From owner-structural-nmr@net.bio.net Thu Aug 01 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!news.sgi.com!enews.sgi.com!EU.net!Portugal.EU.net!news.rccn.net!scsing.switch.ch!swsbe6.switch.ch!news.belnet.be!infoserv.rug.ac.be!bionmr1!kris From: kris@bionmr1.bionmr1.rug.ac.be (Kris Boulez) Newsgroups: bionet.structural-nmr Subject: Diana on Linux ? Date: 2 Aug 1996 07:03:13 GMT Organization: University of Ghent, Belgium Lines: 11 Message-ID: <4ts97h$4ol@infoserv.rug.ac.be> NNTP-Posting-Host: bionmr1.rug.ac.be X-Newsreader: TIN [version 1.2 PL2] Hello, Has anyone gotten Diana, the structure calculation package from Prof. Wuthrich's group, to compile on Linux ? Which compiler/libraries were used ? Kris, -- Kris Boulez (Kris.Boulez@rug.ac.be) Biomolecular NMR unit University of Ghent, Belgium From owner-structural-nmr@net.bio.net Thu Aug 01 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!news.sgi.com!enews.sgi.com!EU.net!Portugal.EU.net!news.rccn.net!scsing.switch.ch!swsbe6.switch.ch!news.belnet.be!infoserv.rug.ac.be!news From: Kris Boulez Newsgroups: bionet.structural-nmr Subject: Diana on Linux ? Date: Fri, 02 Aug 1996 09:08:41 +0200 Organization: University of Ghent, Belgium Lines: 11 Message-ID: <3201A979.41C6@rug.ac.be> NNTP-Posting-Host: bionmr1.rug.ac.be Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP17) Hello, Has anyone gotten Diana, the NMR structure calculation package from Prof. Wuthrich's group, to compile on Linux ? Which versions of compiler/libraries were used ? Kris -- Kris Boulez (Kris.Boulez@rug.ac.be) Biomolecular NMR unit University of Ghent, Belgium From owner-structural-nmr@net.bio.net Fri Aug 02 23:00:00 1996 Path: biosci!BIOC01.UTHSCSA.EDU!raman From: raman@BIOC01.UTHSCSA.EDU (C.S.RAMAN) Newsgroups: bionet.structural-nmr Subject: Announcing ANSIG - Software for assigning Protein NMR spectra Date: 2 Aug 1996 18:40:02 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 72 Sender: daemon@net.bio.net Distribution: world Message-ID: <9608030139.AA04710@bioc01.uthscsa.edu> NNTP-Posting-Host: net.bio.net Dear str-nmr readers: On behalf of Per Kraulis (author of Molscript and Ansig), I am posting the following announcement regarding the program ANSIG. Per had sent me this posting a while back, but, due to an oversight on my part, was unable to post the same. My apologies to Per. Cheers -raman Protein NMR software announcement: The ANSIG (Assignment of NMR Spectra by Interactive Graphics) program, release 3.3 is now available on the web. The entire documentation can be browsed, and the complete distribution can be fetched. There are two alternative sites (with identical content): http://nirvana.bioc.cam.ac.uk/ Follow the link "ANSIG v3.3". http://nmrsgi1.ncifcrf.gov/ansig/doc/ansig.html ANSIG is a program for inspection and assignment of NMR 2D/3D/4D homo- and heteronuclear spectra, mainly but not exclusively geared towards proteins. Literature references: P.J. Kraulis et al, Biochemistry (1994) v 33, pp 3515-3531, and P.J. Kraulis, J. Magn. Reson. (1989), v 24, pp 627-633. The ANSIG program is *not* in the public domain. A signed license is required. However, the program is free for academic institutions. The distribution contains source code, library files, documentation (in HTML format), and several matrix conversion programs. Two different example data sets are available from the FTP sites. The ANSIG program is written for the Silicon Graphics machines using GL and Fortran 77 (the first version of the program was released in 1989). It will compile on IRIX 5.2 and 5.3 systems, and hopefully also on 4.0.5 and 6.2 systems. I thank Dr. Ernest Laue and Dr. Andrew Raine (Cambridge, UK) and Dr. Andrew Byrd and Dr. Paul Dowling (ABL, NCI-FCRDC, USA) for making space available to set up the web sites. -- Per Kraulis, Ph.D. phone: +46 (8) 695 78 34 Pharmacia & Upjohn Inc fax: +46 (8) 695 40 82 Biopharmaceuticals R&D, N62:5 e-mail: krpx@sgikrpe.sto.pharmacia.se S-112 87 Stockholm or p.j.kraulis@bioc.cam.ac.uk SWEDEN --------------------------------------------------------------------- "Nothing is more difficult than simplicity." Unattributed. -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ C.S.RAMAN _/ _/ Department of Biochemistry _/ _/ University of Texas Health Science Center _/ _/ 7703 Floyd Curl Drive _/ _/ San Antonio, TX 78284-7760 _/ _/ USA _/ _/ _/ _/ Tel: (210) 614-0839 _/ _/ Fax: (210) 567-6595 _/ _/ E-mail: raman@bioc01.uthscsa.edu _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ "The real problem in speech is not precise language. _/ _/ The problem is clear language." --Richard Feynman _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From owner-structural-nmr@net.bio.net Sat Aug 03 23:00:00 1996 Path: biosci!sfu.ca!dnaugler From: dnaugler@sfu.ca (David Naugler) Newsgroups: bionet.structural-nmr Subject: Unstructured NMR question Date: 4 Aug 1996 15:01:43 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: <199608042201.WAA24854@beaufort.sfu.ca> NNTP-Posting-Host: net.bio.net Dear str-nmr readers: Many interesting peptides are essentially unstructured or only partly structured. A full treatment of dynamics and polymer statistics would be of great interest. Could someone please recommend a recent review paper which would help me proceed from NMR data to a thorough phys-chem treatment. So far I have already done a great deal of homonuclear and heteronuclear 2D and 3D NMR. I have been studying a 28 amino acid peptide fragment from the alpha subunit of the nicotinic acetylcholine receptor which is only four amino acids removed from the minimal epitope known as the Main Immunogenic Region in the human autoimmune disease Myasthenia Gravis. Thanks in advance. David Naugler Institute of Molecular Biology and Biochemistry Simon Fraser University TEL: (604) 291-5657 FAX: (604) 291-5583 From owner-structural-nmr@net.bio.net Sat Aug 03 23:00:00 1996 Path: biosci!servaly.hobby.nl!wybo From: wybo@servaly.hobby.nl (Wybo Dekker) Newsgroups: bionet.structural-nmr Subject: Re: Unsymmetrical amide NMR question Date: 4 Aug 1996 00:55:46 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net > I am desparately in need of a literature reference > which states that N-methyl amides (-CONHCH3) show restricted rotation on > the NMR timescale (You see two sets of peaks). I have > references which describe disubstituted amides. Are you sure you are not just looking at the NH-CH3 coupling (~5 Hz)? ===================Servalys Analytical Chemistry Services================= Wybo H. Dekker | Deilsedijk 60 | tel (31)345-652164 wybo@servaly.hobby.nl | 4158 CH Deil, The Netherlands | fax (31)345-652383 From owner-structural-nmr@net.bio.net Sun Aug 04 23:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!ubaclu.unibas.ch!ubaclu.unibas.ch!nntp Newsgroups: bionet.structural-nmr Subject: NMR post-doctoral positions -> Biozentrum, U. Basel, Switzerland Message-ID: <32066973.41C6@ubaclu.unibas.ch> From: andrei Date: Mon, 05 Aug 1996 23:36:52 +0200 Nntp-Posting-Host: nmr.bioz.unibas.ch X-Mailer: Mozilla 3.0b5aGold (X11; I; IRIX 5.3 IP17) MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 62 Applications are invited for two Biomolecular-NMR post doctoral positions in the Department of Structural Biology of the Biozentrum, University of Basel - Switzerland. Persons who have received a Ph.D. within the last 6 months, or who expect to receive their Ph.D. within 3 months are strongly preferred. One position is for a person with a technical NMR background. The applicant should have strong computational skills, and extensive experience in programming multidimensional heteronuclear NMR pulse sequences in a UNIX environment. The second position is for an NMR spectroscopist with a molecular biology background. Applicants should ideally have hands-on experience with PCR, mutagenesis, T7 expression systems, 13C/15N isotopic labeling, and protein purification. In addition, outstanding candidates with a primary interest in protein folding and original ideas on how to make progress with THE PROBLEM are also strongly encouraged to apply. Our group's current research interests include: 1) Folding and dynamics of non-homologous proteins that share an OB-fold structural motif. 2) Protein engineering. 3) Isotopically labeled peptides for NMR studies of peptide-protein complexes. 4) NMR structure determination. NMR experiments will be carried out on a dedicated 600 MHz Varian Unity-Plus spectrometer, on which our group (3 NMR users) has 30 % measurement time. This instrument is equipped with pulse field gradients, triple resonance probes, and 4 channels for multidimensional heteronuclear experiments. An SGI Crimson, and INDY computer are available for NMR data processing and analysis. Successful candidate should be highly motivated, and should have a track-record of original publications. Interested and qualified applicants should send a C.V. as well as the names and addresses of 3 referees familiar with the applicant's work to: Dr. Andrei T. Alexandrescu Biozentrum University of Basel Klingelbergstrasse 70 Basel/Switzerland CH-4056 Tel: 41-61-267-2091 Fax: 41-61-267-2109 email: alexandrescu@ubaclu.unibas.ch Use of Fax or e-mail is appreciated, and will expedite responses to inquiries. From owner-structural-nmr@net.bio.net Sun Aug 04 23:00:00 1996 Path: biosci!BIOC01.UTHSCSA.EDU!raman From: raman@BIOC01.UTHSCSA.EDU (C.S.RAMAN) Newsgroups: bionet.structural-nmr Subject: CALL FOR STRUCTURE PREDICTION TARGETS Date: 5 Aug 1996 11:56:08 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 316 Sender: daemon@net.bio.net Distribution: world Message-ID: <9608051854.AA06216@bioc01.uthscsa.edu> NNTP-Posting-Host: net.bio.net Hello everyone: John Moult requested that I post the following to the STR-NMR community in order to solicit structure prediction targets for CASP2. Cheers -raman ---------------------------------------------------------------------------- Appeal for Structure Prediction Targets --------------------------------------- To all Protein NMR Spectroscopists: As you probably know, the second Asilomar protein structure prediction experiment (called CASP2) is well underway, with a prediction season running until October 1, and a meeting in December. The goal of the experiment is to obtain as objective a view as possible of what current protein structure prediction methods are or are not capable of. The method used is to obtain information about soon to be solved structures from experimentalists, to pass that on to the predictors, and to collect their models before the structure becomes public. The first experiment, held during 1994, produced a large amount of interesting and provocative data. A special issue of PROTEINS (vol 23, no 3, November 1995) contains papers describing the outcome. There is also a recent 'Science' 'Research News' (vol 273, 426-428, 26 July, 1996) providing some more background. We hope the second experiment will be as informative as the first. In particular, a big question now is the extent to which the key problems identified have been solved in the intervening two years. You can find out more about the whole process from two web sites: http://iris4.carb.nist.gov/casp2 http://www.mrc-cpe.cam.ac.uk/casp2 If you would like to be get the mailings associated with the experiment, please register there as 'interested'. So far, we have 78 groups registered as intending to make predictions. 35 teams took part last time, so we are on the way to doubling participation. Indeed, at about the half way point in the prediction season, in excess of 300 predictions have been received, more than double the number obtained last time. However, we are still short of prediction targets. In order to get statistically meaningful results, it is important that there is a range of targets predicted in each of the four categories (see below), so we would like predictions on a total of around 50 proteins and protein complexes, but so far have only 30. A number of the deadlines for predictions on those have now passed, and so the number available to predictors at this moment is only about 20. (Information about current and expired targets is available on the web sites.) Thus, the purpose of this message is to ask you to help with target provision, if you can. The rules are spelled out on the general target request below. We need targets in all four categories, and with expiry dates between quite soon and October 1. We are particularly in need of relatively small protein targets suitable for ab initio prediction methods, and hope that the NMR community can be particularly helpful in that area. Even if you do not have any targets available yourself, please pass this message on to other experimentalists you think might be interested. If you have any queries about what is involved in submitting a target, please send me a message. We cannot make this experiment work without again the help of the experimental community. John Moult. jmoult@indigo5.carb.nist.gov ----------------------------------------------------------------------------- Announcement: Call for prediction targets for CASP2 =================================================== This is a call to X-ray crystallographers and NMR spectroscopists. In 1994 the first protein structure prediction experiment was held to evaluate prediction methods through blind prediction. Details of about 33 protein sequences, which were expected to be solved before the end of 1994, were submitted by experimentalists and this allowed 135 blind predictions to be made by 35 different groups, and led to the most objective assessment of prediction methods so far. The results of the experiment are published in the November 1995 issue of Proteins: Structure, Function, and Genetics. This is the announcement of the second prediction experiment, which will run throughout 1996 and culminate in an evaluation meeting in December. As before, for the experiment to succeed, it is essential that we obtain the help of the experimental community. Therefore, we would like to invite Protein crystallographers and NMR spectroscopists who expect to solve a structure before 1st October 1996 to submit the sequence so that attempts can be made to predict it before it is publically announced. Each prediction will be given a deadline prior to the date on which the first information about the structure is to be made public. Targets of all sizes and types are required. Small structures (less than 100 residues) are needed to test some of the ab initio structure prediction methods. Proteins with folds related to those of known structures are needed to test fold identification methods. Proteins with sequences homologous to that of one or more known structures are needed to test comparative modeling methods. Protein-Protein and Protein-Ligand complexes are required to test docking methods. All that is requested is: - the sequence or a sequence accession number of the protein - an estimate of the likely date of public release (and updates if the work proceeds faster or slower) - a commitment to make the coordinates available to the independent assessors not latter than 1st October should the structure be solved by then. Any coordinates provided will be treated with strict confidentiality as requested and used only to evaluate the accuracy of predictions. For further information and on-line forms and documents see: http://iris4.carb.nist.gov/casp2/ http://www.mrc-cpe.cam.ac.uk/casp2/ A Target protein submission form is also attached to this message and can be mailed to casp2@mrc-lmb.cam.ac.uk Tim Hubbard Co-chair Centre for Protein Engineering, Cambridge, UK. Steve Bryant Co-chair NCBI, National Library of Medicine, USA. John Moult President CARB, University of Maryland, USA. Jan T. Pedersen CARB, University of Maryland, USA Krzysztof Fidelis Lawrence Livermore National Laboratory, USA. Richard Judson Sandia National Laboratory, USA. ------------------------------------------------------------------------- CASP2: Second Meeting on the Critical Assessment of Techniques for Protein Structure Prediction Target submission form ====================== Instructions for completing this form ------------------------------------- (0) Please only use this form if you are unable to complete the WWW version at http://iris4.carb.nist.gov/casp2/ or http://www.mrc-cpe.cam.ac.uk/casp2/ (1) Save this page as a text file (2) Complete all sections (3) send by email to casp2@mrc-lmb.cam.ac.uk (4) if you have filled out the form correctly, you should receive an email acknowledgement (though not necessarily immediately) cut here ------------------------------------------------------------------------- CASP2: Second Meeting on the Critical Assessment of Techniques for Protein Structure Prediction Target submission form ====================== This is the text version of the Prediction target submission form for the Second Critical Assessment Techniques for Protein Structure Prediction Experiment (CASP2). Introduction ============ Protein crystallographers and NMR spectroscopists are asked to provide details of structures they expect to have solved before 1st October 1996 using this form. Targets of all sizes and types are required. Small structures (less than 100 residues) are needed to test some of the ab initio structure prediction methods. Proteins with folds related to those of known structures are needed to test fold recognition methods. Proteins with sequences homologous to that of one or more known structures are needed to test comparative modelling methods. To be useful to the predictors, a period of at least a month is required before any details of the structure will be released. Please notify us immediately when the details are going to be made public, so that we can ask the predictors to stop work in a timely manner. This can be done by sending a mail to casp2@mrc-lmb.cam.ac.uk. In order for the predictions to be assessed in time for the meeting in December, we will need a set of co-ordinates by the beginning of October at the latest. If necessary, these can be for limited distribution until the meeting. A. Scientific information ========================= 1. [ ] Protein Name 2. [ ] Organism Name 3. [ ] Number of amino acids (does not need to be exact) Please provide accession number and database of the protein or the actual sequence (both if possible). 4. [ ] Accession number 5. Sequence Database [ ] Swiss-prot [ ] PIR [ ] Genbank [ ] EMBL [ ] Other [ ] 6. Amino acid sequence One letter code (ACEDFTK) is preferred, but three letter code (ala cys glu asp) can also be processed. 7. Are there homologous sequences of known structure to this protein? Yes [ ] No [ ] 8. Current state of the experimental work Please describe briefly where things are at. The more information, the easier it is for a modeler to decide whether to predict your structure. For example, protein supply? interpretable NMR spectra? 9. Do you already have a set of NOE assignments? Yes [ ] No [ ] 10. [ ] Estimated date of obtaining an initial structure. (In order to assess the predictions before the meeting, this date should be before 1st October 1996.) 11. [ ] Estimated date of public release of structure 12. If you have any other useful information about this sequence family please enter it below B. Administrative information ============================= 13. [ ] Name 14. Mailing address: [ ] 15. [ ] Tel 16. [ ] Fax 17. [ ] Email 18. How did you hear about this prediction experiment? [ ] Nature Add [ ] Poster [ ] Newsgroup [ ] Email [ ] Other [ ] ------------------------------------------------------------------------- -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ C.S.RAMAN _/ _/ Department of Biochemistry _/ _/ University of Texas Health Science Center _/ _/ 7703 Floyd Curl Drive _/ _/ San Antonio, TX 78284-7760 _/ _/ USA _/ _/ _/ _/ Tel: (210) 614-0839 _/ _/ Fax: (210) 567-6595 _/ _/ E-mail: raman@bioc01.uthscsa.edu _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ "The real problem in speech is not precise language. _/ _/ The problem is clear language." --Richard Feynman _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From owner-structural-nmr@net.bio.net Mon Aug 05 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!surfnet.nl!swsbe6.switch.ch!scsing.switch.ch!rzunews.unizh.ch!NewsWatcher!user From: zjons@vetbio.unizh.ch (Zophonias O. Jonsson) Newsgroups: bionet.xtallography,bionet.structural-nmr Subject: Protein expression in D2O Date: Tue, 06 Aug 1996 10:29:56 +0000 Organization: Universitat Zurich-Irchel Lines: 23 Message-ID: NNTP-Posting-Host: 130.60.120.10 Xref: biosci bionet.xtallography:2783 bionet.structural-nmr:1426 Dear friends! We want to get large amounts of deuteriated protein by expression in E.coli grown in D2O (for neutron scattering experiments). Because of the price of the substance we would be very thankful for any advice that could save us experimentation. A simple medline search revealed only one paper on the subject. If you have any experience, protocols or references that could be of help we would be very happy. Even educated guesses about what to use as a carbon source for the bacteria would be helpful (as well as other tips about other components of a suitable growth medium). Sincerely Zophonias _____________________________________________________________________ Zophonias O. Jonsson Institut fur Veterinarbiochemie Tel: (41-1)-257-54-75 Universitat Zurich-Irchel Fax: (41-1)-362-05-01 Winterthurerstrasse 190 CH-8057 Zurich Switzerland _____________________________________________________________________ From owner-structural-nmr@net.bio.net Mon Aug 05 23:00:00 1996 Path: biosci!agate!newsgate.duke.edu!solaris.cc.vt.edu!homer.alpha.net!uwm.edu!chi-news.cic.net!news.luc.edu!orion!csriniv From: csriniv@orion.it.luc.edu (Chandra Srinivasan) Newsgroups: bionet.structural-nmr Subject: Postdoctoral Position Date: 6 Aug 1996 04:56:50 GMT Organization: Loyola University Chicago Lines: 11 Message-ID: <4u6jai$9n2@artemis.it.luc.edu> NNTP-Posting-Host: 147.126.1.9 NNTP-Posting-User: csriniv X-Newsreader: TIN [version 1.2 PL2] August 5, 1996 POSTDOCTORAL POSITION available immediately to investigate the pharmacological action of lithium in the treatment of manic-depression in NIMH-funded project. One year appointment that can be extended for a second year subject to performance. Experience in NMR spectroscopy and biochemical methods preferred. Send c.v. and three letters of recommendation to Professor Duarte Freitas, Department of Chemistry, Loyola University, 6525 North Sheridan Road, Chicago, IL 60626. From owner-structural-nmr@net.bio.net Mon Aug 05 23:00:00 1996 Path: biosci!agate!newsxfer2.itd.umich.edu!newsfeed.internetmci.com!in3.uu.net!news2.digex.net!usenet From: numare@cnj.digex.net Newsgroups: bionet.xtallography,bionet.structural-nmr Subject: Re: Protein expression in D2O Date: Tue, 06 Aug 96 16:09:39 PDT Organization: Express Access Online Communications, USA Lines: 65 Message-ID: References: NNTP-Posting-Host: cjc08014.slip.digex.net Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Newsreader: NEWTNews & Chameleon -- TCP/IP for MS Windows from NetManage Xref: biosci bionet.xtallography:2785 bionet.structural-nmr:1430 In article , writes: > Path: news2.digex.net!howland.reston.ans.net!surfnet.nl!swsbe6.switch.ch!scsing.switc h.ch!rzunews.unizh.ch!NewsWatcher!user > From: zjons@vetbio.unizh.ch (Zophonias O. Jonsson) > Newsgroups: bionet.xtallography,bionet.structural-nmr > Subject: Protein expression in D2O > Date: Tue, 06 Aug 1996 10:29:56 +0000 > Organization: Universitat Zurich-Irchel > Lines: 23 > Message-ID: > NNTP-Posting-Host: 130.60.120.10 > Xref: news2.digex.net bionet.xtallography:2680 bionet.structural-nmr:1362 > 08 August 1996, Tuesday, 1625 EDT Dear Zophonias, Don't know about specifice techniques or lit. refs., however, to save funds, why not setup your laboratory as a clearing house for spent deuterium oxide? Seems ashame that this expensive material is most often discarded after use as NMR solvent. Simple filtration and distillation would return it to usable form for your laboratory to use. I imagine that if you offered to pay for shipping, you might very soon have all the D2O that you will ever need. Good luck, Best regards, Lawrence Byrnes, NMR spectroscopist, Numare Spectralab Incorporated, email numare@cnj.digex.net www http://www.cnj.digex.net/~numare/ > Dear friends! > > We want to get large amounts of deuteriated protein by expression in > E.coli grown in D2O (for neutron scattering experiments). Because of the > price of the substance we would be very thankful for any advice that could > save us experimentation. A simple medline search revealed only one paper > on the subject. If you have any experience, protocols or references that > could be of help we would be very happy. Even educated guesses about what > to use as a carbon source for the bacteria would be helpful (as well as > other tips about other components of a suitable growth medium). > > Sincerely > > Zophonias > > _____________________________________________________________________ > Zophonias O. Jonsson > Institut fur Veterinarbiochemie Tel: (41-1)-257-54-75 > Universitat Zurich-Irchel Fax: (41-1)-362-05-01 > Winterthurerstrasse 190 > CH-8057 Zurich > Switzerland > _____________________________________________________________________ > From owner-structural-nmr@net.bio.net Mon Aug 05 23:00:00 1996 Path: biosci!ASCARIS.HEALTH.UFL.EDU!art From: art@ASCARIS.HEALTH.UFL.EDU (Art Edison) Newsgroups: bionet.structural-nmr Subject: USA/FL Postdoc position in biological NMR Date: 6 Aug 1996 11:45:58 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 37 Sender: daemon@net.bio.net Distribution: world Message-ID: <199608061846.OAA03720@ascaris.health.ufl.edu> NNTP-Posting-Host: net.bio.net Postdoctoral positions at the University of Florida and NHMFL I have one or two postdoctoral positions available in my laboratory. The major emphasis of the lab is the use of structural biology to solve exciting neurobiological problems. Thus, I am interested in people with backgrounds in biological NMR, molecular biology, protein expression, or neurobiology. Combinations of these backgrounds is desirable. We are currently working on the following projects: 1. NMR structure determination of neuropeptide precursor proteins. 2. Expression of a neuropeptide-gated sodium-channel receptor for TRNOE conformational studies of the peptide ligand. 3. TRNOE studies of multiple neuropeptide ligands to a membrane extract containing identified receptors. My lab is well-equipped to make proteins, and we have 50-75% time on a fully-equipped 600MHz instrument. In addition, I am a member of the National High Magnetic Field Laboratory (NHMFL), so the successful candidate will have full access to facilities at the NHMFL, including 500, 600, and 720 MHz spectrometers. For further information, please contact me be e-mail. Please send applications (letter of interests, CV, and 3 letters of recommendation) to: ******************************************************* Arthur S. Edison, Ph.D. Department of Biochemistry and Molecular Biology Center for Structural Biology Box 100245 University of Florida Gainesville, FL 32610-0245 352-392-4535 (ph) 352-392-3422 (fax) e-mail: art@ascaris.health.ufl.edu ******************************************************* From owner-structural-nmr@net.bio.net Mon Aug 05 23:00:00 1996 Path: biosci!daresbury!is.bbsrc.ac.uk!news.ox.ac.uk!ocms0001 From: ocms0001@ermine.ox.ac.uk (Dennis Benjamin) Newsgroups: bionet.xtallography,bionet.structural-nmr Subject: Re: Protein expression in D2O Followup-To: bionet.xtallography,bionet.structural-nmr Date: 6 Aug 1996 11:03:02 GMT Organization: Oxford University, England Lines: 12 Message-ID: <4u78p6$rpn@news.ox.ac.uk> References: NNTP-Posting-Host: ermine.ox.ac.uk X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.xtallography:2784 bionet.structural-nmr:1428 Zophonias O. Jonsson (zjons@vetbio.unizh.ch) wrote: : save us experimentation. A simple medline search revealed only one paper : on the subject. If you have any experience, protocols or references that Don't know whether you already found this one, but Vanatalu et. al. Eur. J. Biochem. 216,315-321 (1993) discusses Knud Nierhaus' approach to preparing deuterated ribosomes for neutron scattering. Seems like it would be applicable to soluble proteins as well. From owner-structural-nmr@net.bio.net Mon Aug 05 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!spool.mu.edu!torn!news.ccs.queensu.ca!kone!nott!standby.nrc.ca!BRI.NRC.CA!Feng.Ni From: Feng.Ni@BRI.NRC.CA (Feng Ni) Newsgroups: bionet.structural-nmr Subject: RESEARCHER POSITIONS IN PROTEIN NMR SPECTROSCOPY Date: 5 Aug 1996 22:22:48 GMT Organization: Institut de recherche en biotechnologie, Montréal Lines: 44 Distribution: world Message-ID: <4u5s7o$6a2@standby.nrc.ca> NNTP-Posting-Host: bravais.bri.nrc.ca RESEARCHER POSITIONS IN PROTEIN NMR SPECTROSCOPY The NMR laboratory of the Biotechnology Research Institute (BRI) have openings for self-motivated young researchers in the area of biomolecular/protein NMR spectroscopy. Candidates should have a recent Ph.D. in chemistry, biochemistry or a related field and have demonstrated abilities in carrying out creative research. Experiences include the determination of protein structures and/or the study of protein-ligand interactions by use of triple resonance and multi- dimensional NMR spectroscopy. Knowledge in isotope labelling and protein/pep- tide purification is an important asset. Successful candidates will normally start in the postdoctoral level, or depending on qualifications, may be recruited directly to more senior positions offerred by the National Research Council of Canada. The Research Council offers competitive salaries and other compensation packages commensurate upon your experience and appointment levels. The NMR laboratory at BRI is equipped with one Bruker AMX2-500 MHz spectrometer and shares a Bruker DRX-500 MHz spectrometer with members of the Montreal Joint Centre for Structural Biology. A new state-of-the-art 750 MHz NMR instrument will be added to the facility within the coming year. NMR researchers also have access to excellent computing facilities and work in multidisciplinary teams with expertise in molecular biology, protein/peptide chemistry, molecular design and structural biology. The Biotechnology Research Institute (BRI) is a branch of the National Research Council of Canada, interfacing academia and industry. Your challenge at BRI will be to succeed in high-impact scientific research while generating prac- tical applications transferable to pharmaceutical industry. Qualified indivi- duals are invited to submit your resume, along with the names and addresses of three references, to: Feng Ni, Ph.D. Head of Biomolecular NMR Biotechnology Research Institute 6100 Royalmount Avenue Montreal, Quebec, H4P 2R2, Canada phone: (514)-496-6729; fax: (514)-496-5143 e_mail: fengni@bri.nrc.ca Applications will be accepted until the positions are filled. We thank all applicants for their interests, however, only those being considered will be contacted. From owner-structural-nmr@net.bio.net Tue Aug 06 23:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news.ox.ac.uk!nmrsjm.ocms!sjm From: sjm@bioch.ox.ac.uk (Stephen Matthews) Newsgroups: bionet.structural-nmr Subject: POSTDOC POSITION IN LONDON Date: 7 Aug 1996 10:46:14 GMT Organization: Oxford University Lines: 16 Message-ID: <4u9s5m$seh@news.ox.ac.uk> NNTP-Posting-Host: nmrsjm.ocms.ox.ac.uk Imperial College is presently strengthening structural biology. In addition to augmenting X-ray and electron diffraction expertise a biological NMR facility is being installed within the biochemistry department. Applications are invited for a postdoctoral position within this Wellcome funded laboratory. The position is available from January 1 1997 and will run for at least three years. Applicants should have several years experience of NMR and knowledge of applications in macromolecular structure determination. NMR spectroscopists from any discipline who wish to move in a biological direction are also encouraged to apply. A CV, list of publications, summary of research achievements and aims should be sent to Dr Stephen Matthews, Department of Biochemistry, Imperial College of Science Technology and Medicine, South Kensington, London SW7 2AY. Tel 44 (0)171 594 5315, email sjm@bioch.ox.ac.uk From owner-structural-nmr@net.bio.net Tue Aug 06 23:00:00 1996 Path: biosci!agate!newsxfer2.itd.umich.edu!newsfeed.internetmci.com!in3.uu.net!ott.istar!istar.net!tor.istar!east.istar!news.nstn.ca!thor.atcon.com!apollo.isisnet.com!eru.mt.luth.se!news.kth.se!news From: Arne Elofsson Newsgroups: bionet.structural-nmr Subject: Re: Diana on Linux ? Date: 07 Aug 1996 11:41:28 +0200 Lines: 25 Message-ID: References: <3201A979.41C6@rug.ac.be> NNTP-Posting-Host: rune.biokemi.su.se Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit To: Kris.Boulez@rug.ac.be X-Newsreader: Gnus v5.2.37/XEmacs 19.14 Kris Boulez writes: > > Hello, > > Has anyone gotten Diana, the NMR structure calculation package from > Prof. Wuthrich's group, to compile on Linux ? Which versions of > compiler/libraries were used ? > Just for fun, I compiled diana and it worked without any problems (I deleted the timing but who cares about that) I used gcc-2.7.2 and g77-0.5.18 the binary is available from http://www.biokemi.su.se/~arne/export/diana However I have not tested it since I haven't used diana in years Hope this helps arne -- ----------------------------------------------------------------- From: Arne Elofsson Email: arne@rune.biokemi.su.se Tel:+46(0)8-161553 WWW: http://www.biokemi.su.se/~arne/ From owner-structural-nmr@net.bio.net Wed Aug 07 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: ramakrishna Newsgroups: bionet.structural-nmr Subject: test Date: 8 Aug 1996 05:50:17 +0100 Lines: 2 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4ubrm9$f6u@mserv1.dl.ac.uk> MIME-Version: 1.0 Original-To: Structural-nmr group this is a test mail. From owner-structural-nmr@net.bio.net Thu Aug 08 23:00:00 1996 Path: biosci!biosci!not-for-mail From: Petar_Stojadinovic@sequana.com (Petar Stojadinovic) Newsgroups: bionet.biophysics,bionet.genome.chromosomes,bionet.neuroscience,bionet.protista,bionet.software,bionet.software.acedb,bionet.software.gcg,bionet.software.srs,bionet.software.staden,bionet.software.x-plor,bionet.structural-nmr,bionet.toxicology,bionet.users.addresses,bionet.women-in-bio,bionet.xtallography Subject: Clinical Lab Automation & Development, Computational Biology,Biotech Engineering Date: 8 Aug 1996 22:36:25 -0700 Organization: Sequana Therapeutics, Inc. Lines: 13 Sender: biohelp@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Xref: biosci bionet.biophysics:2205 bionet.genome.chromosomes:1303 bionet.neuroscience:15213 bionet.protista:584 bionet.software:16272 bionet.software.acedb:956 bionet.software.gcg:1948 bionet.software.srs:286 bionet.software.staden:221 bionet.software.x-plor:680 bionet.structural-nmr:1434 bionet.toxicology:849 bionet.users.addresses:3079 bionet.women-in-bio:5326 bionet.xtallography:2789 Wanted: Abstracts, Interested members to Join Engineers in Biotechnology Subchapter of Assoc. of Laboratory Automation (ALA) or ICAR in Europe. please send email to : petar@sequana.com PS: Do you know how I may enter a new newsgroup in alt as alt.biotech.engineers? Thank you. Petar Stojadinovic Sequana Therapeutics Inc. Engineering Dept. Phone: 619-6468263 email: petar@sequana.com From owner-structural-nmr@net.bio.net Sun Aug 11 23:00:00 1996 Path: biosci!GUITAR.ROCKEFELLER.EDU!ilya From: ilya@GUITAR.ROCKEFELLER.EDU (Ilya Vakser) Newsgroups: bionet.structural-nmr Subject: Announcement - protein docking program GRAMM Date: 12 Aug 1996 15:16:26 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 92 Sender: daemon@net.bio.net Distribution: world Message-ID: <320FAE76.41C6@guitar.rockefeller.edu> NNTP-Posting-Host: net.bio.net ----------- GRAMM v1.03 ----------- This note is to announce the availability of GRAMM (Global RAnge Molecular Matching) software. GRAMM is a program for protein docking. To predict the structure of a complex, it requires only the atomic coordinates of the two molecules (no information about the binding sites is needed). The program performs an exhaustive 6-dimensional search through the relative translations and rotations of the molecules. The molecular pairs may be: two proteins, a protein and a smaller compound, two transmembrane (TM) helices, etc. GRAMM may be used for high- resolution molecules, for inaccurate structures (where only the gross structural features are known), in cases of large conformational changes, etc. The Global Range Molecular Matching (GRAMM) methodology is an empirical approach to smoothing the intermolecular energy function by changing the range of the atom-atom potentials. The technique allows to locate the area of the global minimum of intermolecular energy for structures of different accuracy. The quality of the prediction depends on the accuracy of the structures. Thus, the docking of high-resolution structures with small conformational changes yields an accurate prediction, while the docking of ultralow-resolution structures will give only the gross features of the complex. _________________ I am making GRAMM publicly available following a number of requests from different labs. I would like to make it clear, however, that both the methodology and the program, at present, are in the process of active development and validation, especially in the area of the low-resolution docking, and have to be viewed like that. The program is free. However, I would expect proper references. I will also appreciate bug reports. To get GRAMM, send the request to ilya@guitar.rockefeller.edu. The GRAMM site on the Web is http://guitar.rockefeller.edu/. GRAMM was created during my stay in the Weizmann Institute (1991-1993), in the Washington University (1993-1995), and in the Rockefeller University (1995-1996). I deeply appreciate the assistance of my colleagues in all these institutions (especially, Profs. Ephraim Katchalski-Katzir, Garland Marshall, and Andrej Sali). Platforms Presently, GRAMM is compiled on SGI R4000, SGI R4400, SGI R8000, and SGI R10000 Unix workstations. In the near future I will expand this list, so check the GRAMM site for the updates. Interestingly, GRAMM also works on a PC platform under Windows95 (the performance on P5-120 with 16 MB RAM is only two times slower than on SGI 250 MHZ Indigo2 R4400). Papers on GRAMM methodology * E. Katchalski-Katzir, I. Shariv, M. Eisenstein, A. A. Friesem, C. Aflalo, I. A. Vakser, 1992, Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques, Proc. Natl. Acad. Sci. USA, 89, 2195-2199. (Basic algorithm of protein recognition by correlation technique with Fast Fourier transform. High-resolution 'geometric' docking). * I. A. Vakser, C. Aflalo, 1994, Hydrophobic docking: A proposed enhancement to molecular recognition techniques, Proteins, 20, 320-329. (High-resolution 'hydrophobic' docking). * I. A. Vakser, G. V. Nikiforovich, 1995a, Protein docking in the absence of detailed molecular structures, in: Methods in Protein Structure Analysis (M. Z. Atassi & E. Appella, eds.), Plenum Press, New York, pp. 505-514. * I. A. Vakser, 1995b, Protein docking for low-resolution structures, Protein Eng., 8, 371- 377. ('Low-resolution' protein docking). * I. A. Vakser, 1996a, Long-distance potentials: An approach to the multiple-minima problem in ligand-receptor interaction, Protein Eng., 9, 37-41. (Interpretation of the low-resolution docking in terms of energy potentials). * I. A. Vakser, 1996b, Low-resolution docking: Prediction of complexes for underdetermined structures, Biopolymers, in press (39, No.3). (Validation of the low-resolution docking). * I. A. Vakser, 1996c, Main-chain complementarity in protein-protein recognition, Protein Eng., in press (9, No.7). (Docking of Ca structures). ------------------------------------------------------------------------ Ilya A. Vakser The Rockefeller University, Box 270 1230 York Avenue, New York, NY 10021 Phone: (212) 327-7206; Fax: (212) 327-7540 Email: ilya@guitar.rockefeller.edu ------------------------------------------------------------------------ From owner-structural-nmr@net.bio.net Sun Aug 11 23:00:00 1996 Path: biosci!PHOENIX.PRINCETON.EDU!ipelczer From: ipelczer@PHOENIX.PRINCETON.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: H2O sidebands Date: 12 Aug 1996 13:58:46 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Netters, One of our users has experienced strange sidebands flanking the residual water signal using presaturation of about 250 Hz distance. THey are not very large, but are comparable with protein resonances at the millimolar range. This happened on our 600 MHz Varian. Any hints? Thanks, best regards, Istvan wwww,wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww Istvan Pelczer, Ph.D. Email: ipelczer@princeton.edu Senior NMR Spectroscopist Princeton University Department of Chemistry ph# (609) 258 2342 Frick Laboratory fax# (609) 258 6746 Washington Road Princeton, NJ 08544 From owner-structural-nmr@net.bio.net Mon Aug 12 23:00:00 1996 Path: biosci!biosci!not-for-mail From: jmack@acpub.duke.edu (Joseph Mack) Newsgroups: bionet.xtallography,bionet.structural-nmr,misc.forsale.computers.workstation,misc.forsale.computers.other.systems,comp.os.linux.hardware,triangle.forsale Subject: Announce: Group Purchase of DEC Alpha Lite Linux Boxes $750 Date: 13 Aug 1996 11:50:17 -0700 Organization: Duke University, Durham, NC, USA Lines: 128 Sender: daemon@net.bio.net Distribution: world Message-ID: <4untjf$nf4@news.duke.edu> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.xtallography:2794 bionet.structural-nmr:1439 misc.forsale.computers.workstation:34350 misc.forsale.computers.other.systems:13838 comp.os.linux.hardware:51971 Subject: Group purchase of DEC Multia Unix Box for $750 We at Duke are currently using 8 of these running pvm3 to do parallel processing. They are a general purpose unix box (complete specs/info available from DEC at http://www.digital.com:80/.i/info/udb/). At a price of $750 you can use these as a cheap home computer, as a gateway, www server or print server. DEC liquidated the last 8000 of these Jul 1 and they are now available on the surplus market. A local store Computer Outlet (Durham, NC, 919-361-9878, fax 919-544-0794, contact person Eric Westrom) is willing to do a group purchase of these machines at $750 ea. I believe that these machines cost DEC $1700 to produce. The computer is small (about the size of a telephone book for a town of 100,000 people), single board, and uses IBMPC style peripherals and connectors. The version available for the group purchase has: 166 MHz 21066 Alpha chip (approx equal to 100MHz Pentium for integer, better for floating point) PCI bus, one slot (small, we're using that slot for a 100Mbit ether card) 64 bit bus width (approx, there are parity and other lines) 24M memory (72pin 70nsec SIMMS) expandable to 128M 340M internal scsi disk, 1.44M floppy drive on board: graphics accelarator (1280x1024, 2M VRAM) VGA connector, scsi II controller and scsiII external connector, parallel and serial ports, PS/2 keyboard connector, 10Mbit ethercard (twisted pair, AUI and BNC ports). You will need to supply a mouse, keyboard and monitor. Memory upgrades will be available at current prices (which are running about $85 for parity 8M SIMMS, $65 for non-parity, for $16M SIMMS, $135/$125). The machine runs Craftwork Linux (we're using v2.1AXP, with Linux kernel 1.3.89, which we have upgraded to 2.0.x. Craftwork is expecting to release v2.2AXP Sept 1, with Linux kernel v2.0.x, projected price of $95.) Linux AXP is a fully functional Unix, with compilers, X, networking, appletalk, apache WWW server, Mosaic, DNS name services. For further details of the Craftwork Linux AXP see http://www.craftwork.com/ Linux uses GNU and other freely available developement tools, which are readily available from the net, eg gcc (includes objective C), gnu fortran. The machine originally was supplied with Windows NT installed, but the state of the disks in the surplus machines (NT, or unformatted) is unknown. Presumably there is/was support at DEC for NT, but I don't know how to get it. It is my understanding that the Windows NT CDROM has the OS for Alpha. Because the architecture of the CPU is not Intel, Windows NT programs compiled for Intel will not run on this machine. You'll need NT binaries compiled for this chip or you'll need the sources and will have to compile them yourself. I can't offer any help on NT sorry. The Multia has a 1 year warrantee from DEC, however _NO_ manuals are available. I have a copy of the manual and will attempt to make it available, probably for a copying fee. For a starter look on the webpage (address below). I am putting out this announcement because we at Duke are going to buy some of these machines and would like to get a good price. I have dealt with Computer Outlet for about a year, and have found them helpful, reliable and with good prices, so I send them my business when I can. In posting this offer I accept no responsibility for the usefullness or suitability of the machines for any purpose whatever. The specs I have posted here to the best of my knowledge are correct, but again I accept no responsibility for them - please check with Computer Outlet, DEC and Crafwork to make sure. You will be responsible for installing the operating system. If anyone wishes, the Craftwork Linux AXP operating system will be installed for $50 before shipping to the level that the system boots, recognises all its hardware and is capable of connecting to the network via thinwire. You will need to configure the machine beyond this level using the Craftwork CD. These machines will be shipped following shipment of the machines without the installed OS. If anyone is interested please e-mail me, giving contact info (name, organisation, ph#, email, number of computers) Progress on the group purchase (including names and number of computers requested) will be posted on http://www.xray.duke.edu/multia/. On Sep 15 (or there abouts), I will post a notice on this web site as to whether the number of orders is slowing down or not and the projected date for sending your money to the Computer Outlet. Qualified organisations can send a PO. Otherwise a 50% deposit is required, with the remainder paid COD. I'm happy to talk about our experiences with these machines by phone/email or talk about technical issues. As well, after the purchase I will give free phone help (as my time permits) to anyone trying to get the system up. All monies and issues regarding the details of the purchase will be handled through Computer Outlet, (contact person Eric Westrom) who will be responsible for delivering a working machine. Please reply with Name : Organisation : Address : Ph#/timezone : e-mail : number of computers @ $750ea: number of OS installed @ $ 50ea: number of manuals @ $ 20ea: memory upgrades (Mb) : Please note these prices my best estimate at the moment. A final binding price will be posted on the multia web page at the time for sending in the orders. If there's enough interest (200 units) the price will be about $600. Joseph Mack Sysadmin, Xray Group Duke University Medical Center Durham, NC, 27710 (919)-613-8890 (UTC-5hrs) mack@xray.duke.edu From owner-structural-nmr@net.bio.net Mon Aug 12 23:00:00 1996 Path: biosci!rutgers!uwm.edu!chi-news.cic.net!ddsw1!news.mcs.net!nntp04.primenet.com!news.shkoo.com!nntp.primenet.com!news.cais.net!mr.net!newshub.tc.umn.edu!fu-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!news From: "David S. Stephenson" Newsgroups: bionet.structural-nmr Subject: Re: Unsymmetrical amide NMR question Date: Tue, 13 Aug 1996 18:11:30 +0200 Organization: UNiversity of Munich Lines: 22 Distribution: world Message-ID: <3210A932.41C6@org.chemie.uni-muenchen-de> References: NNTP-Posting-Host: cicum21.org.chemie.uni-muenchen.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.2 IP22) To: "[31mThe Brewer [37m" CC: dss [31mThe Brewer [37m wrote: > > I am desparately in need of a literature reference > which states that N-methyl amides (-CONHCH3) show restricted rotation on > the NMR timescale (You see two sets of peaks). I have > references which describe disubstituted amides. > Help... > -- check out H.Kessler, Angew.Chem.,Int.Ed.Engl. 9,219 (1970) He quotes L.A.LaPlanche and M.T.Rogers, J.Amer.Chem.Soc. 86, 337 (1964) and R.H.Barker and G.J.Bondreaux, Spectrochim. acta 23A, 727 (1967) -- David S. Stephenson Institute of Organic Chemistry FON +49-89-5902-229 University of Munich FAX +49-89-5902-483 Karlstrasse 23 EMAIL dss@org.chemie.uni-muenchen.de 80333 Munich URL http://www.chemie.uni-muenchen.de/cicum From owner-structural-nmr@net.bio.net Tue Aug 13 23:00:00 1996 Path: biosci!NMR.UTMB.EDU!david From: david@NMR.UTMB.EDU (David Gorenstein) Newsgroups: bionet.structural-nmr Subject: NMR Faculty and post-doctoral Positions Date: 14 Aug 1996 09:52:37 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 65 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear colleague: I would greatly appreciate it if you could bring to the attention of colleagues in your organization various NMR junior faculty and post-doctoral positions in the Sealy Center for Structural Biology at the University of Texas Medical Branch at Galveston. The recently established Sealy Center for Structural Biology and the Department of Human Biological Chemistry currently have 10 faculty in biomolecular NMR spectroscopy, x-ray crystallography, molecular modeling and macromolecular assembly. We are still expanding the Center in these areas. The NMR and Computer Centers of the Sealy Center for Structural Biology are located in their own building on the UTMB campus. The Center includes Varian Unity Plus 750, 600 and a wide-bore 400 MHz NMR spectrometers. A Cray J91 supercomputer, SGI Power Challenge and 13 SGI and Sun workstations are available. We anticipate hiring another junior faculty member in biomolecular NMR spectroscopy. The individual should have a Ph.D. and post-doctoral experience in modern biomolecular NMR. In addition, I personally have grant funds for hiring several new post-doctoral fellows in the area of protein and nucleic acid NMR structure. Triple resonance, multidimensional NMR is currently being carried out on various DNA and RNA binding proteins and their oligonucleotide complexes. This includes several transcription factors, HIV-1 proteins and human beta-polymerase. Part of our program is oriented towards the rational design, synthesis and structural characterization of oligonucleotide analogues and other agents directed towards HIV-1 and oncogenes (this includes antisense, aptamer and ribozyme oligonucleotides). I would appreciate any nominations or applications of candidates for these positions. Interested candidates for the post-doctoral positions should send their curriculum vitae and names, phone numbers and addresses of at least four references to me. Additional details on the faculty position will shortly be announced. I will be attending the Keystone Biological NMR meeting August 18-23, 1966, and if there are any candidates for the post-doctoral or faculty positions who would be interested in talking with me about these positions, I would be pleased to arrange some time for our discussion. Please leave a message for me at the meeting. Thanks very much for your help in these matters. ----------------------------------------------------------- David Gorenstein Director, Sealy Center for Structural Biology Professor, Dept. of Human Biological Chemistry and Genetics Professor, Dept. of Physiology and Biophysics University of Texas Medical Branch Galveston, TX 77555-1157 Office: (409) 747 6801 Main Office: (409) 747 6800 Voice Mail: (409) 747 6801 Fax: (409) 747 6850 E-MAIL ADDRESS: david@nmr.utmb.edu http://www.nmr.utmb.edu/ From owner-structural-nmr@net.bio.net Tue Aug 13 23:00:00 1996 Path: biosci!EDV1.BOKU.AC.AT!wilson From: wilson@EDV1.BOKU.AC.AT (Iain Wilson) Newsgroups: bionet.structural-nmr Subject: EGC-2 STARTS 9th SEPTEMBER - Register Now! Date: 14 Aug 1996 11:03:07 -0700 Organization: Universit=?iso-8859-1?Q?=E4t f=FC?=r Bodenkultur Wien Lines: 28 Sender: daemon@net.bio.net Distribution: world Message-ID: <3212937A.5ED9@edv1.boku.ac.at> NNTP-Posting-Host: net.bio.net The Second Electronic Glycoscience Conference starts in just under four weeks - it takes place on the Internet from Monday 9th September until Friday 20th September. The timetable for realtime electronic discussions is already taking shape and over 100 abstracts have been received - papers are currently being sent in. Abstracts have been submitted on a wide range of topics related to carbohydrates and glycobiology including molecular modelling and NMR. There will also be a special session on molecular modelling techniques and force fields. In order to view the posters and partake in the discussion sessions, please register as soon as possible - preferably by 1st September (otherwise no guarantee of your registration being processed in time!). Point your WWW-browser now to http://bellatrix.pcl.ox.ac.uk/egc2/ and proceed to the registration page. Once you've selected your username and password, you'll receive an automatic acknowledgement giving details on how to pay. Cheque, bank transfer and credit card payments are available. Once your payment has been processed, then you'll receive another acknowledgement informing you of the activation of your password. Attending EGC-2 is not expensive: normal registration being US$50, with a reduced fee of US$30 for students. If you have any queries, please e-mail egc2org@bellatrix.pcl.ox.ac.uk From owner-structural-nmr@net.bio.net Tue Aug 13 23:00:00 1996 Path: biosci!biol.uni.torun.pl!treder From: treder@biol.uni.torun.pl (Krzysztof Treder) Newsgroups: bionet.structural-nmr Subject: Spectrophotometer Date: 14 Aug 1996 00:26:33 -0700 Organization: Inst. Biol. & Environment Protection Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: <199608140726.JAA03753@biol.uni.torun.pl> NNTP-Posting-Host: net.bio.net Hello . I am looking for manufacture/dealler making or offers spectrofpotometers. Can you advise me in this qestion ? Thenk you for some help! Krzysztof From owner-structural-nmr@net.bio.net Wed Aug 14 23:00:00 1996 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!howland.erols.net!newsfeed.internetmci.com!in2.uu.net!EU.net!news.eunet.fi!newsmaster From: piero pollesello Newsgroups: bionet.structural-nmr Subject: DCOOD anydrous: IS IT A DREAM? Date: 15 Aug 1996 11:10:43 GMT Organization: POLYbios, Area Science Park, Trieste, Italy Lines: 22 Message-ID: <4uv0jj$f5o@idefix.eunet.fi> NNTP-Posting-Host: protein.orion.fi Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12(Macintosh; I; 68K) X-URL: news:bionet.structural-nmr Dear collegues! To make a long story short, I can solve a 20 a.a. very lipophylic peptide only in 1:1 CHCl3:formic acid. If the formic acid is not of hyghest purity (means if it contains 5% water e.g.) the mixture of solvents will split in two phases and the peptide will precipitate. I will run NMR spectra and I have CDCl3 and DCCOD (with 5% D2O !!!). How to take away the water from the DCOOD?). Molecular sieves give out cations: not good! Anhydrous CaSO4 cannot take out water from DCOOD:D2O, but maybe from the mixture CDCL3:DCCOD:D2O. I suspect that also part of the DCOOD will enter CaSO4. Some ideas? Thanks for comments Piero Piero Pollesello From owner-structural-nmr@net.bio.net Wed Aug 14 23:00:00 1996 Path: biosci!AL.NMR.VARIAN.COM!georgeg From: georgeg@AL.NMR.VARIAN.COM (georgeg) Newsgroups: bionet.structural-nmr Subject: Varian User Meeting at ICMRBS Date: 15 Aug 1996 08:47:56 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <9608151546.AA26073@lal600.al.nmr.varian.com> NNTP-Posting-Host: net.bio.net In conjunction with the ICMRBS meeting next week, Varian is hosting a User Meeting at the Keystone Lodge (3rd Floor) from 9am to 5pm. Presentations from Varian scientists and users will be given, covering new techniques and applications, as well as giving an update on current technology and products. Oxford Instruments will present current progress at 800 and 900 MHz. The program agenda is available on the Web at www.nmr.varian.com. Just select the "events" section. If you plan to attend and have not registered you may do so over the Web either today or Friday. This will permit us to know how many lunches to provide. Even if you do not have time to register please drop by on Sunday anyway. George A. Gray NMR Applications Laboratory Palo Alto, CA (george.gray@nmr.varian.com) From owner-structural-nmr@net.bio.net Wed Aug 14 23:00:00 1996 Path: biosci!AL.NMR.VARIAN.COM!georgeg From: georgeg@AL.NMR.VARIAN.COM (georgeg) Newsgroups: bionet.structural-nmr Subject: subscribe Date: 15 Aug 1996 08:48:46 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 3 Sender: daemon@net.bio.net Distribution: world Message-ID: <9608151547.AA26076@lal600.al.nmr.varian.com> NNTP-Posting-Host: net.bio.net subscribe (george.gray@nmr.varian.com) From owner-structural-nmr@net.bio.net Wed Aug 14 23:00:00 1996 Path: biosci!fmp.fta-berlin.de!schultz From: schultz@fmp.fta-berlin.de (Johan Schultz) Newsgroups: bionet.structural-nmr Subject: (none) Date: 15 Aug 1996 04:14:11 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 64 Sender: daemon@net.bio.net Distribution: world Message-ID: Reply-To: schultz@fmp.fta-berlin.de NNTP-Posting-Host: net.bio.net POSITIONS AVAILABLE AT THE EMBL, HEIDELBERG ------------------------------------------- The European Molecular Biology Laboratory (EMBL) is an international research organization with its Headquarters Laboratory in Heidelberg (Germany), Outstations situated in Grenoble (France), Hamburg (Germany) and Hinxton (UK) and a Research Programme at Monterotondo (Italy). The EMBL Headquarters Laboratory in Heidelberg has two vacancies in the NMR facility: (1) GROUP LEADER ref. no.: 96/37 NMR SPECTROSCOPY The European Molecular Biology Laboratory in Heidelberg, Germany, has a wide research programme in the areas of structural biology, developmental biology, cell biology, cell regulation, gene expression and instrumentation. The Structural Biology (incl. Biocomputing) Programme maintains a multidisciplinary approach to study structural basis of biological problems. Its research groups are currently using X-ray crystallography, NMR spectroscopy, high-resolution electron microscopy and biocomputing methods, supported by broad expertise in biochemistry and molecular biology, to study membrane, cytoskeletal and signalling proteins, protein/nucleic acid interactions, and protein folding. The NMR facility is equipped with a 500 MHz and a 600 MHz spectrometer used by several groups. The new group leader is expected to use this facility to study the solution structures and function of important biological macromolecules. Candidates should have a PhD and substantial post-doctoral training, with significant research accomplishments, and should demonstrate the ability to establish and run an independent research group within the Programme. The contract will be for five years in the first instance. (2) STAFF SCIENTIST ref. no.: 96/38 NMR SPECTROSCOPY The Staff Scientist will serve as a facilities manager for the two high-field spectrometers which are used by several research groups. He/She will be responsible for maintenance and upgrades as well as development and inplementation of pulse programs in close collaboration with the NMR group leader. The position also gives an opportunity for development of an independent research project and collaboration with other research groups. The candidates should have a PhD, post-doctoral training and research accomplishments, and demonstrated expertise in NMR spectroscopy. The contract will be for three years in the first instance. Closing date for each position: 31 October 1996 EMBL is an inclusive, equal opportunity organization. To apply please send your CV, quoting appropriate ref. no., to: Head of Human Resources, EMBL, Postfach 10.2209, D-69012 Heidelberg, Germany. Fax: +49 6221 387555 Ann Cooper Senior Personnel Officer European Molecular Biology Laboratory Meyerhofstr. 1, Postfach 10.2209 69012 Heidelberg, Germany Tel: +49 6221 387 208 Fax: +49 6221 387 555 email: cooper@EMBL-Heidelberg.de jobs@EMBL-Heidelberg.de From owner-structural-nmr@net.bio.net Thu Aug 15 23:00:00 1996 Path: biosci!SMI.STANFORD.EDU!holbrook From: holbrook@SMI.STANFORD.EDU (Robin Holbrook) Newsgroups: bionet.structural-nmr Subject: Symposium: 50 Years of NMR at Stanford Date: 16 Aug 1996 13:28:45 -0700 Organization: SMRL, Stanford University Lines: 40 Sender: daemon@net.bio.net Distribution: world Message-ID: <3214779D.47D6@camis.stanford.edu> Reply-To: holbrook@SMI.Stanford.EDU NNTP-Posting-Host: net.bio.net Announcing WHAT: "50 Years of NMR" - a one day Symposium celebrating the discovery of Nuclear Magnetic Resonance at Stanford University WHEN: Friday, October 4, 1996 (~8:30 am-5:15 pm with evening Banquet & Historic Roundtable ~6:30-9:00 pm) WHERE: Fairchild Auditorium, Stanford University Medical Center Co Sponsored by Stanford University and Varian Associates MORE INFO: http://cmgm.stanford.edu/SMRL/50.html EXHIBIT AND DAYTIME SCIENTIFIC SESSIONS WILL BE FREE AND OPEN TO THE PUBLIC - NO REGISTRATION REQUIRED Preliminary Program All Day: Historical Exhibit Morning and Afternoon Scientific Session: Milestones and Current Trends in NMR Speakers: Richard Ernst (ETH-Zentrum, Zurich), Ray Freeman (Phys. Chem., Cambridge, England), Gary Glover (Lucas MR Center, Stanford), Erwin Hahn (Physics, UC Berkeley), James Hyde (Med. College, Wisc.), Oleg Jardetzky (SMRL, Stanford), Albert Macovski (MRSRL, Stanford), Harden McConnell (Chemistry, Stanford), Martin Packard (Varian, retired), Jonathan Stebbins (Geol. Sci., Stanford), Henry Taube (Chemistry, Stanford) ------- Banquet & Historical Session: Felix Bloch Memorial (~6:30-9:00 pm) - REQUIRES PREPAID RESERVATION ($40/person) contact Robin Holbrook (Tel: 415/723-6270, Fax: 415/723-2253, Email: holbrook@camis.stanford.edu or web page - address above) Reminiscences of Early NMR Invited Speakers: Wes Anderson (Varian), J. T. Arnold (Varian), Bob Codrington (Varian), Arthur Schawlow (Stanford), Barry Shapiro (TAMU, NMR Newsletter), James Shoolery (Varian), Harry Weaver (Varian, H-P) and others From owner-structural-nmr@net.bio.net Thu Aug 15 23:00:00 1996 Path: biosci!OXBOW.BIOPHYSICS.ROCHESTER.EDU!pascal From: pascal@OXBOW.BIOPHYSICS.ROCHESTER.EDU (Steve Pascal) Newsgroups: bionet.structural-nmr Subject: Postdoc Date: 16 Aug 1996 14:32:05 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 31 Sender: daemon@net.bio.net Distribution: world Message-ID: <9608162112.AA02357@oxbow.biophysics.rochester.edu> NNTP-Posting-Host: net.bio.net Protein NMR Postdoctoral Position A fully funded postdoctoral position will be available in my laboratory beginning this fall. Available projects include the use of NMR spectroscopy to examine the structure and dynamics of protein and substrate molecules involved in transcriptional regulation and cytotoxicity. The Department of Biophysics at the University of Rochester has recently hired two NMR spectroscopists (Shohei Koide and myself), an X-ray crystallographer (Ravi Basavappa) and installed a fully equipped Varian Unity+ 600 MHz spectrometer as part of a structural biology initiative. Applicants should have experience in multi-nuclear NMR spectroscopy as well as protein expression and purification. Those with strengths in one of these areas and motivation to acquire the rest are also encouraged to apply. For further information, please contact me by email: pascal@oxbow.biophysics.rochester.edu #########################################################################Steve Pascal Assistant Professor Department of Biochemistry and Biophysics University of Rochester Medical Center 601 Elmwood Ave Phone: (716)273-4832 Rochester, NY 14642 Fax: (716)275-6007 ######################################################################### From owner-structural-nmr@net.bio.net Fri Aug 16 23:00:00 1996 Path: biosci!aecom.yu.edu!girvin From: girvin@aecom.yu.edu (Mark Girvin) Newsgroups: bionet.structural-nmr Subject: POSTDOCTORAL POSITION IN MEMBRANE PROTEIN STRUCTURE BY NMR Date: 17 Aug 1996 11:30:25 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 88 Sender: daemon@net.bio.net Distribution: world Message-ID: <199608171816.OAA19871@medusa.bioc.aecom.yu.edu> NNTP-Posting-Host: net.bio.net POSTDOCTORAL POSITION IN MEMBRANE PROTEIN STRUCTURE BY NMR PROJECTS: Membrane proteins are responsible for transmembrane signaling, energy transduction, and ion and metabolite transport. Despite their importance, and the need for structure to understand their function, few structures are available. Membrane proteins have resisted routine crystallographic analysis, and have been thought difficult candidates for NMR. The overall goals of research in this laboratory are to continue to develop and apply new solution conditions and new NMR methods to tease structural details out of these secretive proteins. Present work focuses on subunit c of the F1FO ATP synthase, both as a model system and as an interesting protein in its own right. In the ATP synthase, H+ translocation across the membrane through FO provides the driving force for ATP synthesis on F1. Subunit c is responsible for both H+ translocation through FO (via ionization of the buried Asp61 residue), and transmission of long range (~100 =C5) conformational changes to the ATP binding sites on F1. We have shown that subunit c retains native folding in organic/aqueous solvent mixtures, permitting structural study by NMR. Introduction of a nitroxide at a unique site allowed us to measure distances over a 10-20 =C5 range, and, from 2D difference NMR, to rapidly determine the detailed structure of the region of the protein within 16 =C5 of the probe. We are presently determining the complete structure of subunit c via 1H13C15N 3D and 4D NMR. Structures will be determined above and below the pKa of the essential Asp61, to understand the nature of the conformational change linked to energy transduction. We are developing a convenient system to assay native folding of membrane proteins in mixed solvents and detergent micelles, allowing us to optimize for proper folding and for favorable NMR properties before undertaking lengthy structural studies. We will analyze the structural features which stabilize the folding of membrane proteins. Membrane proteins stand some of the normal folding rules on their heads - e.g. they don=92t bury hydrophobic surface the way that= water soluble proteins do. We expect that clusters of aromatic residues, intricate van der Waals packing, and connecting loops will contribute to folding stability. Each of these elements will be varied by mutagenesis, and folding stability will be assayed by NMR distance and dynamics measurements. All these methods will be extended to other important membrane proteins in the future. SELECTED REFERENCES: M.E. Girvin & R.H. Fillingame (1995) Determination of Local Protein Structure by Spin Label Difference 2D NMR, Biochemistry 34, 1635. M.E. Girvin (1994) Increased Sensitivity of COSY Spectra by Use of Constant Time t1 Periods (CT-COSY), J. Magnetic Resonance Ser. A. 108, 99. M.E. Girvin & R.H. Fillingame (1994) Hairpin Folding of Subunit c of F1Fo ATP Synthase: 1H Distance Measurements to a Nitroxide-Derivatized Asp61 Biochemistry 33, 665. INSTRUMENTATION: The new Structural NMR Resource at Albert Einstein College of Medicine (AECOM) occupies a space constructed to house the new Bruker DRX-600 4-channel and DRX-300 2-channel systems, along with substantial computational resources (hardware & software). The new Resource complements the existing 500, 400, and 200 MHz instruments which are used for physiological NMR.=20 ENVIRONMENT & LOCATION: AECOM provides an interactive, collaborative, friendly, and stimulating environment. The Biochemistry Department is particularly strong in mechanistic and structural biochemistry. The Albert Einstein College of Medicine campus is located in a "pleasant residential neighborhood" of the North Bronx. Many faculty and staff live in the surrounding neighborhoods. Others live in Manhattan, or in Westchester County, which is an easy 10-30 minute commute from AECOM, depending on the location. Check us out at:=20 http://leper1.ca.aecom.yu.edu/sggd/pages/overview/bulltext.htm APPLICATION: The preferred starting date is September to November 1996. Please send Curriculum Vitae and three letters of reference to: Mark Girvin, Biochemistry Department, Albert Einstein College of Medicine, Jack and Pearl Resnick Campus, 1300 Morris Park Ave., Bronx, NY 10461. AECOM is an Equal Opportunity Employer. ______________________________________________________________ Mark Girvin =20 Biochemistry Department =20 Albert Einstein College of Medicine girvin@aecom.yu.edu 1300 Morris Park Ave. Tel:(718) 430-2025/2021 Bronx, NY 10461 FAX:(718) 430-8565 ______________________________________________________________ From owner-structural-nmr@net.bio.net Sun Aug 18 23:00:00 1996 Path: biosci!RIGEL.BIOCHEM.UALBERTA.CA!kkr From: kkr@RIGEL.BIOCHEM.UALBERTA.CA (Krishna Rajarathnam) Newsgroups: bionet.structural-nmr Subject: subscribe Date: 19 Aug 1996 12:15:15 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <9608191914.AA21955@rigel.biochem.ualberta.ca> NNTP-Posting-Host: net.bio.net ________________________________________________________________________ Krishna Rajarathnam PENCE 713 Heritage Building University of Alberta Edmonton, Alberta Canada T6G 2S2 Phone:(403) 492 7540 FAX:(403) 492 1473 From owner-structural-nmr@net.bio.net Sun Aug 18 23:00:00 1996 Path: biosci!biosci!not-for-mail From: Mogens Kjaer Newsgroups: bionet.structural-nmr Subject: Senior NMR Scientist at Carlsberg Laboratory Date: 19 Aug 1996 10:51:07 -0700 Organization: Carlsberg Laboratory Lines: 53 Sender: daemon@net.bio.net Distribution: world Message-ID: <32180ABC.41C6@unidhp.uni-c.dk> NNTP-Posting-Host: net.bio.net Carlsberg Laboratory Senior NMR Scientist At the Carlsberg Laboratory a National Instrument Centre for NMR Spectroscopy of Biological Macromolecules will be opened in 1997 with 800 and 500 MHz Varian UNITY INOVA equipment. The Chemistry Department of the Carlsberg Laboratory has Bruker 600 AMX and 250 DRX instruments also available for research activities. Two research groups are active in the structural determination of biological macromolecules by NMR spectroscopy at the Carlsberg Laboratory, i) the Protein Structure and NMR group and ii) the Carbohydrate NMR group. In order to strengthen the research at the National Centre a 5 years position for a senior research scientist is open. The senior scientist position will be filled with a NMR spectroscopist, who can complement the present structure research at the Carlsberg Laboratory by developing NMR methods for NMR spectroscopy of biological molecules. The successful candidate will have the opportunity to develop an independent research project, but will be committed to collaborate with the existing research groups at the Carlsberg Laboratory and with external users of the instrument centre. For the same period a junior scientific position at the Instrument Centre will be available at the Laboratory. The candidate for the senior research position should have a Ph.D. and substantial post-doctoral training and research accomplishments and should have demonstrated expertise in NMR spectroscopy. A 5 years contract will be offered to the successful candidate by a grant from the Carlsberg Foundation and with a salary level as a research professor. An appointment committee will be established by the Carlsberg Foundation and applications and CV should be sent before October 1, 1996 to: Professor Klaus Bock Department of Chemistry, Carlsberg Laboratory Gamle Carlsberg Vej 10 DK-2500 Valby, Copenhagen, Denmark Telephone: +45 3327 5220 Fax: +45 3327 4708 e-mail: carlkb@unidhp.uni-c.dk From owner-structural-nmr@net.bio.net Wed Aug 21 23:00:00 1996 Path: biosci!news.alaska.edu!newsfeed.acns.nwu.edu!math.ohio-state.edu!cs.utexas.edu!howland.erols.net!newsfeed.internetmci.com!castle.nando.net!news From: forte@nando.net (Milton Forte II) Newsgroups: bionet.xtallography,bionet.structural-nmr,misc.forsale.computers.workstation,misc.forsale.computers.other.systems,comp.os.linux.hardware,triangle.forsale Subject: Re: Announce: Group Purchase of DEC Alpha Lite Linux Boxes $750 Date: 21 Aug 1996 17:25:46 GMT Organization: Forte Associates Lines: 14 Message-ID: <4vfgqq$c3d@castle.nando.net> References: <4untjf$nf4@news.duke.edu> Reply-To: forte@nando.net (Milton Forte II) NNTP-Posting-Host: grail803.nando.net X-Newsreader: IBM NewsReader/2 v1.2 Xref: biosci bionet.xtallography:2807 bionet.structural-nmr:1453 misc.forsale.computers.workstation:34442 misc.forsale.computers.other.systems:13923 comp.os.linux.hardware:52148 In <4untjf$nf4@news.duke.edu>, jmack@acpub.duke.edu (Joseph Mack) writes: x>Subject: Group purchase of DEC Multia Unix Box for $750 x> x> We at Duke are currently using 8 of these running x>pvm3 to do parallel processing. They are a general purpose x>unix box (complete specs/info available from DEC at x>http://www.digital.com:80/.i/info/udb/). At a price of $750 x>you can use these as a cheap home computer, as a gateway, x>www server or print server. x> This machine is available at auction with software on CDROM for LINUX or NT on http://www.onsale.com/. Milton From owner-structural-nmr@net.bio.net Wed Aug 21 23:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!infobiogen.fr!pasteur.fr!univ-lyon1.fr!howland.erols.net!newsfeed.internetmci.com!hunter.premier.net!news.cais.net!news.hkt.net!news.asiaonline.net!usenet From: armins@asiaonline.net (Armin Schon) Newsgroups: bionet.structural-nmr Subject: nmr for low-cost food analysis? Date: Fri, 16 Aug 1996 01:20:16 GMT Organization: Asia On-Line Limited, Hong Kong. Lines: 13 Message-ID: <4uv82u$r23@news.asiaonline.net> Reply-To: armins@asiaonline.net NNTP-Posting-Host: 202.85.14.120 X-Newsreader: Forte Free Agent 1.0.82 I am a physicist but have no experience in nmr whatsoever, so please forgive me if this question seems unreasonable: I suppose that a cw nmr system could be used to do a chemical analysis of food samples, to look for traces of heavy metals (as long as they give a signal, that is) etc. Are there commercial systems available to do that? THeoretically that should be a fairly simple system, so cost should be low? Any good literature about that around? Thanks. Dr. Armin Schon, Hong Kong From owner-structural-nmr@net.bio.net Wed Aug 21 23:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.structural-nmr Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 22 Aug 1996 02:00:06 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 239 Sender: daemon@net.bio.net Distribution: world Message-ID: <199608220900.CAA29572@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. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-structural-nmr@net.bio.net Fri Aug 23 23:00:00 1996 Newsgroups: bionet.structural-nmr Path: biosci!faseb.org!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!newsfeed.internetmci.com!in3.uu.net!sangam!iitb!powai!n1403305 From: n1403305@powai.cc.iitb.ernet.in (ramakrishna) Subject: error analysis Message-ID: Date: Sat, 24 Aug 1996 05:49:00 GMT Organization: Computer Centre, Indian Institute of Technology, Bombay X-Newsreader: TIN [version 1.2 PL2] Lines: 7 dear netters, I am looking for monte carlo simulation program for estimating error in experimental data. could some one provide me information about availability of such a program. thanks in advance From owner-structural-nmr@net.bio.net Fri Aug 23 23:00:00 1996 Path: biosci!BIOC01.UTHSCSA.EDU!raman From: raman@BIOC01.UTHSCSA.EDU (C.S.RAMAN) Newsgroups: bionet.structural-nmr Subject: Re: error analysis Date: 24 Aug 1996 09:28:53 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 37 Sender: daemon@net.bio.net Distribution: world Message-ID: <9608241626.AA17913@bioc01.uthscsa.edu> References: <"ramakrishna"@Aug> NNTP-Posting-Host: net.bio.net Ramakrishna: > I am looking for monte carlo simulation program for estimating error > in experimental data. could some one provide me information > about availability of such a program. Art Palmer's group at Columbia U., distributes a suite of programs that might meet your needs. In particular, you might be interested in MODELFREE and CURVEFIT which have the capability to do MC simutations for estimating the precision limits of the derived parameters. More information can be found in: http://cuhhca.hhmi.columbia.edu/palmer/palmer_group.html Alternatively, you can reach Art at agp6@columbia.edu. Cheers -raman -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ C.S.RAMAN _/ _/ Department of Biochemistry _/ _/ University of Texas Health Science Center _/ _/ 7703 Floyd Curl Drive _/ _/ San Antonio, TX 78284-7760 _/ _/ USA _/ _/ _/ _/ Tel: (210) 614-0839 _/ _/ Fax: (210) 567-6595 _/ _/ E-mail: raman@bioc01.uthscsa.edu _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ "The real problem in speech is not precise language. _/ _/ The problem is clear language." --Richard Feynman _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From owner-structural-nmr@net.bio.net Sat Aug 24 23:00:00 1996 Path: biosci!PHOENIX.PRINCETON.EDU!ipelczer From: ipelczer@PHOENIX.PRINCETON.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: nmr for low-cost food analysis? Date: 25 Aug 1996 07:12:03 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 36 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <4uv82u$r23@news.asiaonline.net> NNTP-Posting-Host: net.bio.net Bruker has a small instrument, "Minispec", which is used for food analysis -- although I doubt that it could do analysis of heavy metals. Oxford may have a small system for industrial use as far as I recall. Hope others will have some more advice. Good luck, Istvan wwww,wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww Istvan Pelczer, Ph.D. Email: ipelczer@princeton.edu Senior NMR Spectroscopist Princeton University Department of Chemistry ph# (609) 258 2342 Frick Laboratory fax# (609) 258 6746 Washington Road Princeton, NJ 08544 On Fri, 16 Aug 1996, Armin Schon wrote: > I am a physicist but have no experience in nmr whatsoever, so please > forgive me if this question seems unreasonable: > > I suppose that a cw nmr system could be used to do a chemical analysis > of food samples, to look for traces of heavy metals (as long as they > give a signal, that is) etc. > Are there commercial systems available to do that? THeoretically that > should be a fairly simple system, so cost should be low? Any good > literature about that around? > Thanks. > > Dr. Armin Schon, Hong Kong > > > From owner-structural-nmr@net.bio.net Mon Aug 26 23:00:00 1996 Path: biosci!aecom.yu.edu!girvin From: girvin@aecom.yu.edu (Mark Girvin) Newsgroups: bionet.structural-nmr Subject: nmrPipe data -> XEASY Date: 27 Aug 1996 05:54:41 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <199608271241.IAA04186@medusa.bioc.aecom.yu.edu> NNTP-Posting-Host: net.bio.net Hello all, Does anyone have a suggestion for getting data processed by nmrPipe into XEASY format? Thanks in advance, Mark ______________________________________________________________ Mark Girvin Biochemistry Department Albert Einstein College of Medicine girvin@aecom.yu.edu 1300 Morris Park Ave. Tel:(718) 430-2025/2021 Bronx, NY 10461 FAX:(718) 430-8565 ______________________________________________________________ From owner-structural-nmr@net.bio.net Mon Aug 26 23:00:00 1996 Path: biosci!mmd.com!vladimirsaudek From: vladimirsaudek@mmd.com (Vladimir Saudek) Newsgroups: bionet.structural-nmr Subject: NMR job Date: 27 Aug 1996 01:38:54 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 33 Sender: daemon@net.bio.net Distribution: world Message-ID: <199608270838.AA08850@gate.mmd.com> NNTP-Posting-Host: net.bio.net Applications are invited for a permanent position of NMR spectroscopist at Marion Merrell Research Institute, Strasbourg, France. The successful candidate will be in charge of running, maintaining and upgrading Bruker 500 and 600 DMX spectrometers. His/her duties will include development and implementation of pulse sequences necessary for pharmaceutical and biomolecular research, assistance to other members of the group with NMR experiments and carrying independent research projects. NMR laboratory is an integral part of Biophysical Group (x-ray crystallography, NMR, optical spectroscopy and molecular modeling). Requirements: PhD, postdoctoral experience in MNR, excellent knowledge of NMR theory and proven practice with multidimensional spectroscopy. Previous experience with biomolecular NMR would be an asset but is not necessary. Interested candidates, please send your CV and a letter of interest to the address bellow. -- *---------------------------------------------------------------------* | Vladimir Saudek email: VladimirSaudek@mmd.com | | biophysics phone: (+33) 88 41 47 46 (lab) | | (+33) 88 41 46 93 (office) | | (+33) 88 41 45 00 (swichboard) | | fax: (+33) 88 45 90 70 | | Marion Merrell 16 rue d'Ankara | | Research Institute 67080 Strasbourg CEDEX | | Group Hoechst France | *---------------------------------------------------------------------* ~ From owner-structural-nmr@net.bio.net Thu Aug 29 23:00:00 1996 Path: biosci!agate!howland.erols.net!nntp04.primenet.com!nntp.primenet.com!news.mathworks.com!newsfeed.internetmci.com!news.ycc.yale.edu!news From: Elias Fernandez Newsgroups: bionet.molbio.proteins,bionet.xtallography,bionet.neuroscience,sci.med.immunology,bionet.structural-nmr Subject: Pro-dicon protein concentrator Date: Fri, 30 Aug 1996 10:24:38 -0400 Organization: Yale University Lines: 16 Message-ID: <3226F9A6.794B@pharm.med.yale.edu> NNTP-Posting-Host: pharm.med.yale.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP20) Xref: biosci bionet.molbio.proteins:8619 bionet.xtallography:2841 bionet.neuroscience:15518 sci.med.immunology:7312 bionet.structural-nmr:1475 Hi, Are the Pro-dicon protein solution concentrators still available? Where? They used to be manufactured/marketed/both by a company called Bio-molecular Dynamics in Oregon, but there doesn't seem to be a firm by that name anymore. -- Elias J. Fernandez Yale University Dept. of Pharmacology New Haven, CT 06520. Tel. No.: (203)-785-6232 Fax No. : (203)-785-7670. From owner-structural-nmr@net.bio.net Thu Aug 29 23:00:00 1996 Path: biosci!agate!spool.mu.edu!usenet.eel.ufl.edu!news.ultranet.com!homer.alpha.net!uwm.edu!cs.utexas.edu!howland.erols.net!nntp.crl.com!news.zNET.net!news From: laradex3@sj.znet.com (Larry Adams) Newsgroups: bionet.structural-nmr Subject: Structure of Magnetosomes? Date: 30 Aug 1996 21:33:14 GMT Organization: none Lines: 12 Message-ID: <507mmq$lum@news> NNTP-Posting-Host: capts-19.znet.com Mime-Version: 1.0 X-Newsreader: WinVN 0.93.14 Are there any magnetic resonance experiments that have determined the structure of the magnetosomes in magnetotactic bacteria? The magnetosomes contain the ferrite, Magnetite. Thanks, Larry