From owner-structural-nmr@net.bio.net Sun Dec 01 22:00:00 1996 Path: biosci!CURLY.BIOP.UMICH.EDU!weidong From: weidong@CURLY.BIOP.UMICH.EDU Newsgroups: bionet.structural-nmr Subject: MRI position in China Date: 2 Dec 1996 15:17:52 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 34 Sender: daemon@net.bio.net Distribution: world Message-ID: <199612022336.SAA10922@curly.biop.umich.edu> NNTP-Posting-Host: net.bio.net Dear fellows: The following is an ad for a MRI position in Wuhan Institute of Physics. Please contact Professor Chaohui Ye if you are interested in this position. ********************************************************************* The State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physic, Wuhan Institute of Physics, The Chinese Academy of Science, is looking for a staff member on MRI research. The lab. has been equipped with MSL-400 for soild and micro-imaging, ARX-500 for solution, a home made Dynamic Nuclear Polarization spectrometer with 80MHz for Proton and 54GHz for electron, a home made machine for Xe-129 and He-3 super-polarization, and a Biospec with 4.7T, bore size 300 mm will be installed in Jan. 1997. Please write to Professor Chaohui Ye or Professor Xi-an Mao, P.O. Box 71010, Wuhan 430071, China or send an e-mail at ye@nmr.whcnc.ac.cn to Prof. Chaohui Ye ********************************************************************** Weidong ****************************************************** Dr. Weidong Hu email: weidong@curly.biop.umich.edu 4028, Biophysics Division Tel: (313) 747-3234(H) 930 N. University (313) 936-3851(O) Univ. of Michigan FAX: (313) 764-3323 Ann Arbor, MI 48109-1055 ****************************************************** From owner-structural-nmr@net.bio.net Sun Dec 01 22:00:00 1996 Path: biosci!agate!spool.mu.edu!uwm.edu!news-peer.gsl.net!news.gsl.net!EU.net!Norway.EU.net!sn.no!nntp.uio.no!news.apfel.de!nntp.zit.th-darmstadt.de!fu-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!ipp-garching.mpg.de!usenet From: Bas Vogt Newsgroups: bionet.structural-nmr Subject: Re: 31 P - NMR of Biomembranes Date: Mon, 02 Dec 1996 14:49:24 +0100 Organization: Max-Planck-Institute for Biochemistry Lines: 21 Message-ID: <32A2DE64.167E@biochem.mpg.de> References: NNTP-Posting-Host: acca.biochem.mpg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; IRIX 5.3 IP22) Try: Biological magnetic resonance. Plenum Press, New York (1990) ISBN 0-306-43341-9 or J.Seelig Biochim. Biophys. Acta 515 (1978) 105-140. Good luck. -- Dr. T.C.B. Vogt, (Bas) Max-Planck-Institute for Biochemistry Dep. for Solid-State NMR Spectroscopy AG. Bechinger Am Klopferspitz 18a 82152 Martinsried Germany Tel: +49-89-8578-2486 Fax: +49-89-8578-2876 email:vogt@biochem.mpg.de From owner-structural-nmr@net.bio.net Sun Dec 01 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: Marc-Andre.Delsuc@cbs.univ-montp1.fr (Marc-Andre Delsuc) Newsgroups: bionet.structural-nmr Subject: Re: TPPI, what type of FFT ? Date: 2 Dec 1996 16:17:56 -0000 Lines: 85 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <57uvfk$8ot@mserv1.dl.ac.uk> X-Sender: mad@tome.cbs.univ-montp1.fr (Unverified) Original-To: str-nmr@dl.ac.uk > From: Alexej.Jerschow@jk.uni-linz.ac.at (Alexej Jerschow) >Dear NMR Spectroscopists! Hi Alexej, >I have problems with figuring out how to FFT TPPI-acquired data. I try to do >it myself (without the spectrometer software) on simulated data. > >I have some conceptual difficulty understanding what kind of FFT I should use. > >My simulated data (1D) is: > >fid(t)=[exp(-i*t*omega)+exp(i*t*omega)]*exp(-t/T2) > >where the 1st term in is I+ coherence and the second I- (or the other way >round). The fid is now amplitude modulated, the imaginary parts cancel. >When I do a complex (ordinary) FFT I get 2 peaks, one at +omega and one at >-omega corresponding to the 2 coherences. > >Using TPPI (increment the pulse phase before evolution by 90 deg. wrt the >previous point) I have to phase shift the I- coherence by -90 and the I+ >coherence by +90 (or the other way round). In this way the 2 peaks are moved >by f(Nyquist)/2 to the left and right, respectively. This I can observe by >complex FFT again. > >The books say that I have to use a *real* FFT to get the 2 coherences folded >onto each other in a way that only absorptive signals remain. But when I use a >*real* FFT (which is a cosine transform in my interpretation) I get the same >pattern, i.e. 2 peaks. (the same happens when I use a sine transform). This is were you make the mistake. First remember that we are talking Digital Fourier Transform here DFT (The Fourier transform applied to a discrete sampled series, playing the sampling/periodizing trick). FT: Xn = sum[k=0; N-1; xk * exp(2 * i * PI * k * n / N ) ] where i^2 = -1 FFT is an implementation of the DFT that permits to compute it much faster ( Nlog(N) )than the N^2 time you would think of by simply writting down the algorithm. This very clever algorithm (the so-called butterfly algorithm, or Cooley-Tukey algorithm) uses a recursive decomposition of the DFT to do so, that is usually implemented for N equal to a power of 2. Real FT (RFT) is NOT cosine (or sine) FT. Cosine and Sine FT are well mathematically defined transformation that are defined as Complex -> Complex. cosFT Xn = sum[k=0; N-1; xk * cos( PI * k * n / N ) ] Real FT (RFT), is the computer trick wich permits to compute the Fourier Transform of a real series. The simplest way of doing it is by stuffing your real series (N data values) into a complex series (2*N data values, out of which half is zero values (the imaginary part)) doing a FFT, so obtaining a spectrum symmetrical around the 0 frequency (2*N data values), finally throwing away the redundant part of the spectrum (for instance the w<0 part), ( N data values) so RFT is nothing that the N real values => N/2 complex values transform. This operation appears to be (nearly) inversible. The whole idea of RFT, is simply that there is a better algorithm that the one just described above, which uses 2*N values for the FFT. The better algorithm, called RFT, gets the same result on place, using only N values all the time, thus gaining about twice the computationnal time. >Which FFT should I use, or where did I make an error ? Just use your Complex FFT, and chop out the redudant part of the spectrum, it's fine. If you wish to implement RFT, you will find it in Numerical recipes for instance. It is simply a preprocessing, post processing pair around the FFT Complex-Complex transform. I hope this helps. _________________________________________________________________________ NOTE THAT TELEPHONE NUMBERS IN FRANCE HAVE CHANGED ON THE 18th OCTOBER MY NEW TELEPHONE NUMBERS ARE GIVEN BELOW _________________________________________________________________________ Marc-Andre' Delsuc Centre de Biochimie Structurale Marc-Andre.Delsuc@cbs.univ-montp1.fr Faculte de Pharmacie tel : (33) (0) 467 04 34 36 15 av, Charles Flahault fax : (33) (0) 467 52 96 23 34060 Montpellier cedex www : http://www.cbs.univ-montp1.fr FRANCE From owner-structural-nmr@net.bio.net Mon Dec 02 22:00:00 1996 Path: biosci!GPC.IBC.WUSTL.EDU!gregory From: gregory@GPC.IBC.WUSTL.EDU (Gregory Nikiforovich) Newsgroups: bionet.structural-nmr Subject: Conformational calculations for peptides Date: 3 Dec 1996 09:25:38 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 38 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear all: One of the best approaches to conformational computations of peptides includes combination of a build-up protocol and the ECEPP force field (see Nikiforovich GV (1994) Int.J.Pept.Prot.Res.vol.44,pp. 513-531). For many years, we have developed a technology of calculations using this approach. The main advantages are that the user can handle a bunch of different conformers simultaneously ensuring rather comprehensive yet not random sampling of the conformational space. This technology is implemented in various pieces of software, allowing to select general strategy of build-up protocol in terms of sequences considered (i.e., start from VYVH to VYVHPF to RVYVHPF to DRVYVHPF - angiotensin II) and to push the button starting calculations. The results are the sets of low-energy backbone conformers with optimized spatial arrangements of side chains. We are considering possibility to assemble these various pieces into a single automatic program running under various computer systems, and to make it accessible to others. Now the question: would anybody be interested in such program? We do not want to waste our time and money on the "non-marketable" project. Thank you in advance for your response. Please e-mail it directly to my e-mail address. Your response will really help us. ___________________________________________________________________________ Gregory V. Nikiforovich Research Professor Phone (314) 362-1566 Center for Molecular Design FAX (314) 362-0234 Washington University E-mail address: Institute for Biomedical Computing gregory@ibc.wustl.edu Box 8036, 700 South Euclid Ave. St. Louis, MO 63110 ___________________________________________________________________________ From owner-structural-nmr@net.bio.net Mon Dec 02 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: herve@afmb85.cnrs-mrs.fr (Herve DARBON) Newsgroups: bionet.structural-nmr Subject: NMR POSTDOCTORAL POSITION Date: 3 Dec 1996 09:40:28 -0000 Lines: 72 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <580sic$c6j@mserv1.dl.ac.uk> Original-To: str-nmr@dl.ac.uk ********************************************************************** NMR POSTDOCTORAL POSITION - PROTEIN STRUCTURE/FUNCTION ********************************************************************** WHERE? MARSEILLE (FRANCE), Herve Darbon's NMR group, WHEN? October 1997. The position will be open for one year, possibly renewable. The salary will be 10,000 FF/month FOR WHOM? This position is for foreign young Post-docs (PhD obtained in 1994 and later). French citizens are disallowed as well as people having already got a french salary in the past. RESEARCH TOPIC? NMR Protein structure. EXPERIENCE REQUIRED Applicants should have strong experience in solving protein structures by multi dimensional homo and heteronuclear NMR. Experience in any of the following areas would be an distinct advantage. Pulsed field gradient NMR 3D heteronuclear NMR FACILITIES AVAILABLE A fully equipped biochemistry/molecular biology lab. A DRX500 Bruker spectrometer with pulsed field gradients (3-axis gradients). The group gets 50% time on this instrument. An extensive network of Silicon Graphics ans Suns workstations with softwares ranging from graphic assignment to structure calculation is available FURTHER DETAILS (1) See our world wide web page: http://afmb.cnrs-mrs.fr/ (2) Contact Herve DARBON TO APPLY Please submit full CV, cover letter, and names and addresses (including telephone, fax, email) of at least two referees. The selected applicant will have to fill an application form before 1st of february 1997. The final decision will be avalaible by 1st of March 1997. Herve Darbon ------------------------------------------------------------------- www: http://afmb.cnrs-mrs.fr/nmr/ ------------------------------------------------------------------- E-Mail: herve@afmb.cnrs-mrs.fr ------------------------------------------------------------------- Phone: (33)491-16-45-35 Fax: (33)491-16-45-36 Mail: CNRS Laboratoire AFMB 31 chemin Joseph-Aiguier F-13402 MARSEILLES cedex 20 France ------------------------------------------------------------------- ------------------------------------------------------------------- From owner-structural-nmr@net.bio.net Mon Dec 02 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: herve@afmb85.cnrs-mrs.fr (Herve DARBON) Newsgroups: bionet.structural-nmr Subject: NMR POSTDOCTORAL POSITION Date: 3 Dec 1996 09:21:20 -0000 Lines: 70 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <580reg$amq@mserv1.dl.ac.uk> Original-To: str-nmr@dl.ac.uk ********************************************************************** NMR POSTDOCTORAL POSITION - PROTEIN STRUCTURE/FUNCTION ********************************************************************** WHERE? MARSEILLE (FRANCE), Herve Darbon's NMR group, WHEN? Early 1997. The position is open for one year, possibly renewable. The salary will be 10,000 FF/month RESEARCH TOPIC? The position will involve investigation of the solution structure and structure-function relationships of immunoglobulin fragments from llama, as well as conformational changes induced by the binding of antigens. The group is located in an X-ray cristallography lab which is already deeply involved in the crystal structure determination of such proteins (see Nature Structural Biology, 3, 752-757). EXPERIENCE REQUIRED Applicants should have strong experience in solving large protein structures by multi dimensional homo and heteronuclear NMR. Experience in any of the following areas would be an advantage. Pulsed field gradient NMR 3D heteronuclear NMR protein expression and purification FACILITIES AVAILABLE A DRX500 Bruker spectrometer with pulsed field gradients (3-axis gradients). The group gets 50% time on this instrument. An extensive network of Silicon Graphics ans Suns workstations with softwares ranging from graphic assignment to structure calculation. A fully equipped biochemistry/molecular biology lab. FURTHER DETAILS (1) See our world wide web page: http://afmb.cnrs-mrs.fr/ (2) Contact Herve DARBON TO APPLY Please submit full CV, cover letter, and names and addresses (including telephone, fax, email) of at least two referees to: Herve Darbon ------------------------------------------------------------------- www: http://afmb.cnrs-mrs.fr/nmr/ ------------------------------------------------------------------- E-Mail: herve@afmb.cnrs-mrs.fr ------------------------------------------------------------------- Phone: (33)491-16-45-35 Fax: (33)491-16-45-36 Mail: CNRS Laboratoire AFMB 31 chemin Joseph-Aiguier F-13402 MARSEILLES cedex 20 France ------------------------------------------------------------------- ------------------------------------------------------------------- From owner-structural-nmr@net.bio.net Mon Dec 02 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.erols.net!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!news From: Mike Gradwell Newsgroups: bionet.structural-nmr,sci.techniques.mag-resonance Subject: Re: Shigemi tubes Date: Tue, 03 Dec 1996 10:14:22 +0100 Organization: National Institute for Medical Research Lines: 20 Message-ID: <32A3EF6E.41C67EA6@nimr.mrc.ac.uk> References: <329EFFE9.41C67EA6@nimr.mrc.ac.uk> NNTP-Posting-Host: nmrsn44.nimr.mrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (X11; I; SunOS 4.1.3 sun4m) Xref: biosci bionet.structural-nmr:1628 sci.techniques.mag-resonance:1869 I have received many helpful suggestions for dealing with Shigemis. So many in fact that it's not going to be possible to thank everyone in person! However, many thanks to all the people who very kindly helped me out - I now seem to have got the hang of it. The general consensus seems to be that you can get the bubble out by pushing the upper barrel down suddenly or tapping it, or both. Holding the tube at an angle whilst doing this also seems to help. Sudha Veeraraghav and Kevin Gardner particularly emphasised the importance of practising with a non-precious sample, something which I'm doing at present! Many thanks to you all again. Mike. -- Mike Gradwell, MRC Biomedical NMR Centre, National Institute for Medical Research, Mill Hill, London NW7 1AA. Tel. +44181 959 3666 ext. 2026 Fax. +44181 906 4477 From owner-structural-nmr@net.bio.net Tue Dec 03 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: Werner Kremer Newsgroups: bionet.structural-nmr Subject: subscribe Date: 4 Dec 1996 10:53:58 -0000 Lines: 1 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <583l86$fvq@mserv1.dl.ac.uk> Original-To: str-nmr please subscribe me to the structural nmr newsgroup From owner-structural-nmr@net.bio.net Tue Dec 03 22:00:00 1996 Path: biosci!agate!spool.mu.edu!newspump.sol.net!news.mindspring.com!mindspring!news.bbnplanet.com!cpk-news-hub1.bbnplanet.com!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!lyra.csx.cam.ac.uk!warwick!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!cpca3.uea.ac.uk!cpca7.uea.ac.uk!c362 From: Ruth Boetzel Newsgroups: bionet.structural-nmr Subject: VLI Research Date: Thu, 28 Nov 1996 11:12:42 +0000 Organization: University of East Anglia, Norwich, Norfolk, NR47TJ, UK Lines: 17 Message-ID: NNTP-Posting-Host: cpca7.uea.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: c362@cpca7.uea.ac.uk Hi! Does anybody have a contact address (preferably email) for VLI Research who prepare isotopically compounds? Thanks in advance Ruth Dr Ruth Boetzel School of Chemical Sciences University of East Anglia Norwich UK E-Mail: r.boetzel@uea.ac.uk From owner-structural-nmr@net.bio.net Thu Dec 05 22:00:00 1996 Path: biosci!SBMM1.UCSB.EDU!BLASKO From: BLASKO@SBMM1.UCSB.EDU (Andrei Blasko) Newsgroups: bionet.structural-nmr Subject: Employers check this Web page Date: 5 Dec 1996 16:37:35 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 3 Sender: daemon@net.bio.net Distribution: world Message-ID: <961205163250.20e4a92a@sbmm1.ucsb.edu> NNTP-Posting-Host: net.bio.net US employers check out my home page: http://www.chem.ucsb.edu.Andrei/Andrei.html Andrei@sbmm1.ucsb.edu From owner-structural-nmr@net.bio.net Sun Dec 08 22:00:00 1996 Path: biosci!rutgers!uwm.edu!news-peer.gsl.net!news.gsl.net!EU.net!sun4nl!surfnet.nl!swidir.switch.ch!serra.unipi.it!sirio.cineca.it!gopher From: Andrea Bernini Newsgroups: bionet.structural-nmr Subject: Problems with TPPI Date: Mon, 09 Dec 1996 11:27:12 +0100 Organization: Università di Siena Lines: 8 Message-ID: <32ABE980.3A6D63C1@neriserv.chim.unisi.it> NNTP-Posting-Host: neriserv.chim.unisi.it Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; Linux 1.2.13 i586) We are processing peptide TPPI 2D spectra acquired on a Bruker AMX600 with Sybyl TRIAD software, but we had some problems while processing roesy and noesy spectra (pulse sequence "roesyprtp" and "noesyprtp" respectively), probably due to data treatments. What type of data treatments (like Redfield, singlature ...) should we apply to this type of spectra? Does anyone know where to find the recipies for processing 2D spectra? Thanks in advance. From owner-structural-nmr@net.bio.net Sun Dec 08 22:00:00 1996 Path: biosci!BIOC01.UTHSCSA.EDU!raman From: raman@BIOC01.UTHSCSA.EDU (C.S.RAMAN) Newsgroups: bionet.structural-nmr Subject: POST-DOC POSITION Date: 9 Dec 1996 12:13:31 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 27 Sender: daemon@net.bio.net Distribution: world Message-ID: <9612092016.AA01277@bioc01.uthscsa.edu> NNTP-Posting-Host: net.bio.net POST-DOC POSITION IN BIOMOLECULAR NMR AT THE "ETH ZURICH" In the group of Prof. Kurt Wuthrich at the Swiss Federal Institute of Technology in Zurich, Switzerland, (ETH Zurich) a post-doctoral position is available for one year (renewable for up to 3 years). Applicants should have experience in modern NMR spectroscopy and a strong interest in technical aspects of NMR applied to biological macromolecules. The position has been funded for a project to optimize NMR experiments with aqueous samples at high salt concentrations. We operate four NMR machines: 400, 500, 600 and 750 MHZ. All instruments are of the newest design and fully equipped for all applications in high resolution biomolecular NMR. The position will be available immediately. Applications will be accepted until the position is filled. We thank all applicants in advance for their interest. Qualified individuals are invited to submit their resume, along with two letters of references to: Prof. Dr. Kurt Wuthrich Institute for Molecular Biology and Biophysics ETH Hoenggerberg CH-8093 Zurich / Switzerland Fax.: (..41) (1) 633 1151 www-homepage: http://www.mol.biol.ethz.ch/wuthrich/ From owner-structural-nmr@net.bio.net Sun Dec 08 22:00:00 1996 Path: biosci!PHOENIX.PRINCETON.EDU!ipelczer From: ipelczer@PHOENIX.PRINCETON.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: Problems with TPPI Date: 9 Dec 1996 09:20:29 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 38 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <32ABE980.3A6D63C1@neriserv.chim.unisi.it> NNTP-Posting-Host: net.bio.net Dear Andrea, Back in time while I was working for NMRi/Tripos we put together processing examples/recipes including TPPI spectra to my best recollection, which were presented in the manual. Should I be mistaken or if the manual was changed since then I am sure people at Tripos will be ready to help you out. The actual data structure, and therefore the processing protocol can be different according to the acquisition mode (qsim or qseq in for the directly acquired dimension) and the conversion. It would be quite useful, however, if you would describe the nature of the problems you experience. Good luck, Istvan wwww,wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww Istvan Pelczer, Ph.D. Email: ipelczer@princeton.edu Senior NMR Spectroscopist Princeton University Department of Chemistry, Frick Lab., ph# (609) 258 2342 Washington Road fax# (609) 258 6746 Princeton, NJ 08544, USA On Mon, 9 Dec 1996, Andrea Bernini wrote: > We are processing peptide TPPI 2D spectra acquired on a Bruker AMX600 > with Sybyl TRIAD software, but we had some problems while processing > roesy and noesy spectra (pulse sequence "roesyprtp" and "noesyprtp" > respectively), probably due to data treatments. > What type of data treatments (like Redfield, singlature ...) should we > apply to this type of spectra? Does anyone know where to find the > recipies for processing 2D spectra? > Thanks in advance. > > From owner-structural-nmr@net.bio.net Mon Dec 09 22:00:00 1996 Path: biosci!mol.biol.ethz.ch!gsw From: gsw@mol.biol.ethz.ch (Gerhard Wider) Newsgroups: bionet.structural-nmr Subject: POST-DOC POSITION IN BIO-NMR Date: 10 Dec 1996 01:22:34 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 31 Sender: daemon@net.bio.net Distribution: world Message-ID: <9612100921.AA18829@freya.biol.ethz.ch> NNTP-Posting-Host: net.bio.net POST-DOC POSITION IN BIOMOLECULAR NMR AT THE "ETH ZURICH" In the group of Prof. Kurt Wuthrich at the Swiss Federal Institute of Technology in Zurich, Switzerland, (ETH Zurich) a post-doctoral position is available for one year (renewable for up to 3 years). Applicants should have experience in modern NMR spectroscopy and a strong interest in technical aspects of NMR applied to biological macromolecules. The position has been funded for a project to optimize NMR experiments with aqueous samples at high salt concentrations. We operate four NMR machines: 400, 500, 600 and 750 MHZ. All instruments are of the newest design and fully equipped for all applications in high resolution biomolecular NMR. The position will be available immediately. Applications will be accepted until the position is filled. We thank all applicants in advance for their interest. Qualified individuals are invited to submit their resume, along with two letters of references to: Prof. Dr. Kurt Wuthrich Institute for Molecular Biology and Biophysics ETH Hoenggerberg CH-8093 Zurich / Switzerland Fax.: (..41) (1) 633 1151 www-homepage: http://www.mol.biol.ethz.ch/wuthrich/ From owner-structural-nmr@net.bio.net Mon Dec 09 22:00:00 1996 Path: biosci!Roche.COM!alfred.ross From: alfred.ross@Roche.COM (Alfred Ross) Newsgroups: bionet.structural-nmr Subject: chemical shift - cis-trans Date: 10 Dec 1996 00:50:18 -0800 Organization: Roche Basel AG Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <32AD23D2.41C6@roche.com> NNTP-Posting-Host: net.bio.net Hi netters, does anybody know anything/ has a reference concerning the influence of a cis/trans isomeristation in a protein/peptide on the chemical shift of the Ha, HN, etc. proton of the residue. Thanks in advance -- ************************************* Alfred Ross NMR-Spectroscopist e-mail: alfred.ross@roche.com ******* Phone: CH-(0)61-6887029 * * Fax: CH-(0)61-6887408 * ROCHE * * * Mail: F. Hoffmann-LaRoche AG ******* (A. Ross - PRPS) Postfach CH-4070 Basel ************************************* From owner-structural-nmr@net.bio.net Mon Dec 09 22:00:00 1996 Path: biosci!SHORE.NET!kautz From: kautz@SHORE.NET (Roger Kautz) Newsgroups: bionet.structural-nmr Subject: Re: chemical shift - cis-trans Date: 10 Dec 1996 08:07:11 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: <199612101606.LAA22262@northshore.shore.net> NNTP-Posting-Host: net.bio.net In response to: "does anybody know anything/ has a reference concerning the influence of a cis/trans isomeristation in a protein/peptide on the chemical shift of the Ha, HN, etc. proton of the residue. """""""""""""""""""""""""" Staph nuclease has two different folded forms which give separate sets of histidine peaks; the difference depended largely on a proline cis/trans isomerization. There's a series of papers on it, start with two in Protein Science 2:838-858 (1993); Biochemistry 28:362 (1989). The two conformations are in equilibrium, making it possible to measure the energy differences between them, and study the effects of mutations in side chain interactions that stabilized one conformation or the other. I would be very interested if you would be willing to post a list of the other responses you get to this question. -- Roger Kautz (kautz@shore.net) From owner-structural-nmr@net.bio.net Mon Dec 09 22:00:00 1996 Path: biosci!BIOC01.UTHSCSA.EDU!raman From: raman@BIOC01.UTHSCSA.EDU (C.S.RAMAN) Newsgroups: bionet.structural-nmr Subject: Re: chemical shift - cis-trans Date: 10 Dec 1996 13:01:04 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 59 Sender: daemon@net.bio.net Distribution: world Message-ID: <9612102103.AA02153@bioc01.uthscsa.edu> References: <32AD23D2.41C6@roche.com> NNTP-Posting-Host: net.bio.net Alfred: > does anybody know anything/ has a reference concerning the influence of > a cis/trans isomeristation in a protein/peptide on the chemical shift of > the Ha, HN, etc. proton of the residue. You may want to consult the published work(s) from the research groups of Walter Chazin (Scripps), Bob Fox (UTMB), John Markley (UWisc) and Joel Morrisett (Baylor). Here are a few citations to get you started: Hope it helps -raman O'Neal KD; Chari MV; Mcdonald CH; Cook RG; Yu-Lee LY; Morrisett JD; Shearer WT. Multiple cis-trans conformers of the prolactin receptor proline-rich motif PRM) peptide detected by reverse-phase HPLC, CD and NMR spectroscopy. Biochemical Journal, 1996 May 1, 315 ( Pt 3):833-44. Hodel A; Rice LM; Simonson T; Fox RO; Brunger AT. Proline cis-trans isomerization in staphylococcal nuclease: multi-substrate free energy perturbation calculations. Protein Science, 1995 Apr, 4(4):636-54. Wang JF; Mooberry ES; Walkenhorst WF; Markley JL. Solution studies of staphylococcal nuclease H124L. 1. Backbone 1H and 15N resonances and secondary structure of the unligated enzyme as identified by three-dimensional NMR spectroscopy. Biochemistry, 1992 Jan 28, 31(3):911-20. Hinck AP; Eberhardt ES; Markley JL. NMR strategy for determining Xaa-Pro peptide bond configurations in proteins: mutants of staphylococcal nuclease with altered configuration at proline-117. Biochemistry, 1993 Nov 9, 32(44):11810-8. Kordel J; Forsen S; Drakenberg T; Chazin WJ. The rate and structural consequences of proline cis-trans isomerization in calbindin D9k: NMR studies of the minor (cis-Pro43) isoform and the Pro43Gly mutant. Biochemistry, 1990 May 8, 29(18):4400-9. Amodeo P; Morelli MA; Castiglione Motta A. Multiple conformations and proline cis-trans isomerization in salmon calcitonin: a combined nuclear magnetic resonance, distance geometry, and molecular mechanics study. Biochemistry, 1994 Sep 6, 33(35):10754-62. ______________________________________________________________________ C.S.Raman Tel: (210) 614-0839 Dept. of Biochemistry Fax: (210) 567-2490 University of Texas email:raman@bioc01.uthscsa.edu Health Science Center 7703 Floyd Curl Drive San Antonio, TX, 78284-7760 U.S.A. ---------------------------------------------------------------------- The real problem in speech is not precise language. The problem is clear language. --Richard Feynman ______________________________________________________________________ From owner-structural-nmr@net.bio.net Mon Dec 09 22:00:00 1996 Path: biosci!PHOENIX.PRINCETON.EDU!ipelczer From: ipelczer@PHOENIX.PRINCETON.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: chemical shift - cis-trans Date: 10 Dec 1996 05:42:18 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 47 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <32AD23D2.41C6@roche.com> NNTP-Posting-Host: net.bio.net Dear Alfred, I am sure there are more, and more traditional sources to answer your question, too, but David Case (Scripps) and Mike Williamson (Sheffield University, UK) have done extensive studies on calculating chemical shifts in proteins. I am sure you can find something relevant in their results. All the best, Istvan wwww,wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww Istvan Pelczer, Ph.D. Email: ipelczer@princeton.edu Senior NMR Spectroscopist Princeton University Department of Chemistry, Frick Lab., ph# (609) 258 2342 Washington Road fax# (609) 258 6746 Princeton, NJ 08544, USA On 10 Dec 1996, Alfred Ross wrote: > Hi netters, > does anybody know anything/ has a reference concerning the influence of > a cis/trans isomeristation in a protein/peptide on the chemical shift of > the Ha, HN, etc. proton of the residue. > > Thanks in advance > > -- > ************************************* > Alfred Ross > NMR-Spectroscopist > > e-mail: alfred.ross@roche.com ******* > Phone: CH-(0)61-6887029 * * > Fax: CH-(0)61-6887408 * ROCHE * > * * > Mail: F. Hoffmann-LaRoche AG ******* > (A. Ross - PRPS) > Postfach > CH-4070 Basel > ************************************* > > From owner-structural-nmr@net.bio.net Tue Dec 10 22:00:00 1996 Newsgroups: bionet.structural-nmr Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!news.bbnplanet.com!cam-news-hub1.bbnplanet.com!uunet!in2.uu.net!128.100.1.3!utcsri!utgpu!utinfo!nntp From: Sebastien Vincent Subject: Re: chemical shift - cis-trans X-Nntp-Posting-Host: ernst.med.utoronto.ca Content-Type: text/plain; charset=us-ascii To: Alfred Ross Message-ID: <32AEFBD1.385D@redfield.med.utoronto.ca> Sender: nntp@utcc.utoronto.ca (News) Content-Transfer-Encoding: 7bit Cc: vincent Organization: UTCC Campus Access References: <32AD23D2.41C6@roche.com> <9612102103.AA02153@bioc01.uthscsa.edu> Mime-Version: 1.0 Date: Wed, 11 Dec 1996 18:22:09 GMT X-Mailer: Mozilla 3.0 (X11; I; SunOS 5.5.1 sun4c) Lines: 54 > does anybody know anything/ has a reference concerning the influence of > a cis/trans isomeristation in a protein/peptide on the chemical shift of > the Ha, HN, etc. proton of the residue. I do have a few additional references: A Polinsky et al., Minimum Energy Conformations of Proline-Containing Helices Biopolymers 32 (1992) 399-406 L.-N. Lin and J. F. Brandts, Determination of Cis-Trans Proline Isomerization by Trypsin Proteolysis. Application to a Model Pentapeptide and to Oxidized Ribonuclease A Biochemistry 22 (1983) 553-559 L.-N. Lin and J. F. Brandts, Isomerization of Proline-93 during the Unfolding and Refolding of Ribonuclease A Biochemistry 22 (1983) 559-563 T. Kiefhaber et al., Replacement of a Cis Proline Simplifies the Mechanism of Ribonuclease T1 Folding Biochemistry 29 (1990) 6475-6480 F. L. Texter et al., Intramolecular Catalysis of a Proline Isomerization Reaction in the Folding of Dihydrofolate Reductase Biochemistry 31 (1992) 5687-5691 D. P. Raleigh et al., A Peptide Model for Proline Isomerism in the Unfolded State of Staphylococcal Nuclease J. Mol. Biol. 228 (1992) 338-342 S.-C. Li et al., alpha-Helical, but not beta-Sheet, Propensity of Proline is Determined by Peptide Environment Proc. Natl. Acad. Sci. USA 93 (1996) 6676-6681 Good luck, Sebastien (::) (::) (::) (::) (::) (::) (::) (::) (::) (::) (::) (::) (::) (::) (::) Sebastien Vincent University of Toronto vincent@redfield.med.utoronto.ca Department of Medical Genetics, Voice: ++(416) 978-0642 1, King's College Circle, Fax: ++(416) 978-6885 Toronto, Ontario, CANADA M5S 1A8 www: http://abragam.med.utoronto.ca/~vincent/ "I need something to fly over my gravity" (M. Stipes) From owner-structural-nmr@net.bio.net Wed Dec 11 22:00:00 1996 Path: biosci!aecom.yu.edu!girvin From: girvin@aecom.yu.edu (Mark Girvin) Newsgroups: bionet.structural-nmr Subject: Gordon Conference Date: 12 Dec 1996 08:05:28 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: <199612121604.LAA05554@medusa.bioc.aecom.yu.edu> NNTP-Posting-Host: net.bio.net Dear Colleagues: Please note that the Gordon Conference on Magnetic Resonance in Biology and Medicine has moved from the summer conference series to the winter series. The next conference will be in Ventura, CA from Jan. 26-31, 1997. For the conference program see the Gordon Conference Web site at http://www.grc.uri.edu. You can also get the application form on the GRC web site. For more information contact the conference chair, Hans Thomann, at: email: hthoman@erenj.com phone: 908-730-2898 fax: 908-730-3031 ______________________________________________________________ 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 Wed Dec 11 22:00:00 1996 Path: biosci!SOCKS.BIOPHYSICS.ROCHESTER.EDU!shohei From: shohei@SOCKS.BIOPHYSICS.ROCHESTER.EDU ("Shohei Koide") Newsgroups: bionet.structural-nmr Subject: Postdoc in protein NMR Date: 12 Dec 1996 06:44:27 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 48 Sender: daemon@net.bio.net Distribution: world Message-ID: <9612120933.ZM4895@socks.biophysics.rochester.edu> NNTP-Posting-Host: net.bio.net Postdoctoral Position Available Immediately RESEARCH INTEREST We are interested in characterizing the solution conformation of a surface antigen protein from the Lyme disease spirochete, Borrelia burgdorferi and its interactions with antibodies. We have already established expression and purification protocols. The project involves resonance assignments using triple resonance experiments, solution structure determination, defining the binding sites of monoclonal antibodies, and characterizing conformational dynamics WHERE Dr. Shohei Koide's laboratory Department of Biochemistry and Biophysics University of Rochester Medical Center For information on the University of Rochester, see http://www.rochester.edu. The University has a growing structural biology community including three NMR and two crystallography groups. RESOURCES The Koide group has 50% machine time on a Varian Unity Inova 600 spectrometer with 4 RF channels and PFG. A GE Omega 400 is also available. The group has several SGI/SUN workstations for processing, structure calculation and modeling. The group has a fully equipped biochemistry and molecular biology laboratory. EXPERIENCE REQUIRED A successful candidate should have experience in biophysical analysis, in particular high-resolution NMR, of macromolecules and strong interest in protein structure. Strong background in one or more of the following fields is advantageous: triple resonance NMR spectroscopy solution structure determination molecular modeling protein expression and purification TO APPLY: Please send a CV and two reference letters to: Shohei Koide Department of Biochemistry and Biophysics University of Rochester Medical Center Box: 712 601 Elmwood Ave. Rochester, NY 14642 U.S.A. From owner-structural-nmr@net.bio.net Wed Dec 11 22:00:00 1996 Path: biosci!rutgers!uwm.edu!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!surfnet.nl!swidir.switch.ch!scsing.switch.ch!elna.ethz.ch!igc.chem!abonvin From: abonvin@igc.chem.ethz.ch (Alexandre Bonvin) Newsgroups: bionet.structural-nmr Subject: GROMOS96 release Date: 12 Dec 1996 08:15:45 GMT Organization: Computational Chemistry, ETH, Zuerich Lines: 69 Sender: abonvin@shiraz (Alexandre Bonvin) Distribution: world Message-ID: <58oevh$p1@elna.ethz.ch> NNTP-Posting-Host: shiraz.ethz.ch Keywords: GROMOS molecular dynamics ***************************************************************** ***************************************************************** ** ** ** A N N O U C I N G T H E R E L E A S E O F ** ** ** ** G R O M O S 9 6 ** ** ** ***************************************************************** ***************************************************************** For general information on GROMOS and information on how to get GROMOS96 visit the GROMOS home page at http://igc.ethz.ch/gromos or contact us at BIOMOS b.v Laboratory of Physical Chemistry ETH Zentrum CH-8092 Zuerich Phone : +41.1.632 5501 Fax : +41.1.632 1039 e-mail: biomos@igc.phys.chem.ethz.ch What is GROMOS ? **************** GROMOS is a general-purpose molecular dynamics computer simulation package for the study of biomolecular systems. Its purpose is threefold: - Simulation of arbitrary molecules in solution or crystalline state by the method of molecular dynamics (MD), stochastic dynamics (SD) or the path-integral method. - Energy minimisation of arbitrary molecules. - Analysis of conformations obtained by experiment or by computer simulation. The simulation package comes with the GROMOS force field (proteins, nucleotides, sugars, etc.) the quality of which should be judged from the scientific literature concerning its application to chemical and physical systems, ranging from glasses and liquid crystals to polymers and crystals and solutions of biomolecules. Interesting applications of GROMOS96 (the latest version of GROMOS) are: - prediction of the dependence of a molecular conformation on the type of environment (water, methanol, chloroform, DMSO, apolar solvent, crystal, etc.); - calculation of relative binding constants by evaluating free energy differences between various molecular complexes using thermodynamic integration, perturbation and extrapolation; - prediction of energetic and structural changes caused by modification of amino acids in enzymes or of base pairs in DNA; - derivation of three-dimensional (3D) molecular structure on the basis of NMR data by using restrained MD techniques including time-averaged distance- and J-value restraining; - dynamic modelling of molecular complexes by searching configuration space using MD or SD in 3- or 4-dimensions, soft-core interaction, local elevation search; - prediction of properties of materials under extreme conditions of temperature and pressure, which may be experimentally inaccessible. From owner-structural-nmr@net.bio.net Wed Dec 11 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!www.nntp.primenet.com!nntp.primenet.com!feed1.news.erols.com!howland.erols.net!news-peer.gsl.net!news.gsl.net!news-lond.gsl.net!news.gsl.net!netcom.net.uk!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!daresbury!not-for-mail From: gsw@mol.biol.ethz.ch (Gerhard Wider) Newsgroups: bionet.structural-nmr Subject: POST-DOC in Bio-NMR Date: 10 Dec 1996 15:25:56 -0000 Lines: 32 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <58jve4$f21@mserv1.dl.ac.uk> X-Sun-Charset: US-ASCII Original-To: str-nmr@dl.ac.uk POST-DOC POSITION IN BIOMOLECULAR NMR AT THE "ETH ZURICH" In the group of Prof. Kurt Wuthrich at the Swiss Federal Institute of Technology in Zurich, Switzerland, (ETH Zurich) a post-doctoral position is available for one year (renewable for up to 3 years). Applicants should have experience in modern NMR spectroscopy and a strong interest in technical aspects of NMR applied to biological macromolecules. The position has been funded for a project to optimize NMR experiments with aqueous samples at high salt concentrations. We operate four NMR machines: 400, 500, 600 and 750 MHZ. All instruments are of the newest design and fully equipped for all applications in high resolution biomolecular NMR. The position will be available immediately. Applications will be accepted until the position is filled. We thank all applicants in advance for their interest. Qualified individuals are invited to submit their resume, along with two letters of references to: Prof. Dr. Kurt Wuthrich Institute for Molecular Biology and Biophysics ETH Hoenggerberg CH-8093 Zurich / Switzerland Fax.: (..41) (1) 633 1151 www-homepage: http://www.mol.biol.ethz.ch/wuthrich/ From owner-structural-nmr@net.bio.net Sun Dec 15 22:00:00 1996 Newsgroups: bionet.structural-nmr Path: biosci!daresbury!nntp-trd.UNINETT.no!online.no!sn.no!nntp.uio.no!www.nntp.primenet.com!nntp.primenet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!cam-news-hub1.bbnplanet.com!uunet!in3.uu.net!128.100.1.3!utcsri!utgpu!utinfo!bloch!gardner From: gardner@bloch (Kevin Gardner) Subject: Re: Gordon Conference X-Nntp-Posting-Host: bloch.med.utoronto.ca Message-ID: Sender: nntp@utcc.utoronto.ca (News) Organization: UTCC Campus Access X-Newsreader: TIN [version 1.2 PL2] References: <199612121604.LAA05554@medusa.bioc.aecom.yu.edu> Date: Mon, 16 Dec 1996 17:07:51 GMT Lines: 32 Hi all: Mark Girvin (girvin@aecom.yu.edu) wrote: : Please note that the Gordon Conference on Magnetic Resonance in Biology and : Medicine has moved from the summer conference series to the winter series. : The next conference will be in Ventura, CA from Jan. 26-31, 1997. Can anyone provide some information about what led to this meeting being switched from the summer to winter series? Regrettably, this year's meeting falls quite close to two highly similar meetings (Keystone: 2/6-11, ENC: 3/23-27). Although I can see where this might save some airfare for those travelling to North America for both of the Gordon and Keystone meetings, I'm not sure that this is the best arrangement for the rest of the macromolecular NMR community. On a personal note along this line, I greatly enjoyed attending the 1994 version of this conference as a graduate student; the Gordon Conference format nicely complemented the larger sizes of other meetings in the field and made it easier for me as a young scientist to meet and interact with people in the field. I fear some of that benefit may be lost if this meeting is scheduled too close to larger meetings such as those listed above as time and financial constraints will limit many to attending only one (if any) of this group. My CA$0.02, Kevin -- ************************************************************************* Kevin Gardner gardner@bloch.med.utoronto.ca University of Toronto http://abragam.med.utoronto.ca/~gardner Dept. of Medical Genetics & Microbiology phone: 416-978-0642/FAX: -6885 From owner-structural-nmr@net.bio.net Mon Dec 16 22:00:00 1996 Path: biosci!rutgers!uwm.edu!www.nntp.primenet.com!nntp.primenet.com!nntp.uio.no!voskovec.radio.cz!btnet-feed2!unlisys!blackbush.xlink.net!scsing.switch.ch!elna.ethz.ch!usenet From: Peter Guentert Newsgroups: bionet.structural-nmr Subject: DYANA 1.1 Date: Tue, 17 Dec 1996 10:54:51 +0100 Organization: Swiss Federal Institute of Technology (ETHZ) Lines: 21 Message-ID: <32B66DEB.53BF@mol.biol.ethz.ch> NNTP-Posting-Host: baldur.ethz.ch Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; SunOS 5.4 sun4m) CC: guentert@mol.biol.ethz.ch ************************* DYANA 1.1 *************************** An improved version of the program package DYANA for NMR structure calculation is available via the Internet, free of charge, to everyone! For further details, please see the DYANA home page at http://www.mol.biol.ethz.ch/wuthrich/software/dyana/ Compared to the first version 1.0 there have been many small bugs fixed, new features added, and the manual substantially extended (see "improvements" on the DYANA home page). Peter ---------------------------------------------------------------------- Dr. Peter Guentert phone +41 1 633 34 54 Institut fuer Molekularbiologie & Biophysik fax +41 1 633 11 51 ETH-Hoenggerberg, HPM G22 guentert@mol.biol.ethz.ch CH-8093 Zuerich (Switzerland) http://www.mol.biol.ethz.ch/~guentert ---------------------------------------------------------------------- From owner-structural-nmr@net.bio.net Wed Dec 18 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!www.nntp.primenet.com!nntp.primenet.com!ix.netcom.com!news From: Elizabeth Finkelstein Newsgroups: bionet.structural-nmr Subject: CF1 Particals in a thylakoid disk? Date: Thu, 19 Dec 1996 04:51:25 GMT Organization: Netcom Lines: 4 Message-ID: <59ahmn$glk@dfw-ixnews12.ix.netcom.com> NNTP-Posting-Host: whp-ny5-12.ix.netcom.com X-NETCOM-Date: Wed Dec 18 10:52:39 PM CST 1996 X-Newsreader: NETCOMplete/3.2 I am looking for an approximate number of CF1 particals in a thylakoid disk. If anyone knows the answer, I would appreciate a response at doorframe@imaginetech.com as I will most likely not be able to return to this newsgroup. TIA. From owner-structural-nmr@net.bio.net Fri Dec 20 22:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!news-stkh.gsl.net!news.gsl.net!news-lond.gsl.net!news.gsl.net!tank.news.pipex.net!pipex!arclight.uoregon.edu!enews.sgi.com!news.sgi.com!mr.net!news.idt.net!news.stealth.net!solace!news.ind.mh.se!usenet From: Dominique MARION Newsgroups: bionet.structural-nmr Subject: Junior research scientist in structural protein NMR Date: Fri, 20 Dec 1996 17:27:57 +0100 Organization: Institut de Biologie Structurale - Grenoble Lines: 44 Message-ID: <32BABE8D.103F@ibs.fr> NNTP-Posting-Host: rmn-dominique.ibs.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; PPC) ------------------------------------------------------------------- Junior research scientist in structural protein NMR Charge de recherche en RMN structurale des proteines ------------------------------------------------------------------- A permanent research position is likely to be open next year at the Institut de Biologie Structurale in Grenoble (France). This position will involve the development of new methods in nuclear magnetic resonance of proteins, with special emphasis on dynamical aspects. Over the recent years, the laboratory of nuclear magnetic resonance has focused its interest on both the implementation of new techniques in multidimensional heteronuclear NMR in solution and its application to various proteins such as cytochromes, snake venom toxins or cellulose binding domains. The laboratory has full access to two NMR spectrometers (Bruker AMX-600 and AMX-400) as well as to a range of work stations (SGI). The institute has recently been selected by the french public research institutions as a national facility for a high field NMR spectrometer (800 MHz spectrometer) that will be delivered in 1997. The opening of this position is related to installation of this new equipment. This position corresponds to a permanent appointment at CNRS (Centre National de la Recherche Scientifique) as a "Charge de Recherche 2eme Classe". Therefore, the selection procedure will follow the rules of the french public civil service. The candidate should have extensive practice of multidimensional NMR on labelled biological macromolecules, and preferably have a physical background with a two-year postdoctoral experience. A minimum of five publications in peer-review journals is required. This is no citizenship requirement for this position (although EC citizenship would be prefered), but knowledge of the french language is essential. Interested candidates can obtain further information from: Dr Dominique Marion Institut de Biologie Structurale C.N.R.S.- C.E.A. 41, Avenue des Martyrs 38027 Grenoble Cedex 1 - France Fax: (33) 4 76 88 54 94 E-mail: marion@ibs.fr The deadline for the application is January 10, 1997. From owner-structural-nmr@net.bio.net Sat Dec 21 22:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.structural-nmr Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 22 Dec 1996 02:00:56 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 239 Sender: daemon@net.bio.net Distribution: world Message-ID: <199612221000.CAA08570@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. 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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 Sun Dec 22 22:00:00 1996 Path: biosci!BIOC01.UTHSCSA.EDU!raman From: raman@BIOC01.UTHSCSA.EDU (C.S.RAMAN) Newsgroups: bionet.structural-nmr Subject: Happy Holidays...!!!! Date: 23 Dec 1996 08:28:41 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <9612231630.AA07697@bioc01.uthscsa.edu> NNTP-Posting-Host: net.bio.net I would like to extend my warmest holiday wishes to all participants of this newsgroup. I would also like to wish everyone a spectacular and productive new year, 1997. Let us hope it brings success to all of us. As Alfred de Vigny (the great French poet) said, HOPE (l'espoir) is what keeps us on the move. Sending best regards, -raman ______________________________________________________________________ C.S.Raman Tel: (210) 614-0839 Dept. of Biochemistry Fax: (210) 567-2490 University of Texas email:raman@bioc01.uthscsa.edu Health Science Center 7703 Floyd Curl Drive San Antonio, TX, 78284-7760 U.S.A. ---------------------------------------------------------------------- The real problem in speech is not precise language. The problem is clear language. --Richard Feynman ______________________________________________________________________ From owner-structural-nmr@net.bio.net Tue Dec 31 22:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!swrinde!news.uh.edu!usenet From: Hong Yu Liu Newsgroups: bionet.structural-nmr Subject: 3D NMR processing on Felix950 Date: Wed, 01 Jan 1997 11:49:30 -0600 Organization: University of Houston, Chemistry Department Lines: 72 Message-ID: <32CAA3AA.41C6@tracer.chem.uh.edu> NNTP-Posting-Host: dad.chem.uh.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 5.3 IP22) Dear Newsgroup fellows: Merry Christmas and Happy new year. I was wondering if someone could give me some help on 3D NMR processing using Felix950. I acquired the NOESY-HMQC data on a bruker600 AMX instrument with the following TD: t3 X t2 X t1: 1024 X 32 X 256. I used the conversion program supplied by felix X32 New to convert the bruker format to felix format. It seems to went through fine ( at least no complaining messages). Then I used the felix950 ND Mode to process it as following: User EZ 3D transform D1 States-TPPI Data file format: New format Matrix dimension: D1 X D2 X D3: 512 X 32 X 256 Acquisition Data acquisition type: Quartets 1st incremented: t2 # of t2 exps: 32 # of t1 exps: 256 Phasing Mode: interactive processing Paramenters Correct DC-offset: No Correct 1st point: none Solvent Suppression: none D1 window function: sinebell Transform type: complex (I tried bruker as well) baseline correction: No Info/interrupt: on After applying th window function of 512, 90 sinebell and phasing, the 1D trace obtained looks good. Then I used User EZ 3D transform ND States ( I tried TPPI as well) Dimension: 2( then 3) processing mode: bundle correct 1st point: none window function sinebell liner prediction: off reverse vector: no info/interrupt: on phasing mode: use parameter. phase 0: 0 phase 1: 0 There is no complaining messages all through the process. But when I opened the mat file. It's mainly t3(t2?) noise. I know my data is good b/c I processed it on bruker. and I tried the example offered by felix, it works fine. I'm lost. Pls help. Any suggestion will be greatly appreciated. Thanks in advance. My e-mail address is hong@tracer.chem.uh.edu Thanks HY