From owner-molec-model@net.bio.net Tue Jun 02 23:00:00 1998 Path: biosci!INTEK.PPDI.COM!Jami.Grossfield From: Jami.Grossfield@INTEK.PPDI.COM ("Jami Grossfield") Newsgroups: bionet.molec-model Subject: input please! Date: 3 Jun 1998 10:50:55 -0700 Organization: PPD Pharmaco Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: <35758CB6.E4FA9596@intek.ppdi.com> NNTP-Posting-Host: net.bio.net we're looking for reccommendations/ warnings about any sort of software (windows based) for modeling DNA secondary structure. thanks in advance! jami :) From owner-molec-model@net.bio.net Sun Jun 07 23:00:00 1998 Path: biosci!GR8HEALTH.COM!rella From: rella@GR8HEALTH.COM Newsgroups: bionet.molec-model Subject: AD: Lose Weight Now -- Ask Me How! 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Drop us a line and let us know how you like it! *************************************************** The information contained here was derived from many medical, nutritional and media sources and is for informational and educational purposes only. No medical claims are implied or intended. Testimonies are offered voluntarily and are not paid for. Your results may vary. Consult a physician before using Thermo-Lift if you have high blood pressure, are pregnant, lactating, or are being treated for a medical condition. *************************************************** //////////////////////////////////////////////////////////////////// If you wish to be removed from all future mailings, reply with the subject "Remove" and accept my apologies for the intrusion. //////////////////////////////////////////////////////////////////// From owner-molec-model@net.bio.net Sun Jun 07 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!newsfeed.nacamar.de!dispose.news.demon.net!demon!delos!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!antares!alan From: Alan Robinson Newsgroups: bionet.molec-model Subject: Conference on Bioinformatics Date: Mon, 8 Jun 1998 11:38:29 +0100 Organization: MRC Human Genome Mapping Project Resource Centre Message-ID: NNTP-Posting-Host: antares.ebi.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: alan@antares Lines: 98 --ooOOoo-- Objects in Bioinformatics '98 Object-Oriented Technology, Software Components and Distributed Computing for Bioinformatics and Genomics. ***************************** http://www.ebi.ac.uk/oib98/ ***************************** 3rd and 4th August, 1998. Wellcome Trust Genome Campus, Hinxton, near Cambridge, UK. Following last years successful OiB-97 conference, OiB-98 has been set for August 3rd-4th, 1998. The conference is organised by the European Bioinformatics Institute and will be held in the conference facilities at the Wellcome Trust Genome Campus in the grounds of Hinxton Hall, Cambridge, UK. 'Objects in Bioinformatics' focuses upon the role of object-oriented technology, software components, design patterns and distributed computing in bioinformatics and genomics. The conference is aimed at those who are interested in, are developing, or have developed object-oriented software that will be of use to the bioinformatics and genomics community in both academia and industry. The conference aims to address the problems now facing our scientific community of: o Heterogeneous computing environments o Effective standards for the representation of data o The distributed nature of applications, resources and data across computer networks (i.e. intranets, extranets and the Internet) o The ever-present data deluge that is hitting biology o The development of tools and resources to aid the biologist and bioinformatician A theme of this year's conference will be the implication and application of distributed object technology (such as CORBA) to biology and bioinformatics, and the work of the Life Sciences Research Task Force of the Object Management Group in promoting standards. The conference will include lectures and poster sessions on the rapidly expanding and developing fields of object-oriented software and distributed computing from both an academic and industrial perspective. Invited talks will cover the application of reusable components, tools, software libraries, distributed object technology and the role of Life Sciences Research Task Force. Speakers will also include specialists from outside the domain of biology that have already experienced our current data problems. Poster stands (including a limited number with a dedicated networked computer), are available upon which delegates may showcase their work and projects. Participants are encouraged to submit a brief abstract for a poster relevant to the conference themes to promote and display their work in the field, and fuel dialogue. In the same spirit as OiB-97, the cost of registration for the conference has been kept as low as possible with a nominal fee of 50 GBP for early registration. The closing date for early registration and submission of abstracts is July 1st, 1998. Late registration will be possible from July 2nd onwards, however the registration fee will increase to 100 GBP. N.B. Following OiB-98, the Life Sciences Research (LSR) group will be holding a technical meeting with work groups where efforts will continue in encouraging the formation of domain standards. Interested OiB participants are encouraged to attend these (and other) meetings of the LSR group, although numbers will be limited for logistic reasons. Registration for this meeting is separate from OiB - details can be found in the group's web pages. OiB-98 is supported by BioInform, Millennium Pharmaceuticals, NetGenics, Object Design, Silicon Graphics and Synomics. Details of registration and accommodation may be found at the conference Web site - http://www.ebi.ac.uk/oib98/ Yours sincerely, Alan Robinson. -- ============================================================ Alan J. Robinson Tel:+44-(0)1223 494625 EMBL Outstation Fax:+44-(0)1223 494468 European Bioinformatics Institute Email: alan@ebi.ac.uk Wellcome Trust Genome Campus Hinxton, Cambridge, CB10 1SD, UK http://industry.ebi.ac.uk/~alan/ ============================================================ From owner-molec-model@net.bio.net Sun Jun 07 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!la-news-feed1.bbnplanet.com!news.bbnplanet.com!newsfeed1.earthlink.net!feed2.news.erols.com!erols!woodstock.news.demon.net!demon!dispose.news.demon.net!demon!newsfeed.nacamar.de!news-hh.maz.net!fu-berlin.de!jussieu.fr!not-for-mail From: Michel Seigneuret Newsgroups: bionet.molec-model Subject: molecular modeling on linux Date: Mon, 08 Jun 1998 17:02:03 +0200 Organization: Universites Paris VI/Paris VII - France Message-ID: <357BFCEB.167E@lpbc.jussieu.fr> NNTP-Posting-Host: lpbcsun2.lpbc.jussieu.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.3 IP20) Lines: 22 Dear Collegues, I am thinking of purchasing a 2 processors Pentium2 350 or 400Mhz PC to perform bioinformatics and molecular modelling studies under Linux. I would therefore be interested to hear from people already using similar machines for similar works. 1)Are the performances satisfactory for "standard" modeling tasks (e.g. sequence or structure database searching, molecular dynamics or conformational searching on peptides)? Comparison of performances with e.g. an SGI R10000 would be helpful. 2)It seems that a big problem with Linux is hardware compatibility. I would thus be interested if some people would advise me on specific hardware configurations that work (specially on high-end 3D OpenGL compatible graphic cards). Thank you in avance for your help. Michel Michel Seigneuret Universite Paris 6, Lab. de Physicochimie Biomoleculaire et Cellulaire 4, place Jussieu, 75252 Paris cedex 05, France tel 33 1 44277545, fax 33 1 44277560 From owner-molec-model@net.bio.net Mon Jun 08 23:00:00 1998 Path: biosci!LCBVAX.CCHEM.BERKELEY.EDU!DUBCHAK From: DUBCHAK@LCBVAX.CCHEM.BERKELEY.EDU Newsgroups: bionet.molec-model Subject: DIMACS Workshop on Combinatorial Clustering and Multi-Domain Proteins Date: 9 Jun 1998 14:58:08 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 62 Sender: daemon@net.bio.net Distribution: world Message-ID: <980609145623.20209caf@LCBVAX.CCHEM.BERKELEY.EDU> NNTP-Posting-Host: net.bio.net DIMACS Workshop on Combinatorial Clustering and Multi-Domain Protein Structure Analysis June 26-27, 1998 DIMACS Center, CoRE Building (Room 431), Rutgers University, Busch Campus, Piscataway, NJ URL: http://dimacs.rutgers.edu/Workshops/CombCluster/announcement.html Principal Organizers: * Sylvia Spengler, Lawrence Berkeley NationalLaboratory * Manfred D. Zorn, Lawrence Berkeley National Laboratory * Inna Dubchak, Lawrence Berkeley National Laboratory * Fred Roberts, Rutgers University, DIMACS * Ilya Muchnik, Rutgers University, DIMACS * Casimir A. Kulikowski, Rutgers University, CS Department Presented under the auspices of the Special Year on Massive Data Sets and the Special Year in Mathematical Support for Molecular Biology. ---------------------------------------------------------------------------- The combinatorics, graph theory and algorithms branches of discrete mathematics are powerful techniques for use in analysis of diverse sets of data. Combinatorics introduces clustering models, forms a basis for the interpretation of results, and brings new ideas to clustering methods. The area of combinatorial clustering provides new opportunities for systematic (routine) and comprehensive study of very large databases containing highly complex non-regular elements. However, researchers developing methods for combinatorial clustering often do not collaborate with specialists in the creation, management and analysis of large, complex databases. The goal of this workshop is to foster and facilitate such a collaboration by focusing on a particular application. The specific problem we wish to address is in the area of protein structure and analysis of multi-domain proteins (as an example for other type of interactions among large bio-molecules). By hosting this workshop, our aim is not only to stimulate research at the interface between these disciplines, but also stimulate development of ideas and methods in each field. We plan to have two type of sessions: theoretical, devoted to mathematical models and clustering procedures, and practical, concentrated on sequence-structure relations in biomolecular systems, mostly on multi-domain protein analysis. Following applications of clustering to the multi-domain protein analysis will be discussed among others: * amino acid sequence segmentation which determines domain structures of proteins, * automatic procedure to collect libraries of protein domains, * contact map method for protein 3D-structure analysis and protein fold classification, * inter-domain contact aggregates, * correlation between contact structures and sequence segmentation. URL: http://dimacs.rutgers.edu/Workshops/CombCluster/announcement.html From owner-molec-model@net.bio.net Wed Jun 10 23:00:00 1998 Path: biosci!agate!howland.erols.net!europa.clark.net!128.158.254.10!news.msfc.nasa.gov!cnn.nas.nasa.gov!bross From: bross@nospamb.nas.nasa.gov (Bill Ross) Newsgroups: bionet.molec-model Subject: Re: molecular modeling on linux Date: 11 Jun 1998 10:48:31 GMT Organization: Numerical Aerodynamic Simulation Facility/NASA Ames Research Ctr. Lines: 13 Message-ID: <6loclv$7cb$1@sun500.nas.nasa.gov> References: <357BFCEB.167E@lpbc.jussieu.fr> NNTP-Posting-Host: splatter.nas.nasa.gov |> I am thinking of purchasing a 2 processors Pentium2 350 or 400Mhz PC |> to perform bioinformatics and molecular modelling studies under Linux. |> I would therefore be interested to hear from people already using |> similar machines for similar works. |> 1)Are the performances satisfactory for "standard" modeling tasks |> (e.g. sequence or structure database searching, molecular dynamics or |> conformational searching on peptides)? Comparison of performances with |> e.g. an SGI R10000 would be helpful. See www.amber.ucsf.edu/amber/ for benchmarks. Bill Ross From owner-molec-model@net.bio.net Thu Jun 11 23:00:00 1998 Path: biosci!biosci!not-for-mail From: Ann Newsgroups: bionet.molec-model, Subject: Q: Role of methionin Date: 12 Jun 1998 09:49:45 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: <6lrm79$ja0@net.bio.net> NNTP-Posting-Host: net.bio.net Dear bionetters, Except for the obvious role as ligand to Fe and Cu ions in redox enzymes, does anyone know of other specific roles of methionin in proteins? Any specific properties, like dielectric constant etc? Is there any pattern for the distribution of Met in certain types of proteins? Differences between eucharyots and procaryots? Any info is welcome! Thanks, Ann Magnuson From owner-molec-model@net.bio.net Fri Jun 12 23:00:00 1998 Path: biosci!news.Stanford.EDU!newsfeed.concentric.net!netnews.com!news.internetsat.com!not-for-mail From: "A Van de Wiele " Newsgroups: bionet.molec-model Subject: who can help me with Rasmol ? Date: 13 Jun 1998 18:58:46 GMT Organization: none Lines: 8 Message-ID: <01bd96fc$b4b49360$f1f706c3@a.-van-de-wiele> NNTP-Posting-Host: gate4-241.nordnet.fr X-Newsreader: Microsoft Internet News 4.70.1155 Who can help me with Rasmol ? What is the command to oblige the machine to name some groups in a molecule, for example atoms number: 32-33-34-35-38-39-40-41-90-91-92-93-94-95 = residu Asparagine ? That is a new peptid built with another soft and that is a ent file. Thanks. e.mail : avandewiele@nordnet.fr From owner-molec-model@net.bio.net Fri Jun 12 23:00:00 1998 Path: biosci!agate!howland.erols.net!woodstock.news.demon.net!demon!dispose.news.demon.net!demon!news.demon.co.uk!demon!mail2news.demon.co.uk!not-for-mail From: Paul@pdchem.demon.co.uk (Paul Davis) Newsgroups: bionet.molec-model Subject: Re: who can help me with Rasmol ? Date: Sat, 13 Jun 98 21:41:09 GMT Organization: Myorganisation Message-ID: <897774069snz@pdchem.demon.co.uk> References: <01bd96fc$b4b49360$f1f706c3@a.-van-de-wiele> Reply-To: Paul@pdchem.demon.co.uk X-Trace: mail2news.demon.co.uk 897774785 mail2news:27856 mail2news mail2news.demon.co.uk X-Complaints-To: abuse@demon.net X-Mail2News-Path: news.demon.net!pdchem.demon.co.uk X-Newsreader: Demon Internet Simple News v1.30 Lines: 25 In article <01bd96fc$b4b49360$f1f706c3@a.-van-de-wiele> avandewiele@nordnet.fr "A Van de Wiele " writes: > Who can help me with Rasmol ? What is the command to oblige the machine to > name some groups in a molecule, for example atoms number: > 32-33-34-35-38-39-40-41-90-91-92-93-94-95 = residu > Asparagine ? That is a new peptid built with another soft and that is a > ent file. > Thanks. > e.mail : avandewiele@nordnet.fr > > You may be interested to know that there is a RasMol home page at http://klaatu.oit.umass.edu/microbio/rasmol/ There you can find help files, tutorials, examples and pointers to the RasMol Email Discussion List. The Discussion List has a searchable archive, and this is also a mine of useful information. I hope this helps. -Paul -- -------------------------------------------------------------------- Paul Davis paul@pdchem.demon.co.uk From owner-molec-model@net.bio.net Sun Jun 14 23:00:00 1998 Path: biosci!MSN.COM!zea60 From: zea60@MSN.COM (MN1) Newsgroups: bionet.molec-model Subject: Earn $100 every time OUR phone rings...test Date: 14 Jun 1998 21:41:18 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: <19980615131RAA41044@post.msn.com> Reply-To: marketn@msn.com NNTP-Posting-Host: net.bio.net Testing...PR From owner-molec-model@net.bio.net Sun Jun 14 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!194.72.7.126!btnet-peer!btnet!nntp.news.xara.net!xara.net!server5.netnews.ja.net!news.york.ac.uk!not-for-mail From: Stuart Priest Newsgroups: bionet.molec-model Subject: Re: molecular modeling on linux Date: Mon, 15 Jun 1998 15:22:36 +0100 Organization: Protein Structure Group, University of York Lines: 40 Sender: sap1@york.ac.uk Message-ID: <35852E2C.31DF@yorvic.york.ac.uk> References: <357BFCEB.167E@lpbc.jussieu.fr> NNTP-Posting-Host: heffalump.chem.york.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.2 IP22) To: Michel Seigneuret Michel Seigneuret wrote: > > Dear Collegues, > I am thinking of purchasing a 2 processors Pentium2 350 or 400Mhz PC > to perform bioinformatics and molecular modelling studies under Linux. > I would therefore be interested to hear from people already using > similar machines for similar works. > 1)Are the performances satisfactory for "standard" modeling tasks > (e.g. sequence or structure database searching, molecular dynamics or > conformational searching on peptides)? Comparison of performances with > e.g. an SGI R10000 would be helpful. > 2)It seems that a big problem with Linux is hardware compatibility. > I would thus be interested if some people would advise me on specific > hardware configurations that work (specially on high-end 3D OpenGL > compatible graphic cards). > Thank you in avance for your help. > > Michel > > > Michel Seigneuret > Universite Paris 6, Lab. de Physicochimie Biomoleculaire et Cellulaire > 4, place Jussieu, 75252 Paris cedex 05, France > tel 33 1 44277545, fax 33 1 44277560 See ... http://www.amber.ucsf.edu/amber/ http://kihp6.ki.si/parallel/summary.html (CHARMM - PII 400 much faster than a R10K SGI) http://www.emsl.pnl.gov:2080/docs/tms/abinitio/cover.html (GAUSSIAN) http://www.chem.joensuu.fi/people/juha_muilu/Misc/benchmarks.html http://www.dl.ac.uk/CCP/CCP4/ccp4onLINUX.html Regards Stuart Priest, Computer Manager, Tel. 44 1904 432592 Protein Structure Group, University of York, UK FAX 44 1904 410519 Interested in Theatre? http://www.users.globalnet.co.uk/~rltc/ From owner-molec-model@net.bio.net Tue Jun 16 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.new-york.net!news.columbia.edu!merhaba.cc.columbia.edu!og32 From: Olgun Guvench Newsgroups: bionet.molec-model Subject: Re: molecular modeling on linux Date: Wed, 17 Jun 1998 16:33:58 -0400 Organization: Columbia University Lines: 70 Message-ID: References: <357BFCEB.167E@lpbc.jussieu.fr> NNTP-Posting-Host: merhaba.cc.columbia.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII To: Michel Seigneuret In-Reply-To: <357BFCEB.167E@lpbc.jussieu.fr> Hi, I do modeling work (specifically molecular dynamics and visualization) on a Linux PC and it works great. I think the other posts to this group address your question regarding benchmarks. Regarding hardware compatibility, check http://www.redhat.com -- there you will find a hardware compatibility list. Also, check www.linux.org for a list of hardware vendors that provide systems with Linux pre-installed. One caveat: as far as I know OpenGL acceleration is not available at the hardware level, so it probably is not worth spending lots of $$ on a video card which has OpenGL acceleration at the hardware level (I think there are some commercial X vendors which claim accleration for OpenGL, but this is done only on the software level). That being said, let me ease your worries that hardware compatibility is a "big problem," as you will see from the above RedHat web site. (for graphics under Linux using X, if you want a recommendation, try a Matrox Millenium II for your graphics board -- it is well supported and has a reputation for excellent performance; I currently use an S3 Virge based card (Diamond 3D 3000, 4 MB memory) and it works quite well). Two excellent (and free) sources for molecular dynamics on Linux are: Theoretical Biophysics Group http://www.ks.uiuc.edu/ Check out their program VMD, which runs under RedHat 5.0 and uses a free version of the OpenGL library called Mesa to provide graphics like you would see on an SGI Ponder Group at U. Washington, St. Louis http://dasher.wustl.edu/tinker/ Fortran 77 code for molecular dynamics, mechanics, etc. (compiles without trouble using g77 2.7.2.3) Best of luck, Olgun Guvench p.s.: Linux is also available on the Alpha architecture (by Digital, which is now owned by Compaq, I believe). The Alpha has the fastest floating point unit on the planet right now, but unfortunately, the math library for Linux is not very good on Alpha's at this point, so the Alpha's full potential cannot be realized (although someone is re-writing the library and it should be ready for use on Alpha in a couple of weeks from what I have heard...). So, if you are running Linux, it is probably better to stick with Intel if you will be compiling your own code using gcc. On Mon, 8 Jun 1998, Michel Seigneuret wrote: > Dear Collegues, > I am thinking of purchasing a 2 processors Pentium2 350 or 400Mhz PC > to perform bioinformatics and molecular modelling studies under Linux. > I would therefore be interested to hear from people already using > similar machines for similar works. > 1)Are the performances satisfactory for "standard" modeling tasks > (e.g. sequence or structure database searching, molecular dynamics or > conformational searching on peptides)? Comparison of performances with > e.g. an SGI R10000 would be helpful. > 2)It seems that a big problem with Linux is hardware compatibility. > I would thus be interested if some people would advise me on specific > hardware configurations that work (specially on high-end 3D OpenGL > compatible graphic cards). > Thank you in avance for your help. > > Michel > > > Michel Seigneuret > Universite Paris 6, Lab. de Physicochimie Biomoleculaire et Cellulaire > 4, place Jussieu, 75252 Paris cedex 05, France > tel 33 1 44277545, fax 33 1 44277560 > > From owner-molec-model@net.bio.net Fri Jun 19 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsxfer3.itd.umich.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: "Ivan Torshin" Newsgroups: bionet.molec-model Subject: Re: Sensitive alkaline phosphatase assay Date: 20 Jun 1998 17:11:53 +0100 Organization: Kinetics and Catalysis Lab. Lines: 29 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6mgn09$5fi@mserv1.dl.ac.uk> References: <98620151059.~INN-YLBa00192.bionet-news@dl.ac.uk> MIME-Version: 1.0 Original-To: molmodel@dl.ac.uk > >but the alkaline phosphatase activity is too low to be useful. > Dear Dudley Page, Could you describe the experiment in more detail ? For example, what APAse do you use (source, another data) ? What is the expression system (E.coli) ? Do you experiment with pH, temperature (APAse is periplasmic protein, therefore, it could be easily regulated by changing 'outside' pH. E.coli Apase is relatively thermostable- the molecule begins to dissociate into subunits with the activity loss at 70-80 C) ? Moreover, E.coli APase activity strongly depends on the MG and Zn ion concentrations -the ions are involved in active site and molecule stabilization) Some of that may help, Regards, Ivan --- From owner-molec-model@net.bio.net Fri Jun 19 23:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!news.ox.ac.uk!not-for-mail From: "Dr M.L.D. Page" Newsgroups: bionet.molec-model Subject: Sensitive alkaline phosphatase assay Date: Sat, 20 Jun 1998 14:51:41 +0100 Organization: Oxford University Department of Biochemistry Lines: 23 Message-ID: <358BBE6D.680E@worf.molbiol.ox.ac.uk> Reply-To: South, Parks, Road, Oxford, OX1, 3QU, United, Kingdom. NNTP-Posting-Host: brunhilde.bioch.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win16; I) Does anyone know of an assay for alkaline phosphatase that is more sensitive than the colorimetric (i.e. p-nitrophenyl phosphate) one? A radiochemical one, perhaps? or could I adapt one of the chemiluminescent southern/northern protocols? A problem I see here is that the luminescent products are (necessarily) insoluble wheras for an enzyme assay it would be better if it were soluble... Alternatively, perhaps the molecular biologists among you can help me.... I am trying to determine the topology of a multi-membrane spanning protein which is pretty toxic, even in small segments. I have made a series of phoA fusions in a low/medium copy number vector. These are stable, but the alkaline phosphatase activity is too low to be useful. I have tried transferring the some of the constructs to a high copy number vector, but the colonies, while nicely blue in parts, develop white sectors suggesting deletion of the inserts. How should I proceed? Should I clone the inserts under the control of a regulated promoter and induce when I am ready to do the measurements? Any ideas gratefully received. Thanks. Dudley Page (mpage@worf.molbiol.ox.ac.uk) From owner-molec-model@net.bio.net Sat Jun 20 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.new-york.net!news.columbia.edu!ciao.cc.columbia.edu!og32 From: Olgun Guvench Newsgroups: bionet.molec-model Subject: Re: molecular modeling on linux Date: Sun, 21 Jun 1998 17:44:24 -0400 Organization: Columbia University Lines: 27 Message-ID: References: <357BFCEB.167E@lpbc.jussieu.fr> NNTP-Posting-Host: ciao.cc.columbia.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII To: Andrew Martin In-Reply-To: On Sat, 20 Jun 1998, Andrew Martin wrote: > I've just heard (though havn't confirmed myself) that the free OpenGL > compatible library, Mesa, now has direct hardware support for Voodoo 3D > graphics cards. This apparently works VERY well.... Do you know if this can be done in an X terminal? This could be quite useful if it can... > > Many of the problems with Alpha Linux maths libraries were ironed out > for the Titanic. Animation for this movie was done on 160 Alpha, over > 100 of which were running Linux (the rest NT). Take a look at the > February 1998 issue of Linux Journal (www.linuxjournal.com) > In the article, the problem they mention is a problem with the kernel, not with the math library, from what I can tell. The library "problem" that I was referring to has to do with the code for certain functions in the math library which do not perform optimally on the Alpha architecture and hence slow down code which uses these functions; I do not think that the library "problem" causes programs to die, only to run slower than if they had been compiled, e.g. under Digitial Unix and linked to the Digital math library. -Olgun From owner-molec-model@net.bio.net Sat Jun 20 23:00:00 1998 Path: biosci!agate!nntp-out.monmouth.com!newspeer.monmouth.com!btnet-peer!btnet!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 Subject: Re: molecular modeling on linux Date: Sat, 20 Jun 1998 09:43:07 GMT Organization: Private Address Message-ID: References: <357BFCEB.167E@lpbc.jussieu.fr> X-Trace: mail2news.demon.co.uk 898402544 mail2news:7144 mail2news mail2news.demon.co.uk X-Complaints-To: abuse@demon.net X-Mail2News-Path: news.demon.net!post-12.mail.demon.net!post.mail.demon.net![194.222.20.72]!stagleys.demon.co.uk X-Newsreader: TIN [version 1.2 PL2] Lines: 31 Olgun Guvench (og32@columbia.edu) wrote: : One caveat: as far as I know OpenGL acceleration is not available at the : hardware level, so it probably is not worth spending lots of $$ on a video : card which has OpenGL acceleration at the hardware level (I think there : are some commercial X vendors which claim accleration for OpenGL, but this : is done only on the software level). I've just heard (though havn't confirmed myself) that the free OpenGL compatible library, Mesa, now has direct hardware support for Voodoo 3D graphics cards. This apparently works VERY well.... : p.s.: Linux is also available on the Alpha architecture (by Digital, which : is now owned by Compaq, I believe). The Alpha has the fastest floating : point unit on the planet right now, but unfortunately, the math library : for Linux is not very good on Alpha's at this point, so the Alpha's full : potential cannot be realized (although someone is re-writing the library : and it should be ready for use on Alpha in a couple of weeks from what I : have heard...). So, if you are running Linux, it is probably better to : stick with Intel if you will be compiling your own code using gcc. Many of the problems with Alpha Linux maths libraries were ironed out for the Titanic. Animation for this movie was done on 160 Alpha, over 100 of which were running Linux (the rest NT). Take a look at the February 1998 issue of Linux Journal (www.linuxjournal.com) Andrew From owner-molec-model@net.bio.net Sun Jun 21 23:00:00 1998 Path: biosci!HERMES.KFUNIGRAZ.AC.AT!kungl From: kungl@HERMES.KFUNIGRAZ.AC.AT ("Kungl, Andreas") Newsgroups: bionet.molec-model Subject: 3rd International Conference on Molecular Structural Biology (ICM SB99) Date: 22 Jun 1998 09:59:11 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 117 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net FIRST ANNOUNCEMENT THIRD INTERNATIONAL CONFERENCE ON MOLECULAR STRUCTURAL BIOLOGY ICMSB99 8.-12. SEPTEMBER 1999 VIENNA, AUSTRIA =20 This conference, organised by the Biophysical Chemistry subgroup of the Austrian=20 Chemical Society (G=D6CH), is the third in the ICMSB series, which aims = to bring together=20 scientists from the fields of X-ray crystallography, NMR spectroscopy, molecular biology,=20 structure prediction, computer modeling and microscopy. The third conference will again=20 cover all these areas, and will in addition feature a session on the industrial use of=20 these techniqes in the design of novel drugs. The beautiful central european city of Vienna is an ideal conference location, not only=20 because of its international airport and excellent public transport system, but also=20 because of its beauty and historical interest.=20 The conference will take place from the evening of Wednesday 8th September to Sunday=20 12th. Following the opening lecture by Robert Huber on Wednesday evening, the next four=20 days will include plenary lectures given by outstanding scientists from all over the=20 world, plus short communications which will be selected from abstract submissions.=20 There will be 2 poster sessions, with a poster prize being awarded to the best poster=20 contribution. In addition, an entertainment and social programme will provide the=20 participants with a taste of the cultural side of Vienna.=20 =20 Preliminary Programme Honorary Lecture Robert Huber =20 Novel Structures Michael Rossmann, Don Wiley, Kurt W=FCthrich Folding and Function Alan Fersht, Paul Sigler, Peter Wright Prediction and Simulation David Eisenberg, John Moult Structure-Based Drug Design Siegfried Reich Advances in Microscopic Methods Werner K=FChlbrandt, Hansgeorg Schindler Structural Molecular Biology Stephen Cusack, Robert = Kaptein, Christoph Kratky Participation Fees=20 Early Fee Late Fee (before July 31. 1999) (after July 31. 1999)=20 Regular.................5.000,- ATS ...........5.500,- ATS=20 G=D6CH Member......4.000,- ATS ...........4.500,- ATS=20 Student.................2.500,- ATS ...........2.500,- ATS=20 Accompanying person.......600,- ATS .............600,- ATS=20 =20 The fee for regular participants, G=D6CH members, and students, = includes the full=20 scientific programme, the Conference Proceedings (which will be published in book form=20 with an ISBN number), lunch from Thursday to Sunday, coffee breaks, and the entertainment=20 programme. Accompanying persons attend only the entertainment = programme. =20 Deadlines=20 =20 Abstract Submission June 30. 1999 Early Registration July 31. 1999 Please complete the Pre-Registration Form on our homepage at=20 http://www.kfunigraz.ac.at/ipcwww/icmsb99 or contact the conference secretariat (see below) in order to receive the Second=20 Announcement for the ICMSB99, which contains the full scientific and social programmes,=20 and all details necessary for attending the conference, including the procedure for=20 submission of abstracts, and accommodation forms. The Second Announcement will be sent=20 out early in 1999. =20 Conference Secretariat Dr. Andreas Kungl=20 Austrian Chemical Society (G=D6CH), Biochemistry Subgroup c/o Institute of Pharmaceutical Chemistry University of Graz, Universit=E4tsplatz 1, A-8010 Graz Tel.: +43 316 380 5373, Fax: +43 316 382541 E-Mail: andreas.kungl@kfunigraz.ac.at =20 From owner-molec-model@net.bio.net Tue Jun 23 23:00:00 1998 Path: biosci!IRIS.BIO.USTC.EDU.CN!zhouli From: zhouli@IRIS.BIO.USTC.EDU.CN (Zhou Li) Newsgroups: bionet.molec-model Subject: [QUESTION] Related news groups? Date: 24 Jun 1998 00:15:20 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: <359179D0.7DE1@iris.bio.ustc.edu.cn> NNTP-Posting-Host: net.bio.net Hi,Netters, Who can post a list of some other news groups dedicated to the topics of molecular simulation or the URLs of the major research institutes (laboratories) working on this field? Thanks. -- Li Zhou Graduate Student on Molecular Modelling Laboratory of Structural Biology Dept. of Cell and Molecular Biology College of Life Sciences Univ. of Science and Technology of China Hefei 230027 CHINA From owner-molec-model@net.bio.net Tue Jun 23 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!spring.edu.tw!news.nctu.edu.tw!newsfeed.nthu.edu.tw!news.nthu.edu.tw!nthuls From: mjhsieh.bbs@bbs.life.nthu.edu.tw (謝孟叡) Newsgroups: bionet.molec-model Subject: Re: [QUESTION] Related news groups? Date: 24 Jun 1998 08:38:09 GMT Organization: 清華生命科學 BBS Lines: 16 Message-ID: <3PE2lY$Deo@bbs.life.nthu.edu.tw> NNTP-Posting-Host: bbs.life.nthu.edu.tw X-Filename: bn.mm/M.898677490.A ==> zhouli@IRIS.BIO.USTC.EDU.CN (Zhou Li) wrote: : Hi,Netters, : Who can post a list of some other news groups : dedicated to the topics of molecular simulation or : the URLs of the major research institutes (laboratories) : working on this field? The easiest way to get your answer is to find them in the search engine like yahoo! or altavista. There are some useful information in "Nee-How" database in your country. -- 謝孟叡,台灣國立清華大學生命科學系 | Francis M.J. Hsieh,Life Science,NTHU,TWN mjhsieh@life.nthu.edu.tw | Life Science BBS: bbs.life.nthu.edu.tw. -- ※ Origin: 生命科學 BBS ◆ From: mjhsieh.life.nth From owner-molec-model@net.bio.net Wed Jun 24 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newshub.northeast.verio.net!fu-berlin.de!news.uni-stuttgart.de!news.urz.uni-heidelberg.de!news.dkfz-heidelberg.de!not-for-mail From: N.N@DKFZ-Heidelberg.de (N.N) Newsgroups: bionet.molec-model Subject: Re: who can help me with Rasmol ? Date: 25 Jun 1998 08:20:01 GMT Organization: DKFZ Lines: 9 Message-ID: <6mt17h$fs3$2@news.inet.dkfz-heidelberg.de> References: <01bd96fc$b4b49360$f1f706c3@a.-van-de-wiele> Reply-To: a.bohne@DKFZ-Heidelberg.de NNTP-Posting-Host: zsp101.inet.dkfz-heidelberg.de X-Trace: news.inet.dkfz-heidelberg.de 898762801 16259 193.174.48.165 (25 Jun 1998 08:20:01 GMT) X-Complaints-To: usenet@news.dkfz-heidelberg.de NNTP-Posting-Date: 25 Jun 1998 08:20:01 GMT X-Newsreader: WinVN 0.92.6+ In article <01bd96fc$b4b49360$f1f706c3@a.-van-de-wiele>, "A Van de Wiele " says: > >Who can help me with Rasmol ? What is the command to oblige the machine to >name some groups in a molecule, for example atoms number: > 32-33-34-35-38-39-40-41-90-91-92-93-94-95 = residu >Asparagine ? That is a new peptid built with another soft and that is a >ent file. well, I would change it in the pdb-file. From owner-molec-model@net.bio.net Thu Jun 25 23:00:00 1998 Path: biosci!news.Stanford.EDU!nntp.cs.ubc.ca!hub.org!newsfeed.direct.ca!newsfeed.internetmci.com!128.174.5.49!vixen.cso.uiuc.edu!not-for-mail From: @staff.uiuc.edu () Newsgroups: bionet.molec-model Subject: VMD-"Visual Molecular Dynamics" 1.2 beta 3 available! Date: 26 Jun 1998 16:24:59 GMT Organization: University of Illinois at Urbana-Champaign Lines: 143 Message-ID: <6n0i0r$870$1@vixen.cso.uiuc.edu> NNTP-Posting-Host: staff1.cso.uiuc.edu Announcing version 1.2b3 release of VMD --------------------------------------- The Theoretical Biophysics group at the University of Illinois and the Beckman Institute would like to announce the availability of version 1.2b3 of the program VMD, a package for the vizualization and analysis of biomolecular systems. This software is being made available to the structural biology research community free of charge, and includes the source code for VMD, documentation, and precompiled binaries for SGIs, HPs, Solaris 2, and Linux. The documentation (still being updated) includes an installation guide, a users guide, and a programmers guide for interested researchers. VMD also provides on-line help through the use of an external HTML viewer. A full description of VMD is available via the VMD WWW home page: http://www.ks.uiuc.edu/Research/vmd/ New in this version ------------------- o VMD now supports AIX 4.x with the native AIX OpenGL implementation o OpenGL rendering speed has been improved by 2-5x on several platforms o OpenGL version now correctly supports stereo-in-a-window o OpenGL/GL versions are now able to interoperate with VMD scripts created in by one or the other. o Upgraded some builds to use newer XForms libraries, which fix some GUI/Mouse bugs o VMD upgraded to compile with the 2.6c release of the CAVE libraries o VMD code now builds with much pickier C++ compilers (i.e. HP aCC) o New Linux binary distributions have working file browser now. o New Linux RPM style binary distribution o New HPUX10-OpenGL binaries for Visualize-FX hardware accelerators o New AIX4-OpenGL binaries for IBM OpenGL hardware accelerators o Many bug fixes Version 1.2b2 features ---------------------- o VMD has been ported to Sun Solaris 2. o Upgraded to support Linux RedHat 5.0 o OpenGL support works with native HP-UX and Sun OpenGL implementations o Added Tk support and upraded to Tcl/Tk 8.0 o Upgraded to Babel 1.6 o Added support for MSMS, a program for calculating molecular surfaces o Added support for Grasp file format o For most commands, typing in a command without arguments will print a help message o Added more commands to Tcl scripting interface o Many bug fixes Version 1.2b1 features ---------------------- o This biggest improvement in version 1.2b1 support for platforms other than GL-based SGIs. In addition to the full source and SGI binary distributions, VMD is now available for HP-UX (tested under 9 and 10) and Linux. o Greatly enhanced Tcl scripting commands for performing molecular analysis, writing scripts, developing tutorials, etc. o New rendering styles, a fast (and cheap) solvent accessible surface and C-alpha and P trace method, and improvements to the existing styles. o New output renderer formats: Postscript, VRML and STL (a stereo-lithography format) o Support for Amber structure and animation file formats ============= Basic information about VMD ================= Features -------- VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. The program has many features, which include: o No limits on the number of molecules, atoms, residues or number of animation frames, excepting available memory. o Many molecular rendering and coloring methods. o Stereo display capability. o Extensive atom selection syntax for choosing subsets of atoms for display (includes boolean operators, regular expressions, and more). o Integration with the program 'Babel' which allows VMD to read many molecular data file formats. Even without the use of Babel, VMD can read PDB files, as well as CHARMM- and X-PLOR compatible binary DCD files and X-PLOR compatible PSF files. o Ability to write the current image to a file which may be processed by a number of popular raytracing and image rendering packages, including POV-Ray, Rayshade, Raster3D, and Radiance. o Extensive graphical and text-based user interfaces, which use the Tcl package to provide full scripting capabilities. o Extensions to the Tcl language which enable researchers to write their own routines for molecular analysis o Modular, extensible source code using an object-oriented design in C++, with a programmer's guide describing the source code o Integration with the program NAMD, a fast, parallel, and scalable molecular dynamics program developed in conjunction with VMD in the Theoretical Biophysics Group at the University of Illinois. See the NAMD WWW home page for more info: http://www.ks.uiuc.edu/Research/namd/ VMD can be used to set up and concurrently display a MD simulation using NAMD. The two programs, along with the intermediary communcations package (called MDComm) constitute the 'MDScope' environment. Availability ------------ The software is available for downloading from http://www.ks.uiuc.edu/Research/vmd/ Please email any questions to vmd@ks.uiuc.edu. VMD, NAMD, and the entire MDScope environment are part of an ongoing project within the Theoretical Biophysics group to help provide free, effective tools for molecular dynamics studies in structural biology. For more information, see http://www.ks.uiuc.edu/Research/MDScope/. This project is funded by the National Institutes of Health (grant number PHS 5 P41 RR05969) and the Roy J. Carver Charitable Trust. John Stone vmd@ks.uiuc.edu June 25, 1998 From owner-molec-model@net.bio.net Thu Jun 25 23:00:00 1998 Path: biosci!PUBLIC.BTA.NET.CN!maxj From: maxj@PUBLIC.BTA.NET.CN (maxuejun) Newsgroups: bionet.molec-model Subject: (no subject) Date: 25 Jun 1998 23:54:02 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 3 Sender: daemon@net.bio.net Distribution: world Message-ID: <35934621.208EDB2F@public.bta.net.cn> NNTP-Posting-Host: net.bio.net Help info FAQ From owner-molec-model@net.bio.net Fri Jun 26 23:00:00 1998 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molec-model Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 27 Jun 1998 02:00:16 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199806270900.CAA04571@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 Mon Jun 29 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!152.163.199.19!portc03.blue.aol.com!audrey01.news.aol.com!not-for-mail From: gtompk2922@aol.com (GTompk2922) Newsgroups: bionet.molec-model Subject: Laborartory Equipment_New and Used Lines: 4 Message-ID: <1998063000112100.UAA04546@ladder01.news.aol.com> NNTP-Posting-Host: ladder01.news.aol.com X-Admin: news@aol.com Date: 30 Jun 1998 00:11:21 GMT Organization: AOL http://www.aol.com Check out our web site for great deals on new and used lab equipment. Use our equipment exchange area to sell your surplus equipment or find equipment you are looking gor. 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