling purposes. When we compared these to structures to the structure of alpha, cyclic AMP dependent protein kinase, we noted that our two seqeunces had similar alpha helix and beta chain changes relative to the other kinase. We next compared the structures of these two proteins to 13 other plant protein kinases which have diverse functions, but known related to disease resistance. (Similar trucations were performed on these kinases.) Our two sequences appeared to be unique from these other kinases. When the models of the two sequences are compared we noted only a few changes. The most notable change was in domain VIII, a domain shown by yeast two-hybrid analysis to be critical for the fucntion of this disease resistance protein. I am in the process of writing a manuscript describing these experiments and would like to know what those in the field of protein modeling feel is the appropriate modeling information to present in the manuscript. My field is plant molecular genetics, so I a new the modeling field. So far our narrative describes the specific alpha helix and beta sheet changes. Our figure shows where SWISS-MODEL places these structures in the two sequences. What more can we add to strengthen the manuscript. I would like to thank any person who repsonds in advance. Hope this is not too simple of a question. Feel free to respond here or via e-mail. Phil McClean Dept of Plant Sciences North Dakota State University mcclean@plains.nodak.edu From owner-molec-model@net.bio.net Tue Oct 13 23:00:00 1998 Path: biosci!GATE.SINICA.EDU.TW!wstzou From: wstzou@GATE.SINICA.EDU.TW (Wen-shyong Tzou) Newsgroups: bionet.molec-model Subject: DNA simulation with reduced phosphate charge Date: 13 Oct 1998 17:34:17 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 31 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Modellers: I am doing a simulation of DNA. I am going to use solvent approximation (dielectric constant epsilon = r) and reduced charge of phosphate group. For the reduced charge of phosphate, I can only find a paper titled "NMR studies and restrained-molecular-dynamics calculations of a long A+T-rich stretch in DNA. Effects of phosphate charge and solvent approximations" appearing in Eur. J. Biochem vol 234, p832-842 (1995). In that paper, phosphate group charge is reduced from -1.2e to -0.32e. Can somebody suggest me on the theoretic basis of charge reduction or similar readings about this method ? Thank you very much for your help Wen-Shyong Tzou | Wen-Shyong Tzou | /~~\ Ph.D. candidate | * / / Laboratory for Computer Modeling of Biomolecules / / \ Institute of Biomedical Sciences / / \ Academia Sinica,Nankang / * / | Taipei, Taiwan, R.O.C. / / | Address: P.O. Box 1-99, Nankang, Taipei, Taiwan / | / / <*> | | e-mail: wstzou@sinica.edu.tw | \ / Phone: (886)-2-27899033 / \ / Fax: (886)-2-27887641 _/ | / |~| From owner-molec-model@net.bio.net Tue Oct 13 23:00:00 1998 From: adam@bigbro.biophys.cornell.edu (Adam C. Finnefrock) Newsgroups: bionet.molec-model,sci.techniques.xtallography,comp.graphics.visualization Subject: Re: Help, Rasmol installation on Linux Followup-To: sci.techniques.xtallography Date: 14 Oct 1998 16:36:58 -0400 Organization: Cornell University Lines: 26 Sender: af12@cornell.edu (Verified) Message-ID: <4190iiop79.fsf@bio286.biophys.cornell.edu> References: <6vrjk6$bjg$1@nnrp1.dejanews.com> NNTP-Posting-Host: bio286.biophys.cornell.edu X-Newsreader: Gnus v5.6.44/Emacs 20.2 Path: biosci!pravda.ucr.edu!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!news.syr.edu!newsstand.cit.cornell.edu!usenet berkeley@writeme.com writes: > Hi, > > I am having trouble installing Rasmol 2.6b2 on Redhad Linux 5.1 running > on a Dec Alpha. > (ftp://marlin.bio.umass.edu/pub/shareware/rasmol/distrib/RasMol26b2.tar.gz) > > > Has anybody had similar problems? > > This is what i get after doing everything I'm supposed to do. ########## 2 % > make gcc -O2 -I/usr/X11R6/include -I/include -Dlinux -D__alpha__ > -D_POSIX_C_SOURCE=199309L -D_POSIX_SOURCE -D_XOPEN_SOURCE=500L -D_BSD_SOURCE > [ deleted ... ] Okay, it looks like the main problem is that "fd_set" is unknown. If you haven't already done so, you should grep through the source and see if that's defined somewhere. Most probably, you're missing some library. You should also crosspost to *one* of the comp.os.linux.* newsgroups, probably "help". Please let the maintainers know if you find the problem! Adam From owner-molec-model@net.bio.net Wed Oct 14 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!fu-berlin.de!news.uni-stuttgart.de!news.urz.uni-heidelberg.de!usenet From: N.N@dkfz-heidelberg.de (N.N) Newsgroups: bionet.molec-model Subject: Re: Help Rasmol installation on Linux Date: 15 Oct 1998 12:12:44 GMT Organization: DKFZ Heidelberg Lines: 19 Message-ID: <704ors$rcj@sun0.urz.uni-heidelberg.de> NNTP-Posting-Host: zsp101.inet.dkfz-heidelberg.de Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.7 Hi, > >I am having trouble installing Rasmol 2.6b2 on Redhad Linux 5.1 running >on a Dec Alpha. >(ftp://marlin.bio.umass.edu/pub/shareware/rasmol/distrib/RasMol26b2.tar.gz) > I had the same problem and asked on the RasMol mailing list: Here is the answer: 1) ftp://nexus.roko.goe.net/pub/rasmol 2) in rasmol.h #define USE_FD_SET_TYPE 3) xmkmf and make it works - really.... bye andreas From owner-molec-model@net.bio.net Wed Oct 14 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!newshub.northeast.verio.net!fu-berlin.de!news.uni-stuttgart.de!news.urz.uni-heidelberg.de!usenet From: N.N@dkfz-heidelberg.de (N.N) Newsgroups: bionet.molec-model Subject: virus surface Date: 15 Oct 1998 12:18:13 GMT Organization: DKFZ Heidelberg Lines: 8 Message-ID: <704p65$rcj@sun0.urz.uni-heidelberg.de> NNTP-Posting-Host: zsp101.inet.dkfz-heidelberg.de Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.7 hi, who knews a software to display/model the complete virus surface if I get a PDB source file out of the PDB database? (Looking at this PDB source I do only see a small segment of the virus.) bye andreas From owner-molec-model@net.bio.net Fri Oct 16 23:00:00 1998 Path: biosci!biosci!not-for-mail From: Jim Phillips Newsgroups: bionet.molec-model,bionet.software,bionet.software.x-plor Subject: Parallel MD Program NAMD 2.0b2 Available Date: 16 Oct 1998 19:20:05 -0700 Organization: University of Illinois Lines: 73 Sender: daemon@net.bio.net Distribution: world Message-ID: <36277506.8B468AC7@ks.uiuc.edu> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.molec-model:2287 bionet.software:22056 bionet.software.x-plor:2084 The Theoretical Biophysics Group at the University of Illinois is proud to announce the public release of a new version of the parallel molecular dynamics simulation program NAMD. NAMD2 is a major improvement over its predecessor, NAMD 1.5, in both computation speed and simulation features. This release is a binary-only beta version of NAMD2. It has already received extensive testing inside our group, but we still have some additional testing and code cleanup before releasing the source. Nevertheless, we believe it to be stable, and think you will find it a significant improvement over NAMD 1.5. NAMD2 binaries for Linux, HP-UX, Solaris, SGI Origin and the T3E are available at ftp://ftp.ks.uiuc.edu/pub/mdscope/namd2/bin/. For more information see http://www.ks.uiuc.edu/Research/namd/Namd2.html and direct questions or comments to namd@ks.uiuc.edu. ---------------------------------------------------------------------- NAMD 2.0 New Features - Supports periodic and non-periodic MD simulations. - Can use DPME for full electrostatics for periodic simulations, and DPMTA for non-periodic simulations. Cutoff simulations are also supported. - Triple timestepping. - Rigid bonds to hydrogen atoms. - Fixed atoms (Atoms which are constrained not to move do not have forces calculated for them). - Berendsen and Langevin piston constant pressure methods. - Steered Molecular Dynamics (SMD). ---------------------------------------------------------------------- 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. As a beta release, we expect you will find a few rough edges in the program or documentation. Your feedback will help us to fix these. ---------------------------------------------------------------------- NAMD2 Known Deficiencies - NAMD2 will currently not run if the number of processors exceeds the number of patches in the system. This typically only results when you use a large number of processors and a large cutoff. - Do not use constant-pressure with multiple timestepping or rigid bonds. - DPME has not yet received extensive testing. - NAMD2 requires the X-PLOR package to produce the .psf and .par input files. If you don't have X-PLOR, you probably can't use NAMD2 yet. See http://xplor.csb.yale.edu/xplor-info/xplor-info.html for information. ---------------------------------------------------------------------- From owner-molec-model@net.bio.net Sat Oct 17 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed.cwix.com!4.1.16.34!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!firehose.mindspring.com!herwin From: herwin@gmu.edu (Harry Erwin) Newsgroups: bionet.molec-model Subject: Q: How DO You Search for an Entry Level Position? Date: Sun, 18 Oct 1998 18:59:46 -0400 Organization: HDE Associates Lines: 17 Message-ID: <1dh3ze0.960czmrku7pgN@user-38lcivj.dialup.mindspring.com> NNTP-Posting-Host: user-38lcivj.dialup.mindspring.com X-Server-Date: 18 Oct 1998 22:59:56 GMT X-Newsreader: MacSOUP 2.3.3 I'm trying to help my son find an entry-level position in computational biology in the USA. He has a new degree in biomedical science, a background in C++ programming, and a senior project that computed primer-template bonding temperatures using a nearest-neighbor algorithm. He's deferring grad school until he knows what specialized field he wants to work in. He's been e-mailing resumes to the human resources offices of companies on the web, but I have the impression that he's getting lost in the hundreds of resumes they must get that way. I'm sure there's a lot of research labs that could use his skills, but most of them don't post their openings on the web. Is there a better way to do this? -- Harry Erwin, Web Page: http://mason.gmu.edu/~herwin Senior Software Analyst supporting the FAA, PhD candidate in computational neuroscience--modeling how bats echolocate--and lecturer for CS 211 (data structures and advanced C++). From owner-molec-model@net.bio.net Sun Oct 18 23:00:00 1998 Path: biosci!biosci!not-for-mail From: herwin@gmu.edu (Harry Erwin) Newsgroups: bionet.jobs.wanted,bionet.microbiology,bionet.software,bionet.molec-model Subject: Q: How DO You Search for an Entry Level Position? Date: 19 Oct 1998 10:18:17 -0700 Organization: HDE Associates Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: <1dh3xln.1grndrz1tytdq8N@user-38lcivj.dialup.mindspring.com> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.jobs.wanted:25007 bionet.microbiology:14730 bionet.software:22078 bionet.molec-model:2290 I'm trying to help my son find an entry-level position in computational biology in the USA. He has a new degree in biomedical science, a background in C++ programming, and a senior project that computed primer-template bonding temperatures using a nearest-neighbor algorithm. He's deferring grad school until he knows what specialized field he wants to work in. He's been e-mailing resumes to the human resources offices of companies on the web, but I have the impression that he's getting lost in the hundreds of resumes they must get that way. I'm sure there's a lot of research labs that could use his skills, but most of them don't post their openings on the web. Is there a better way to do this? -- Harry Erwin, Web Page: http://mason.gmu.edu/~herwin Senior Software Analyst supporting the FAA, PhD candidate in computational neuroscience--modeling how bats echolocate--and lecturer for CS 211 (data structures and advanced C++). From owner-molec-model@net.bio.net Mon Oct 19 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!news.phoenix.good.net!news.good.net!news.sgi.com!newshub.sdsu.edu!franklin.ljcrf.edu!not-for-mail From: greg@franklin.burnham-inst.org (Dr. Greg Quinn) Newsgroups: bionet.jobs.wanted,bionet.microbiology,bionet.software,bionet.molec-model Subject: Re: Q: How DO You Search for an Entry Level Position? Followup-To: bionet.jobs.wanted,bionet.microbiology,bionet.software,bionet.molec-model Date: 20 Oct 1998 01:00:50 GMT Organization: COMPUTATIONAL BIOLOGY at The BURNHAM INSTITUTE Lines: 57 Distribution: world Message-ID: <70gnc2$h34$1@franklin.ljcrf.edu> References: <1dh3xln.1grndrz1tytdq8N@user-38lcivj.dialup.mindspring.com> NNTP-Posting-Host: franklin.ljcrf.edu X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Xref: biosci bionet.jobs.wanted:25017 bionet.microbiology:14735 bionet.software:22082 bionet.molec-model:2291 Harry Erwin (herwin@gmu.edu) wrote: : I'm trying to help my son find an entry-level position in computational : biology in the USA. He has a new degree in biomedical science, a : background in C++ programming, and a senior project that computed : primer-template bonding temperatures using a nearest-neighbor algorithm. : He's deferring grad school until he knows what specialized field he : wants to work in. He's been e-mailing resumes to the human resources : offices of companies on the web, but I have the impression that he's : getting lost in the hundreds of resumes they must get that way. I'm : sure there's a lot of research labs that could use his skills, but most : of them don't post their openings on the web. Is there a better way to : do this? : : -- : Harry Erwin, Web Page: http://mason.gmu.edu/~herwin : Senior Software Analyst supporting the FAA, PhD candidate in : computational neuroscience--modeling how bats echolocate--and : lecturer for CS 211 (data structures and advanced C++). : Harry, you may want to check the bionet.jobs.offered group. There's usually an assortment of computational biology positions to be had. There's a real need for computational biologists, though many of the positions do seek someone with a few years lab experience and many require a Ph.D. If I had to give my personal opinion, it would be that unless your son is desperately interested in getting a Ph.D., try to get into a computational position with his present qualifications (plus some lab experience) or a Masters degree at most. I wouldn't advise anyone to get a Ph.D. simply to get into computational biology, and in fact with the current career/funding structure, I wouldn't advise anyone to get a bio Ph.D., period. If he wants any real financial/career stability, stick with the computing/biocomputing, which in career terms has 'outs' into mainstream commerce. Most of the Ph.D. computational biology positions advertised by companies (and all the ones that I have been contacted about) are usually looking for someone to do very light programming (PERL scripting, etc) and a ton of data analysis, which your son may or may not find interesting. Any real programmer worth his salt won't find such a situation very satisfying, so your son needs to really think this through. Good luck with your search. -- ALL VIEWS EXPRESSED ARE MY PERSONAL VIEWS AND NOT THOSE OF MY EMPLOYER ***************************************** Computational Biology Group The Burnham Institute (formerly La Jolla Cancer Research Inst.) 12901 North Torrey Pines road La Jolla CA92037 Phone:(619) 646 3103 Email: greg@franklin.ljcrf.edu http://franklin.ljcrf.edu/greg http://www.greg.com/ ***************************************** From owner-molec-model@net.bio.net Tue Oct 20 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!news-nyc.telia.net!newsfeed.cwix.com!128.174.5.49!vixen.cso.uiuc.edu!skeel!skeel From: skeel@cs.uiuc.edu Newsgroups: bionet.molec-model Subject: vis.res.programmer/sys.analyst Date: Wed, 21 Oct 98 18:47:30 GMT Organization: Dept. of Computer Sci - University of Illinois Lines: 45 Message-ID: <70lagn$d1m$4@vixen.cso.uiuc.edu> NNTP-Posting-Host: skeel.cs.uiuc.edu NCSA/U of I Computational Biology Group Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign Title: Visiting Research Programmer/Systems Analyst The Computational Biology Group at NCSA/University of Illinois at Urbana-Champaign (bioweb.ncsa.uiuc.edu) is seeking a visiting research programmer/systems analyst. The project funding this position is at the beginning stage of three-year funding. Position Description: The Computational Biology Group has developed the Biology Workbench, a Web-based computational environment for bioinformatics. The new project involves integrating simulation programs for biological molecules, such as molecular dynamics, Monte Carlo, Brownian dynamics, and drift-diffusion theory, into the Workbench environment. Research programming is needed both to integrate these methodologies into the Workbench environment, and for algorithmic refinement and development of the methodologies themselves. The successful candidate will be encouraged to broaden his/her technical skills and scientific knowledge on the job. This position will provide a great opportunity to work at the cutting edge at the development of a new Web-based computational architecture that NCSA director Larry Smarr has termed a "new way of computing for the 21st century." Qualifications: The ideal candidate will be a versatile programmer, since both Web interfaces and simulation algorithms are involved in the project. Experience in scientific programming is a plus. The person who assumes this positon will join a dynamic team of senior scientists, postdocs, programmers, and students who are working in various aspects of computational biology. Application information: The position is available immediately. It will be open until a suitable candidate is found. Minority and women candidates are strongly encouraged to apply. Please send a resume (electronic mail preferred)including three references to: Eric Jakobsson jake@ncsa.uiuc.edu Beckman Institute 405 N. Mathews Ave Urbana, IL 61801 From owner-molec-model@net.bio.net Thu Oct 22 23:00:00 1998 Path: biosci!news.stanford.edu!nntp.stanford.edu!not-for-mail From: reh@leland.Stanford.EDU (Robin E Holbrook) Newsgroups: bionet.microbiology,bionet.molec-model,bionet.cellbiol,bionet.molbio.proteins Subject: Announcing NATO ASI, Spring '99 Date: 23 Oct 1998 15:48:22 -0700 Organization: Stanford University, CA 94305, USA Lines: 97 Message-ID: <70r13m$9ui@elaine6.Stanford.EDU> NNTP-Posting-Host: elaine6.stanford.edu Xref: biosci bionet.microbiology:14794 bionet.molec-model:2294 bionet.cellbiol:10677 bionet.molbio.proteins:13465 Dynamics, Structure and Function of Biological Macromolecules 4th Course of the International School of Structural Biology and Magnetic Resonance - a NATO Advanced Study Institute Location: Ettore Majorana Centre for Scientific Culture, Erice, Italy Dates: May 25-June 5, 1999 Number of working days: 10 days Objective: To summarize the current state of the field of protein studies focusing on the type of information that can be obtained about dynamic processes in proteins by NMR and other physical methods and the implications for protein and drug design. Fee: $1,200 includes Board and Lodging to be arranged by the Centre. Some financial aid available and any request for aid should be indicated in the application. Full support will NOT be available, so please indicate the specific amount of financial aid necessary to attend. Directors: -Oleg Jardetzky, Professor, Department of Molecular Pharmacology, Stanford University School of Medicine, Stanford, CA 94305-5337, USA. Tel: (+1) 650/723-6153, Fax: (+1) 650/723-2253, Email: jardetzky@stanford.edu -Jean-Francois Lefevre, Professor, ESBS, Louis Pasteur University, Bld. Sebastien Brant, 67400 Strasbourg-Illkirch, France. Tel: (+33) 388 65 52 69, Fax: (+33) 388 65 53 43, Email: lefevre@bali.u-strasbg.fr To apply contact Course Registrar: Ms. Robin Holbrook Fax: (1) 650/723-3353 Tel: (1) 650/723-6270 Email: reh@stanford.edu URL: http:// www-leland.stanford.edu/~reh/Erice*99.html No application form is required but applicants must submit: 1) date and place of birth and nationality 2) degree and other academic qualifications 3) list of publications 4) present position and work address, fax and phone numbers and email address Young applicants with only a few years of experience in the field should arrange for a letter of recommendation from the head of their research group. Applicants interested in financial aid should also send an abstract of current research interest. Selected papers will be presented in poster sessions and student workshops. APPLICATION DEADLINE: MARCH 15, 1999. A letter of acceptance will be sent to successful applicants. Lecturers Cheryl H. Arrowsmith (Ontario Cancer Institute, Toronto, Canada) Ivano Bertini (Universita degli Studi di Firenze, Italy) Richard R. Ernst (ETH Zentrum, Zurich, Switzerland) Hans Frauenfelder (Los Alamos National Laboratories, USA) Cornelius W. Hilbers (University of Nijmegen, The Netherlands) Oleg Jardetzky (Stanford University, USA) Jean-Francois Lefevre (Universite Louis Pasteur, France) Michael Levitt (Stanford University, USA) William N. Lipscomb (Harvard University, USA) Dino Moras (Universite Louis Pasteur, France) Joseph D. Puglisi (Stanford University, USA) Paul Rosch (Universitat Bayreuth, Germany) Brian D. Sykes (University of Alberta, Edmonton, Canada) Wilfred van Gunsteren (ETH Zentrum, Zurich, Switzerland) Course Topics EXPERIMENTAL OBSERVATION OF MOLECULAR MOTIONS *Modern NMR techniques: 3D spectroscopy and molecular dynamics *Protein crystallography *Multisubunit allosteric proteins OBSERVATION OF INTERNAL MOTIONS OF BIOLOGICAL MOLECULES *Dynamics and conformational transitions in allosteric proteins *Principles of NMR and dynamics *Protein dynamics and reactions *The energy landscape of proteins THEORETICAL ANALYSIS OF INTERNAL MOTIONS IN BIOLOGICAL MOLECULES *Introduction to molecular dynamics *Simulations of protein folding *Simulating protein and nucleic acid molecular dynamics *New programs in MD simulations *Calculation of free energy and binding constants MOTIONS IN NUCLEIC ACID *Nucleic acids structure and dynamics *RNA NMR spectroscopy ANALYSIS OF SPECIFIC PROTEINS *Interactions of antifreeze proteins with ice *Mechanism of action of calcium-signaling proteins *tat-Protein structure, dynamics and function *Protein-DNA complexes: Heteronuclear strategies of the assignment of larger complexes From owner-molec-model@net.bio.net Fri Oct 23 23:00:00 1998 From: "Pieter van Santen" Newsgroups: bionet.molec-model Subject: Bioreactor Design Program Date: Sat, 24 Oct 1998 13:36:46 +0200 Organization: World Access / Planet Internet Lines: 12 Message-ID: <70sedi$qh7$1@reader3.wxs.nl> NNTP-Posting-Host: ut1312.wxs.nl X-Trace: reader3.wxs.nl 909229298 27175 195.121.73.43 (24 Oct 1998 11:41:38 GMT) X-Complaints-To: abuse@wxs.nl NNTP-Posting-Date: 24 Oct 1998 11:41:38 GMT X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Path: biosci!news.ic.sunysb.edu!news-nysernet-16.sprintlink.net!news-east.sprintlink.net!news-peer1.sprintlink.net!news-backup-east.sprintlink.net!news.sprintlink.net!198.138.0.5!newshub.northeast.verio.net!news.maxwell.syr.edu!newsfeed.cwix.com!195.99.66.215!news-feed1.eu.concert.net!skynet.be!News.Amsterdam.UnisourceCS!news.wxs.nl!not-for-mail Dear colleague, I developed a program which can be used to design new bioreactors, or to calculate parameters of already used bioreactors. If you are interested, you can find more information at: http://home.wxs.nl/~pvsanten/bioreactor/brd.htm Pieter van Santen From owner-molec-model@net.bio.net Sat Oct 24 23:00:00 1998 Path: biosci!TWISTER.SCH.BME.HU!hiorue51 From: hiorue51@TWISTER.SCH.BME.HU (Innovative Lectro Designs) Newsgroups: bionet.molec-model Subject: Cable Descrambler.....NOW Only $7.00 ! Date: 25 Oct 1998 02:38:14 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 179 Sender: daemon@net.bio.net Distribution: world Message-ID: <199810251619IAA49578@FunandEasy.unbsj.ca> NNTP-Posting-Host: net.bio.net This is really cool! PREMIUM CHANNELS........Descrambled! EASY to assemble plans for only $7.00 ! YOU WILL BE WATCHING all your FAVORITE PAY STATIONS featuring MOVIES, SPORTS. Adult entertainment, and any other scrambled signal NEXT WEEK! You can EASILY assemble a cable descrambler in less than 30 minutes! You have probably seen many advertisments for similar plans......... BUT OURS are BETTER! We have compared it to all the others and have actually IMPROVED the quality and SIMPLIFIED the design !!! ** We even include PHOTOS! ** OUR PLANS ARE BETTER! We have NEW, EASY TO READ,EASY to assemble plans for only $7.00! We have seen them advertised for as much as $29.00 and you have to wait weeks to receive them! WHAT THE OTHERS SAY IS TRUE! Parts are available at "The TV HUT" or any electronics store. Trademark rights do not allow us to use a national electronics retail chains' name but there is one in your town! Call and ask them BEFORE you order! They are very familiar with these plans! You will need these easy to obtain parts : 270-235 mini box 271-1325 2.2k ohm resistor 278-212 chasis connectors RG59 coaxial cable #12 copper wire Variable capacitor They may have to special order the variable capacitor, But WHY WAIT for a special order? WE have them! WE have secured a supply of the capacitors directly from the manufacturer and We WILL include one with your plans for an ADDITIONAL $10.00 only! All you need now is the EASY TO ASSEMBLE plans to show you how this educational device in 30 MINUTES! It is LEGAL, providing of course you use these plans for EDUCATIONAL PURPOSES only. See first hand and LEARN how this SIMPLE circuitry works! If you intend to use these plans for any other purpose DO NOT ORDER them. IT'S FUN TO BUILD! We're sure you'll enjoy this project! This is a unique opportunity for hobbiest of ANY skill level to learn simple circuitry! Learn how easy descrambling is! $ 7.00 for plans only $10.00 for variable capacitor only $17.00 for The easy to assemble plans and one variable capacitor! Please send check or money order payable to: Kraftworks P.O. Box 11752 San Rafael, Ca. 94912 WE pay postage and handling! Please allow 14 days for delivery. This is a one time only mailing! You have already been placed on our remove list and will not receive another offer from us! Thank You From owner-molec-model@net.bio.net Mon Oct 26 22:00:00 1998 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molec-model Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 27 Oct 1998 02:00:12 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199810271000.CAA01743@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 Tue Oct 27 22:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.gtei.net!cpk-news-hub1.bbnplanet.com!news.news.gtei.net!wn3feed!worldnet.att.net!135.173.83.225!attworldnet!newsadm From: Abhay Kini Newsgroups: bionet.molec-model Subject: Hardware question Date: 28 Oct 1998 14:21:01 GMT Organization: Purdue University Lines: 10 Message-ID: <3637286C.B36BBA90@worldnet.att.net> Reply-To: kinis@cheerful.com NNTP-Posting-Host: 12.79.165.80 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.05 [en] (Win95; U) Hi, I am looking to purchase a computer which would allow me to run programs such as macromodel and other modeling programs as well. Could any one suggest a site that would help me through this decision? Thanx... Abhay From owner-molec-model@net.bio.net Tue Oct 27 22:00:00 1998 Path: biosci!AOL.COM!Ricf17 From: Ricf17@AOL.COM Newsgroups: bionet.molec-model Subject: NO PRODUCTS TO STOCK ! Date: 28 Oct 1998 14:22:44 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 48 Sender: daemon@net.bio.net Distribution: world Message-ID: <16b4b18f.363795ca@aol.com> NNTP-Posting-Host: net.bio.net This is a multi-part message in MIME format. --part0_909612490_boundary Content-ID: <0_909612490@inet_out.mail.aol.com.1> Content-type: text/plain; charset=US-ASCII --part0_909612490_boundary Content-ID: <0_909612490@inet_out.mail.aol.com.2> Content-type: message/rfc822 Content-transfer-encoding: 7bit Content-disposition: inline From: Ricf17@aol.com Return-path: To: Ricf17@aol.com Subject: here Date: Wed, 28 Oct 1998 16:39:38 EST Mime-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit YES YOU CAN!! Retire in 3 to 6 months or less. Generate a 6 figure income in 6 months or less. Fire your boss and work from home now. NOT MLM For information and personal interview, call me toll free at 1-888-231-4916 Prosperous regards, Sandy For immediate information re: our product and marketing plan call 1-850-654-7727 ext. 2001 and 2002 --part0_909612490_boundary-- From owner-molec-model@net.bio.net Tue Oct 27 22:00:00 1998 Path: biosci!AOL.COM!SName0 From: SName0@AOL.COM Newsgroups: bionet.molec-model Subject: Home Income !! Date: 28 Oct 1998 15:35:48 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 25 Sender: daemon@net.bio.net Distribution: world Message-ID: <20a41eac.3637a73a@aol.com> NNTP-Posting-Host: net.bio.net This is a multi-part message in MIME format. --part0_909616955_boundary Content-ID: <0_909616955@inet_out.mail.aol.com.1> Content-type: text/plain; charset=US-ASCII --part0_909616955_boundary Content-ID: <0_909616955@inet_out.mail.aol.com.2> Content-type: message/rfc822 Content-transfer-encoding: 7bit Content-disposition: inline From: Atlanis31@aol.com Return-path: To: SName0@aol.com Subject: Re: Is this richard's email address? Date: Wed, 28 Oct 1998 17:31:28 EST Mime-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit no this is not richards email adress....duh --part0_909616955_boundary--