From owner-structural-nmr@net.bio.net Sun Mar 02 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!cs.utexas.edu!howland.erols.net!rill.news.pipex.net!pipex!usenet.eel.ufl.edu!warwick!lyra.csx.cam.ac.uk!news.ox.ac.uk!news From: "Simon M. Brocklehurst" Newsgroups: bionet.structural-nmr Subject: IMPORTANT ** Cytokines Web Announcement Date: Mon, 03 Mar 1997 10:23:25 +0000 Organization: University of Oxford Lines: 53 Message-ID: <331AA69D.794BDF32@bioch.ox.ac.uk> NNTP-Posting-Host: nmrv.ocms.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (X11; I; SunOS 4.1.3_U1 sun4m) ********IMPORTANT ANNOUNCEMENT************* *********** THE CYTOKINES WEB************** MAJOR UPDATE, and CHANGE OF LOCATION The Cytokines Web has moved from it's location at the University of Oxford OCMS Web server. The new URL is: http://www.psynix.co.uk/cytweb/ Please update your links and bookmarks to reflect the new location. The Cytokines Web has been updated and extended, as described below: The Cytokines Web provides leading-edge scientific information about cytokines and their receptors, including 3-D structural information and topological and evolutionary relationships (site info available). It also contains information about potential theraputic uses for some Human cytokines. In addition to updates of previously available sections to include up-to-date structural information, new CytWeb areas for 1997 are. o Journal Watch - Up-to-date surveys of the literature at the click of a mouse button (see the icons in the "known structures" areas) o Hot Targets - recently discovered human cytokines that are targets for structure determination by using X-ray/NMR techniques, and/or prediction by computational techniques. o Clinical Significance - potential uses of Human cytokines in diagnosis and treatment of disease Conference Announcements o Check out upcoming events and conferences in a Calendar format. o Commercial Links - products and services of interest to Cytokines Web users. Thanks for reading this message! _____________________________________________________________ | | Simon M. Brocklehurst, | Oxford Centre for Molecular Sciences, | Department of Biochemistry, | University of Oxford, Oxford, UK. | E-mail: smb@bioch.ox.ac.uk |____________________________________________________________ From owner-structural-nmr@net.bio.net Mon Mar 03 22:00:00 1997 Path: biosci!OPAL.TUFTS.EDU!akuliopu From: akuliopu@OPAL.TUFTS.EDU (Athan Kuliopulos) Newsgroups: bionet.structural-nmr Subject: NMR/Signal Transduction Postdoc Avail-BostonPostdoctoral Position Available Center of Hemostasis and Thrombosis Research Tufts University School of Medicine-NEMC Boston, MA We have an immediate opening for a Postdoctoral Fellow to work in the field Date: 4 Mar 1997 08:29:25 -0800 Organization: Tufts-NEMC Lines: 48 Sender: daemon@net.bio.net Distribution: world Message-ID: <331C6198.2AD8@opal.tufts.edu> Reply-To: Department@nemc.org, of@nemc.org, Medicine@nemc.org, Box@nemc.org, 832@nemc.org, 750@nemc.org, Washington@nemc.org, St.@nemc.org, Boston@nemc.org, MA@nemc.org, 02111@nemc.org NNTP-Posting-Host: net.bio.net Postdoctoral Position Available Center of Hemostasis and Thrombosis Research Tufts University School of Medicine-NEMC Boston, MA We have an immediate opening for a Postdoctoral Fellow to work in the field of molecular signaling and peptide-protein recognition. The project focuses on the human thrombin receptor. The thrombin receptor is activated by thrombin cleavage of the receptor exodomain and exposure of an N-terminal tethered ligand that binds to the body of the receptor. Receptor activation precipitates complex signaling events culminating in platelet aggregation, wound healing, and cellular proliferation. Since chronic activation of the receptor may lead to coronary artery disease, stroke, and other vascular diseases, preventing thrombin receptor activation is of pharmacologic interest. NMR structural studies of the thrombin receptor exodomain in activated and resting forms are currently in progress and a preliminary structure has been generated for the activated exodomain. Future projects include solving the structure of the exodomain complexed with extracellular loops and the mechanism of substrate-assisted domain cleavage by thrombin. Insight into the molecular interactions between the exodomain and the body of the receptor should provide leads for the development of novel anti-thrombotic agents. The laboratory is located within the Center of Hemostasis and Thrombosis Research, a modern, state-of-the-art facility with a staff of 20 investigators including technical support. The NMR facility is located in the Medical School Biochemistry Department and current instrumentation include Bruker AMX 500 MHz and 400 MHz magnets along with several SGI workstations. Our lab has a close collaboration with NMR spectroscopist, Dr. James Baleja, who provides additional technical expertise. Qualifications for this position are a Ph.D. degree and US citizenship or permanent residency. Candidates with training in NMR who would like to acquire expertise in molecular biology are encouraged to apply. Interested candidates should e-mail a description of their research interests, a CV, and names of three references to: Athan Kuliopulos, MD., Ph.D. Assistant Professor Departments of Medicine and Biochemistry Tufts-NEMC Box 832 750 Washington Street Boston, MA 02111 617-636-5650 617-636-4833 (fax) akuliopu@opal.tufts.edu From owner-structural-nmr@net.bio.net Tue Mar 04 22:00:00 1997 Path: biosci!NMR.UTMB.EDU!robert From: robert@NMR.UTMB.EDU (Robert Fraczkiewicz) Newsgroups: bionet.structural-nmr Subject: Structural Biology Symposium 1997 Date: 4 Mar 1997 16:07:01 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 48 Sender: daemon@net.bio.net Distribution: world Message-ID: <331CB935.446B@nmr.utmb.edu> NNTP-Posting-Host: net.bio.net ====================================================================== Structural Biology Symposium 1997 April 11-13, 1997 University of Texas Medical Branch at Galveston Sealy Center for Structural Biology Dear Colleagues: We would like to invite you and your colleagues to participate in the UTMB Structural Biology Symposium organized by the Sealy Center for Structural Biology and the Department of Human Biological Chemistry & Genetics of the University of Texas Medical Branch at Galveston, TX. The meeting will start on Friday April 11 afternoon at 4:00 pm and ends on Sunday at noon. For details on the program and electronic registration visit our symposium WEB page http://www.scsb.utmb.edu/symposium.html For further information contact Structural Biology Symposium Shirley Broz Department of Human Biological Chemistry & Genetics University of Texas Medical Branch at Galveston 5.138 Medical Research Building Galveston, TX 77555-1055 Phone: (409) 772-2281 FAX: (409) 772-4298 E-mail: SBroz@mspo1.med.utmb.edu We look forward to your participation. On behalf of the organizing committee Werner Braun Professor Sealy Center for Structural Biology Department of Human Biological Chemistry & Genetics ======================================================================== For Prof. Werner Braun Robert Fraczkiewicz University of Texas Medical Branch Galveston, TX 77555, U.S.A. From owner-structural-nmr@net.bio.net Tue Mar 04 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!cnn.Princeton.EDU!usenet From: Nancy Vogelaar Newsgroups: bionet.molbio.proteins,bionet.xtallography,bionet.structural-nmr Subject: Re: structs vs reality? Date: Thu, 27 Feb 1997 12:14:51 -0500 Organization: Princeton University Lines: 32 Message-ID: <3315C10B.167E@atp.princeton.edu> References: <33134D9A.57D6@spork.niddk.nih.gov> NNTP-Posting-Host: atp.princeton.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) To: John Kuszewski Xref: biosci bionet.molbio.proteins:10168 bionet.xtallography:3256 bionet.structural-nmr:1801 John Kuszewski wrote: > > How well do xray or NMR structures actually model > reality in vivo? > > I've seen some old papers showing that some enzymes > still work in the crystalline state, but there > must be something else about this. > > Can anyone point me toward some references? Hi, John! You may find this paper of interest--especially since it deals with quaternary structure and allostery in crystals vs. solution. D.I. Svergun et al., PROTEINS: Str., Fn., Genet. 27 (1997),pp. 110-117. "Large Differences Are Observed Between the Crystal and Solution Quaternary Structures of Allosteric Aspartate Transcarbamylase in the R State" Nancy --------------------------------------------------------------------- Nancy Vogelaar Department of Chemistry Phone: (609) 258-2927 Princeton University Fax: (609) 258-6746 Princeton, NJ 08544 email: gc@atp.princeton.edu --------------------------------------------------------------------- From owner-structural-nmr@net.bio.net Tue Mar 04 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!newsfeeds.sol.net!feed1.news.erols.com!howland.erols.net!surfnet.nl!ruu.nl!not-for-mail From: Ton Rullmann Newsgroups: bionet.structural-nmr Subject: EMBO Practical Course: Multidimensional NMR in Structural Biology Date: Wed, 05 Mar 1997 10:22:51 +0000 Organization: NMR Spectroscopy, Utrecht University, NL Lines: 102 Message-ID: <331D497B.167E@nmr.chem.ruu.nl> NNTP-Posting-Host: 131.211.51.65 Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) EMBO Practical Course Multidimensional NMR in Structural Biology Il Ciocco, Lucca (Italy), 17 - 21 August, 1997 Co-sponsored by the European Initiative for Training in NMR Organizers: R. Kaptein C. Griesinger H. Oschkinat Speakers and instructors: R. Boelens (Utrecht) S. Glaser (Frankfurt) = C. Griesinger (Frankfurt) = S. Grzesiek (J=FClich) = C.W. Hilbers (Nijmegen) = R. Kaptein (Utrecht) = L. Mitschang (EMBL Heidelberg) = M. Nilges (EMBL Heidelberg) = H. Oschkinat (EMBL Heidelberg) = G. Otting (Stockholm) = A. Palmer (Columbia Un, New York) = G.W. Vuister (Utrecht) = The course will cover NMR theory and methodology for the study of the structure and dynamics of biomolecules in solution. There will be lectures, practical sessions, poster sessions and round table discussions. Topics to be discussed include: = NMR theory (product operator formalism) = Description of pulse sequences including phase cycling and = pulsed field gradients = Multidimensional and multinuclear NMR = Methods for spectral assignment = Relaxation theory and dynamics = Structure calculations (distance geometry, restrained molecular = dynamics, etc) = Isotope labeling = Applications to proteins and nucleic acids = Participation is limited to 55 students (Ph.D students or post-doc's) from European countries, who should have a good basic knowledge of = biomolecular NMR. = Participants must pay a registration fee of Dfl. 400. Board and lodging is covered by EMBO. Participants from industrial companies are required to pay an additional fee to EMBO. = Applications should include a curriculum vitae, a short description of = current research and a letter of recommendation, and should be sent to: = Prof. R. Kaptein Bijvoet Center for Biomolecular Research University of Utrecht Padualaan 8, NL-3584 CH Utrecht The Netherlands Tel. +31-30-253 3787, FAX +31-30-253 7623 E-mail: kaptein@nmr.chem.ruu.nl WWW: http://www-nmr.chem.ruu.nl = Deadline for applications: 20 May, 1997 = (This announcement is also available on the Web as http://www-nmr.chem.ruu.nl/conferences/EMBO97.html) -- J.A.C. Rullmann http://www-nmr.chem.ruu.nl/users/rull/rull.html Bijvoet Center for Biomolecular Research E-mail : rull@nmr.chem.ruu.nl Utrecht University, Padualaan 8, Phone : int+31.30.253 3641 3584 CH Utrecht, the Netherlands Fax : int+31.30.253 7623 From owner-structural-nmr@net.bio.net Wed Mar 05 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: Tim Hubbard Newsgroups: bionet.structural-nmr Subject: ANNOUNCEMENT2: FEBS advanced course: frontiers of protein structure prediction 1997 Date: 6 Mar 1997 12:33:53 -0000 Lines: 75 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5fmdjh$1si@mserv1.dl.ac.uk> X-Sender: th@netra.sanger.ac.uk Original-To: pdb-l@pdb.pdb.bnl.gov, bioforum@dl.ac.uk, bionews@dl.ac.uk, biophys@dl.ac.uk, bio-soft@dl.ac.uk, comp-bio@dl.ac.uk, methods@dl.ac.uk, molmodel@dl.ac.uk, proteins@dl.ac.uk, xtal-log@dl.ac.uk, str-nmr@dl.ac.uk [sorry - with correct web addresses this time] Announcement: Call for applications =================================== FEBS advanced course: frontiers of protein structure prediction 1997 http://predict.sanger.ac.uk/irbm-course97/ The course, which is being run for the second time (see http://predict.sanger.ac.uk/irbm-course95), is directed at young scientists with some experience and a strong interest in protein structure and structure prediction who wish to learn about the latest developments in the field. The aim of the workshop is to predict as much as possible about the structure of a number of proteins of biological interest, taking advantage of the most recent methodologies for fold recognition and ab initio prediction. The participants will be divided into working groups assisted by an instructor. Each group will be equipped with state of the art software and hardware (kindly provided by Silicon Graphics) and assigned the sequences of proteins whose structure has to be predicted. The predictions will be made public as a technical document and also available via World Wide Web. Suggestions for target proteins can also be submitted by non-participants via WWW (see accompanying email) Organizers: Tim Hubbard (Sanger Centre), Anna Tramontano (IRBM) Instructors: G. Barton (Oxford), T. Hubbard (Cambridge), D. Jones (London), M. Sippl (Salzburg), A. Valencia (Madrid) Lecturers: A. Lesk (Cambridge), J. Moult (Rockville), B. Rost (Heidelberg) Dates: 7-20 October 1997 Deadline for applications: 30th June 1997. Registration fee 1200 DM (includes accomodation and meals) Location: IRBM (Istituto di Ricerche di Biologia Molecolare) Pomezia, Rome, Italy Further information and on-line application forms: http://predict.sanger.ac.uk/irbm-course97/ Prof. Anna Tramontano IRBM, Via Pontina Km 30.600 I-00040 Pomezia (Rome) Tel: +39 6 91093207 Fax: +39 6 91093654 email: tramontano@irbm.it Tim Hubbard, Anna Tramontano ------------------------------------------------------------------------- Dr Tim Hubbard email: th@sanger.ac.uk Sanger Centre Tel (direct): +44 1223 494983 Wellcome Trust Genome Campus Tel (switch): +44 1223 834244 Hinxton Fax: +44 1223 494919 Cambridgeshire. CB10 1SA. URL: http://www.sanger.ac.uk/ ------------------------------------------------------------------------- ------------------------------------------------------------------------- Dr Tim Hubbard email: th@sanger.ac.uk Sanger Centre Tel (direct): +44 1223 494983 Wellcome Trust Genome Campus Tel (switch): +44 1223 834244 Hinxton Fax: +44 1223 494919 Cambridgeshire. CB10 1SA. URL: http://www.sanger.ac.uk/ ------------------------------------------------------------------------- From owner-structural-nmr@net.bio.net Wed Mar 05 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: Tim Hubbard Newsgroups: bionet.structural-nmr Subject: ANNOUNCEMENT2: have you a protein to predict? Call for prediction targets Date: 6 Mar 1997 12:33:50 -0000 Lines: 39 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5fmdje$1s9@mserv1.dl.ac.uk> X-Sender: th@netra.sanger.ac.uk Original-To: pdb-l@pdb.pdb.bnl.gov, bioforum@dl.ac.uk, bionews@dl.ac.uk, biophys@dl.ac.uk, bio-soft@dl.ac.uk, comp-bio@dl.ac.uk, methods@dl.ac.uk, molmodel@dl.ac.uk, proteins@dl.ac.uk, xtal-log@dl.ac.uk, str-nmr@dl.ac.uk [sorry - with correct web addresses this time] Announcement: Call prediction targets ===================================== The previous mail to this list announced the FEBS advanced course: frontiers of protein structure prediction 1997. The aim of the workshop is to predict as much as possible about the structure of a number of proteins of biological interest, taking advantage of the most recent methodologies for fold recognition and ab initio prediction. If you are interested in a structure prediction being made on a protein for which there is no sign of an experimental structure and does not appear to be homologous to any known structure, please consider submitting it as a target for this course. For further information and on-line target submission forms see: http://predict.sanger.ac.uk/irbm-course97/ For the automatic analysis carried out on the 113 targets received for the 1995 course and the predictions made for 17 of them see: http://predict.sanger.ac.uk/irbm-course95/ Tim Hubbard, (Sanger Centre) Anna Tramontano, (IRBM) ------------------------------------------------------------------------- Dr Tim Hubbard email: th@sanger.ac.uk Sanger Centre Tel (direct): +44 1223 494983 Wellcome Trust Genome Campus Tel (switch): +44 1223 834244 Hinxton Fax: +44 1223 494919 Cambridgeshire. CB10 1SA. URL: http://www.sanger.ac.uk/ ------------------------------------------------------------------------- From owner-structural-nmr@net.bio.net Wed Mar 05 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: Tim Hubbard Newsgroups: bionet.structural-nmr Subject: ANNOUNCEMENT: FEBS advanced course: frontiers of protein structure prediction 1997 Date: 6 Mar 1997 09:23:02 -0000 Lines: 65 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5fm2dm$ea9@mserv1.dl.ac.uk> X-Sender: th@netra.sanger.ac.uk Original-To: pdb-l@pdb.pdb.bnl.gov, bioforum@dl.ac.uk, bionews@dl.ac.uk, biophys@dl.ac.uk, bio-soft@dl.ac.uk, comp-bio@dl.ac.uk, methods@dl.ac.uk, molmodel@dl.ac.uk, proteins@dl.ac.uk, xtal-log@dl.ac.uk, str-nmr@dl.ac.uk Announcement: Call for applications =================================== FEBS advanced course: frontiers of protein structure prediction 1997 http://predict.sanger.cam.ac.uk/irbm-course97/ The course, which is being run for the second time (see http://predict.sanger.ac.uk/irbm-course95), is directed at young scientists with some experience and a strong interest in protein structure and structure prediction who wish to learn about the latest developments in the field. The aim of the workshop is to predict as much as possible about the structure of a number of proteins of biological interest, taking advantage of the most recent methodologies for fold recognition and ab initio prediction. The participants will be divided into working groups assisted by an instructor. Each group will be equipped with state of the art software and hardware (kindly provided by Silicon Graphics) and assigned the sequences of proteins whose structure has to be predicted. The predictions will be made public as a technical document and also available via World Wide Web. Suggestions for target proteins can also be submitted by non-participants via WWW (see accompanying email) Organizers: Tim Hubbard (Sanger Centre), Anna Tramontano (IRBM) Instructors: G. Barton (Oxford), T. Hubbard (Cambridge), D. Jones (London), M. Sippl (Salzburg), A. Valencia (Madrid) Lecturers: A. Lesk (Cambridge), J. Moult (Rockville), B. Rost (Heidelberg) Dates: 7-20 October 1997 Deadline for applications: 30th June 1997. Registration fee 1200 DM (includes accomodation and meals) Location: IRBM (Istituto di Ricerche di Biologia Molecolare) Pomezia, Rome, Italy Further information and on-line application forms: http://predict.sanger.cam.ac.uk/irbm-course97/ Prof. Anna Tramontano IRBM, Via Pontina Km 30.600 I-00040 Pomezia (Rome) Tel: +39 6 91093207 Fax: +39 6 91093654 email: tramontano@irbm.it Tim Hubbard, Anna Tramontano ------------------------------------------------------------------------- Dr Tim Hubbard email: th@sanger.ac.uk Sanger Centre Tel (direct): +44 1223 494983 Wellcome Trust Genome Campus Tel (switch): +44 1223 834244 Hinxton Fax: +44 1223 494919 Cambridgeshire. CB10 1SA. URL: http://www.sanger.ac.uk/ ------------------------------------------------------------------------- From owner-structural-nmr@net.bio.net Wed Mar 05 22:00:00 1997 Path: biosci!BEAR.BIOCHEM.UBC.CA!mcintosh From: mcintosh@BEAR.BIOCHEM.UBC.CA (Lawrence McIntosh) Newsgroups: bionet.structural-nmr Subject: (none) Date: 5 Mar 1997 22:34:49 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 25 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hello - We are looking for a program to build simple models of DNA, e.g. in a pdb format. We had a program called 'namot' that did this. Somehow we have 'lost' the program and seem to have problems compiling the newer 'namot2' from the Los Alamos site. Does anyone have an early version of 'namot' or a recommendation for a similar program? Thanks! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Lawrence McIntosh 2146 Health Sciences Mall Departments of Biochemistry and Chemistry University of British Columbia Vancouver, BC, Canada V6T 1Z3 mcintosh@otter.biochem.ubc.ca ph: (604) 822-3341 fax: (604) 822-5227 http://www.biochem.ubc.ca/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-structural-nmr@net.bio.net Wed Mar 05 22:00:00 1997 Path: biosci!ggr.co.uk!rhf23484 From: rhf23484@ggr.co.uk (Dr R H Fogh) Newsgroups: bionet.structural-nmr Subject: Varian nD exps in FELIX Date: 6 Mar 1997 02:35:26 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: <5433.199703061034@mailhub.ggr.co.uk> NNTP-Posting-Host: net.bio.net Dear netters, Does anyone know about a set of FELIX processing macros that will process a general arrayed Varian 2D or 3D experiment? I am looking for something that can (ideally) handle any kind and order of arrayed parameters, in the same way as the Varian ft-with-coefficients (e.g. wft2d(1,0,1,0, 0,0,0,0, 0,0,0,0, -1,0,1,0). If you post the answers to me direct, I will send out a resume. Thanks to all, Rasmus Dr. Rasmus H. Fogh Senior Research Scientist, GlaxoWellcome SpA, Via A. Fleming 4, I-37135, Verona, Italia 'Phone: (+39) 45 9218 804 Email : rhf23484@ggr.co.uk From owner-structural-nmr@net.bio.net Wed Mar 05 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: Tim Hubbard Newsgroups: bionet.structural-nmr Subject: ANNOUNCEMENT: have you a protein to predict? Call for prediction targets Date: 6 Mar 1997 09:23:08 -0000 Lines: 29 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5fm2ds$eat@mserv1.dl.ac.uk> X-Sender: th@netra.sanger.ac.uk Original-To: pdb-l@pdb.pdb.bnl.gov, bioforum@dl.ac.uk, bionews@dl.ac.uk, biophys@dl.ac.uk, bio-soft@dl.ac.uk, comp-bio@dl.ac.uk, methods@dl.ac.uk, molmodel@dl.ac.uk, proteins@dl.ac.uk, xtal-log@dl.ac.uk, str-nmr@dl.ac.uk Announcement: Call prediction targets ===================================== The previous mail to this list announced the FEBS advanced course: frontiers of protein structure prediction 1997. The aim of the workshop is to predict as much as possible about the structure of a number of proteins of biological interest, taking advantage of the most recent methodologies for fold recognition and ab initio prediction. If you are interested in a structure prediction being made on a protein for which there is no sign of an experimental structure and does not appear to be homologous to any known structure, please consider submitting it as a target for this course. For further information and on-line target submission forms see: http://predict.sanger.cam.ac.uk/irbm-course97/ For the automatic analysis carried out on the 113 targets received for the 1995 course and the predictions made for 17 of them see: http://predict.sanger.cam.ac.uk/irbm-course95/ Tim Hubbard, (Sanger Centre) Anna Tramontano, (IRBM) From owner-structural-nmr@net.bio.net Wed Mar 05 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!news.sgi.com!swrinde!news.uh.edu!usenet From: "M. Vidakovic" Newsgroups: bionet.structural-nmr Subject: (no subject) Date: 6 Mar 1997 22:32:45 GMT Organization: University of Houston Lines: 21 Message-ID: <5fngmd$u4b@Masala.CC.UH.EDU> NNTP-Posting-Host: mac-11172.sr-building.uh.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) X-URL: news:bionet.structural-nmr Dear Newsgroup users: I have two questions regarding NMR. 1. I have a protein sample: MW ~10,000. How concentrated can be sample be? I can get it up to 10 mM. I want to run DQF_COSY, TOCSY, NOESY. 2. What's be best method for H2O suppression in NOESY and TOCSY? I'm using 'presaturation'. I know about 'jump-return' and 'gradient', but which is better? My purpose is to see the peaks buried under H2O. Any help will be apppreciated. Thanks in advance. Hong Liu e-mail: hong@tracer.chem.uh.edu From owner-structural-nmr@net.bio.net Thu Mar 06 22:00:00 1997 Path: biosci!PHOENIX.PRINCETON.EDU!ipelczer From: ipelczer@PHOENIX.PRINCETON.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: (no subject) Date: 7 Mar 1997 05:32:16 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 64 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <5fngmd$u4b@Masala.CC.UH.EDU> NNTP-Posting-Host: net.bio.net Dear Hong, The minimum concentration required is a function of the sensitivity, in turn the field strength -- and the time you want/can spend on these experiments. Aggregation can be a concern, too. On our 600 MHz system we routinely run experiments in water at the 1 mM concentration, frequently below this level. For water suppression I would recommend the Watergate gradient method. Presaturation may remove/partially suppress important correlations, and may take away sensitivity in general. There are a couple af good halndbook which will give you a lot of useful infirmation about these things, for example: Two-Dimensional NMR Spectroscopy (2nd edition) (Eds.: Croasmun & Carlson), VCH 1994 F. J. M. van de Ven: Multidimensional NMR in Liquids, VCH 1995 John Cavanagh has an excellent book on protein NMR, which I don't have in hand right now, but you'll find it. 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 6 Mar 1997, M. Vidakovic wrote: > Dear Newsgroup users: > > I have two questions regarding NMR. > > 1. I have a protein sample: MW ~10,000. How concentrated can be sample > be? I can get it up to 10 mM. I want to run DQF_COSY, TOCSY, NOESY. > > 2. What's be best method for H2O suppression in NOESY and TOCSY? I'm > using 'presaturation'. I know about 'jump-return' and 'gradient', but > which is better? My purpose is to see the peaks buried under H2O. > > Any help will be apppreciated. > > Thanks in advance. > > Hong Liu > > e-mail: hong@tracer.chem.uh.edu > > > > > From owner-structural-nmr@net.bio.net Thu Mar 06 22:00:00 1997 Path: biosci!COSY.UTMB.EDU!bruce From: bruce@COSY.UTMB.EDU ("Bruce A. Luxon") Newsgroups: bionet.structural-nmr Subject: NMR SOFTWARE UPDATE: MORASS 2.3 Date: 7 Mar 1997 14:46:23 -0800 Organization: Sealy Center for Structural Biology Lines: 34 Sender: daemon@net.bio.net Distribution: world Message-ID: <9703071647.ZM7914@cosy.utmb.edu> Reply-To: bruce@nmr.utmb.edu NNTP-Posting-Host: net.bio.net NMR SOFTWARE ANNOUNCEMENT: MORASS 2.3 is now available for downloading with improved handling of proteins, RNA and DNA over previous versions. MORASS - Multiple Overhauser Relaxation AnalysiS and Simulation - uses a full hybrid matrix eigenvalue/eigenvector solution to the Bloch equations to derive cross-relaxation rates and interproton distances for determining the NMR solution structures of DNA/RNA and proteins. MORASS is available free for academic use from the research laboratories of Prof. David Gorenstein. Distribution is available from: http://www.nmr.utmb.edu/ provides downloading & information via the WWW. nmr.utmb.edu in /pub/morass for standard ftp anonymous protocol. For more information contact: Bruce Luxon bruce@nmr.utmb.edu -- *=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-* * Bruce A. Luxon, Ph.D * * Assistant Professor * * Sealy Center for Structural Biology U * Dept. of Human Biological Chemistry & Genetics T * University of Texas Medical Branch M * Galveston, TX 77555-1157 B * * * (409)747-6802; Fax (409)747-6850 http://www.hbcg.utmb.edu/ * * bruce@nmr.utmb.edu http://www.nmr.utmb.edu/ * *=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-* From owner-structural-nmr@net.bio.net Fri Mar 07 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!csulb.edu!hammer.uoregon.edu!arclight.uoregon.edu!news.maxwell.syr.edu!ais.net!ameritech.net!uunet!in3.uu.net!136.142.185.26!newsfeed.pitt.edu!dsinc!netnews.upenn.edu!taurus.fccc.edu!sauder From: sauder@algol.rm.fccc.edu (John Michael Sauder) Newsgroups: bionet.structural-nmr Subject: labeled protein for NMR studies Date: 8 Mar 1997 19:01:42 GMT Organization: Fox Chase Cancer Center Lines: 2 Message-ID: <5fsd2m$72v@taurus.fccc.edu> NNTP-Posting-Host: algol.rm.fccc.edu Keywords: NMR, ubiquitin, BPTI, nitrogen, carbon, deuterium If anyone is interested in multiply-labeled proteins for benchmarking NMR studies, check out http://www.vli-research.com/ From owner-structural-nmr@net.bio.net Sat Mar 08 22:00:00 1997 Path: biosci!CARIBE.CHEM.UKY.EDU!cammers From: cammers@CARIBE.CHEM.UKY.EDU (Arthur Cammers) Newsgroups: bionet.structural-nmr Subject: water suppression for 2D w/o gradients Date: 8 Mar 1997 19:54:29 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hello NMR Heads: I hope someone out there would like to field this question. What is the best approach for water suppression with 2D nmr that is compatible with Roesy, DQcosy and tocsy in the absence of gradients? Arthur Cammers-Goodwin acgood1@pop.uky.edu From owner-structural-nmr@net.bio.net Sun Mar 09 22:00:00 1997 Path: biosci!PHOENIX.PRINCETON.EDU!ipelczer From: ipelczer@PHOENIX.PRINCETON.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: water suppression for 2D w/o gradients Date: 10 Mar 1997 06:24:09 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 35 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net Dear Arthur, My favourite is used to be the jump-return-echo (JRE; Sklenar & Bax, JMR 74(1987)469-479). Ther is good review on solvent suppression: Gueron, Plateau, and Decorps; Progress in NMR Spectroscopy 23(1991)135-209. 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 8 Mar 1997, Arthur Cammers wrote: > Hello NMR Heads: > I hope someone out there would like to field this question. What > is the best approach for water suppression with 2D nmr that is compatible > with Roesy, DQcosy and tocsy in the absence of gradients? > > > Arthur Cammers-Goodwin > acgood1@pop.uky.edu > > > From owner-structural-nmr@net.bio.net Mon Mar 10 22:00:00 1997 Path: biosci!MRR.COM!jon From: jon@MRR.COM (Jon Webb) Newsgroups: bionet.structural-nmr Subject: New Executive Team Member Date: 11 Mar 1997 13:57:56 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 42 Sender: daemon@net.bio.net Distribution: world Message-ID: <3.0.32.19970311165832.0077e7e8@mrr.com> NNTP-Posting-Host: net.bio.net MR Resources is pleased to announce the addition of Mark Suomala to our team. Mark will occupy the newly created position of Chief Financial Officer. As MR Resources growth and success has increased significantly over the years, we have determined that our need for additional professional leadership has expanded as well. Mark comes to us with both Bachelor and Masters degrees in business administration, as well as numerous years of experience in high tech organizations. This addition is yet one more step in bringing high quality, cost effective goods and services to the NMR industry. As an independent service organization, MR Resources is committed to enhancing and expanding the science of NMR. We all offer Mark a hearty welcome to our winning team. Mark, as well as the rest of us, will be in attendance at the ENC. Stop in and say hi. Best regards, Jon ____________________________________________________________________________ ________ Jon Webb M R Resources, Inc Remanufactured NMR & MRI Systems, Parts and Services 158 R Main Street P.O. Box 880 Gardner, MA 01440 Voice: 508-632-7000 Fax: 508-630-2509 Email: jon@mrr.com Web Site: http://www.mrr.com ____________________________________________________________________________ ________ From owner-structural-nmr@net.bio.net Mon Mar 10 22:00:00 1997 Path: biosci!PHOENIX.PRINCETON.EDU!ipelczer From: ipelczer@PHOENIX.PRINCETON.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: water suppression for 2D w/o gradients Date: 11 Mar 1997 05:48:33 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net Dear Abil, There are some more publications where Sklenar & Bax refer to using the JRE, including one in FEBS Letters (216(1987)249-252). I would also recommend another related publication in JACS (Bax, Sklenar, Clore, & Gronenborn, 109(1987)6511-6513) where avoiding radiation damping is discussed. I am not aware of any further development on this issue; the technique is simple, and is simple to implement -- however, does not offer nearly as much efficiency as gradient methods do. Good luck, 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 From owner-structural-nmr@net.bio.net Tue Mar 11 22:00:00 1997 Path: biosci!Merck.Com!yves_aubin From: yves_aubin@Merck.Com (Yves Aubin) Newsgroups: bionet.structural-nmr Subject: Re: Temperature artifacts Date: 12 Mar 1997 07:33:10 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 100 Sender: daemon@net.bio.net Distribution: world Message-ID: <199703121526.KAA14955@igw2> NNTP-Posting-Host: net.bio.net DearAlfred and Istvan, While I was a grad student at Yale, I recall we had the same problem with our GE omega500 system. If I recall correctly, Jim Prestegard had dropped a thermocouple into the magnet and monitored the temperature only to find that it took about 1 or 2 hours to reach a very stable temperature! The double diagonal problem was traced to the hardware temperature that was fluctuating at low frequency due to the air conditioning system that was too strong for the small room housing the console. The problem was solved partly by raising the room temperature so as to slow down the frequency and bringing the up and down closer, and also adding deflectors to the air inlets of the console. On the instruments, the air intakes were very close to the floor contributing to suck colder air. Look also on the concole side as well as the magnet! Hope this helps, Yves >Dear Alfred, > >There is a paper from Ad Bax's lab in JBN in '95 to my best recollection >about temperature fluctuations due to (13C[!]) spin-lock pulses and its >effect on lock, shim, etc. Sorry not having the exact reference handy. > >However, in a ROESY with sufficiently low power for the spin-lock field >I would not expect such effects (perhaps with the exception of high salt >samples). Those artifacts parallel to the diagonal can be simply a >result of low frequency temperature fluctuations in the lab area. It is >likely to be the case if you see the "parallel diagonal" artifacts along F1. > >I heard of several stories of such effects before; an interesting (and >attractively simple, perhaps partial, however) solution can be to dress >your magnet into a skirt of plastic down to the floor... >Avoiding any direct inlet of conditioned air into the magnet area, or >shields which diffuse it early enough could be helpful, too. >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 12 Mar 1997, Alfred.Ross@Roche.com wrote: > >> Dear Spectroscopists, >> >> I am looking for a reference about artifacts in 2D spectra that are >>induced by >> temperature instability - especially caused by long spinlock pulses like in >> ROESY experiments. I learnd that you get "artifacts" parallel to the >>diagonal, >> but I nerver understood why. >> >> Thanks for any comment from >> >> >> ALfred Ross >> >> -- >> ************************************* >> Dr. 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 >> ************************************* >> >> >> Yves Aubin Ph.D. Merck Frosst Canada Inc. P.O. Box1005 Pointe-Claire--Dorval QC, H9R 4P8 tel: (514) 428-3931 fax: (514) 428-8615 email: yves_aubin@merck.com From owner-structural-nmr@net.bio.net Tue Mar 11 22:00:00 1997 Path: biosci!MAILBOX.SYR.EDU!lpappala From: lpappala@MAILBOX.SYR.EDU (Lucia Pappalardo) Newsgroups: bionet.structural-nmr Subject: ppm vs T Date: 12 Mar 1997 06:08:05 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Netters, I am looking for references on dependence of chemical shifts from temperature, how to analyze them and to relate to conformational changes. I know it is applied to NH of peptide to determine if they are or not involved in H-bond. What about the application to nucleic acids? What about the application to H not involved in H-bond? Usually there is a linear dipendence of ppm vs T, is there explation for this? Thanks, Lucia From owner-structural-nmr@net.bio.net Tue Mar 11 22:00:00 1997 Path: biosci!PHOENIX.PRINCETON.EDU!ipelczer From: ipelczer@PHOENIX.PRINCETON.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: Temperature artifacts Date: 12 Mar 1997 05:51:17 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 63 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <9703121217.ZM24573@sodium.bas.roche.com> NNTP-Posting-Host: net.bio.net Dear Alfred, There is a paper from Ad Bax's lab in JBN in '95 to my best recollection about temperature fluctuations due to (13C[!]) spin-lock pulses and its effect on lock, shim, etc. Sorry not having the exact reference handy. However, in a ROESY with sufficiently low power for the spin-lock field I would not expect such effects (perhaps with the exception of high salt samples). Those artifacts parallel to the diagonal can be simply a result of low frequency temperature fluctuations in the lab area. It is likely to be the case if you see the "parallel diagonal" artifacts along F1. I heard of several stories of such effects before; an interesting (and attractively simple, perhaps partial, however) solution can be to dress your magnet into a skirt of plastic down to the floor... Avoiding any direct inlet of conditioned air into the magnet area, or shields which diffuse it early enough could be helpful, too. 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 12 Mar 1997, Alfred.Ross@Roche.com wrote: > Dear Spectroscopists, > > I am looking for a reference about artifacts in 2D spectra that are induced by > temperature instability - especially caused by long spinlock pulses like in > ROESY experiments. I learnd that you get "artifacts" parallel to the diagonal, > but I nerver understood why. > > Thanks for any comment from > > > ALfred Ross > > -- > ************************************* > Dr. 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 Mar 11 22:00:00 1997 Path: biosci!SODIUM.BAS.ROCHE.COM!rossa From: rossa@SODIUM.BAS.ROCHE.COM ("Alfred.Ross@Roche.com") Newsgroups: bionet.structural-nmr Subject: Temperature artifacts Date: 12 Mar 1997 03:18:35 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 27 Sender: daemon@net.bio.net Distribution: world Message-ID: <9703121217.ZM24573@sodium.bas.roche.com> NNTP-Posting-Host: net.bio.net Dear Spectroscopists, I am looking for a reference about artifacts in 2D spectra that are induced by temperature instability - especially caused by long spinlock pulses like in ROESY experiments. I learnd that you get "artifacts" parallel to the diagonal, but I nerver understood why. Thanks for any comment from ALfred Ross -- ************************************* Dr. 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 Thu Mar 13 22:00:00 1997 Path: biosci!lhc.nlm.nih.gov!not-for-mail From: Chris Hogue Newsgroups: bionet.structural-nmr Subject: Cn3D for 68K Mac is here! Date: Fri, 14 Mar 1997 18:03:52 -0500 Organization: National Library of Medicine Lines: 24 Message-ID: <3329D958.15FB@ncbi.nlm.nih.gov> Reply-To: info@ncbi.nlm.nih.gov NNTP-Posting-Host: glowworm.nlm.nih.gov Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; U; IRIX 5.3 IP20) Greetings, This note is to announce Cn3D (See in 3-D) 1.0 now available for the 680x0 Macintosh platform. Cn3D is a three-dimensional molecular structure viewer which uses MMDB, NCBI's Molecular Modeling Database. Visit the Cn3D homepage: http://www.ncbi.nlm.nih.gov/Structure/cn3d.html There you will find complete downloading and installation instructions, the Cn3D manual, links to Cn3D image galleries, and WWW-based services for structure database searching integrated with NCBI's Entrez system. Christopher Hogue, Ph.D. National Center for Biotechnology Information National Library of Medicine, National Institutes of Health Bldg 38A 8600 Rockville Pike, Bethesda MD 20894 http://www.ncbi.nlm.nih.gov/Structure From owner-structural-nmr@net.bio.net Fri Mar 14 22:00:00 1997 Newsgroups: bionet.structural-nmr Path: biosci!rutgers.rutgers.edu!uwm.edu!cyclic.gsl.net!news.gsl.net!news.maxwell.syr.edu!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!uknet!usenet1.news.uk.psi.net!uknet!uknet!newsfeed.ed.ac.uk!leeds.ac.uk!news From: garyt@bmb.leeds.ac.uk (Gary Sheldon Thompson) Subject: Re: Temperature artifacts Message-ID: <3329B31F.6956@bmb.leeds.ac.uk> NNTP-Posting-Host: bmbsgi14.leeds.ac.uk X-Mailer: Mozilla 3.01 (X11; I; IRIX 5.3 IP22) Content-Type: text/plain; charset=us-ascii Organization: Biochemistry and Molecular Biology, University of Leeds MIME-Version: 1.0 Date: Fri, 14 Mar 1997 20:19:29 +0000 (GMT) References: <9703121217.ZM24573@sodium.bas.roche.com> Lines: 67 CC: rossa@SODIUM.BAS.ROCHE.COM Content-Transfer-Encoding: 7bit Alfred.Ross@Roche.com wrote: > > Dear Spectroscopists, > > I am looking for a reference about artifacts in 2D spectra that are induced by > temperature instability - especially caused by long spinlock pulses like in > ROESY experiments. I learnd that you get "artifacts" parallel to the diagonal, > but I nerver understood why. > > Thanks for any comment from > > ALfred Ross > Hi If these artifacts consist of a 'duplicate of the diagonal' they are indeed caused by a cyclic temperature instability. Quite often they can be caused by your air conditioner cycling you room temperature too violently, which causes the lock to move and adds a extra frequency ontop of you normal data in the indirect dimension. Wurtrich published a paper on this in j mag res a few months back which included a nice little equation to calculate what the length of the cycle that caused the problem. It was based on the diagonal to artifact separation. in actual fact here it is l/w *t1max l = length of experiment[hours] w = distance from diagonal to artefact in hz t1max = dwelltime * no t1 incriments D Braun G. wilder k wurtrich J Mag Res B100 313 (1996) the irony is that in our case the temperature on the front of the machine did not change as the cycling of the room tempeature was affecting the temperture reference for the machine, so the machine always thought the temperature was right. So try watching the lock, signal does it cycle of the same period as the one from the formula . if so look at you room temperature does it cycle on the same timescale if so there is you culprit..... hope this helps gary cures ?? well there are a few -- ********************************************************************* Dr. Gary S. Thompson Address: Wellcome Postdoctoral Fellow Biochemistry and Molecular Biology, Sheena Radford's Laboratory Woodhouse Lane, University of Leeds, Studying the structure and Leeds, LS2 9JT. folding of proteins by nmr. England. e-mail: garyt@bmb.leeds.ac.uk. tel: 0113 233 3134 fax: 0113 233 3167 ********************************************************************* From owner-structural-nmr@net.bio.net Sat Mar 15 22:00:00 1997 Path: biosci!SGI3.MAGNET.FSU.EDU!fengxu From: fengxu@SGI3.MAGNET.FSU.EDU (Feng Xu) Newsgroups: bionet.structural-nmr Subject: Strand Handedness Conversion Date: 16 Mar 1997 10:29:33 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <9703161810.AA23319@sgi3.magnet.fsu.edu> NNTP-Posting-Host: net.bio.net Greetings to all, I have a simple question for those expereinced in molecular modeling: I have a pdb file for a right-handed beta-helix, now for some reason I want to see how its left-handed counterpart looks like. Is that any easy way to convert the pdb file into another file for the left-handed one? Specifically, what kind of software, if any, could I use to do that? Thank you all in advance! FengXu NMR Program National High Magnetic Field Laboratory 1800 E. Paul Dirac Dr. Tallahassee, FL 32306 From owner-structural-nmr@net.bio.net Sun Mar 16 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!csulb.edu!hammer.uoregon.edu!news-xfer.netaxs.com!news.maxwell.syr.edu!news.apfel.de!fu-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!not-for-mail From: "David S. Stephenson" Newsgroups: bionet.structural-nmr Subject: Re: Strand Handedness Conversion Date: Mon, 17 Mar 1997 13:29:44 +0100 Organization: University of Munich Lines: 31 Distribution: world Message-ID: <332D3938.41C6@org.chemie.uni-muenchen.de> References: <9703161810.AA23319@sgi3.magnet.fsu.edu> 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 3.0 (X11; I; IRIX 5.2 IP22) Feng Xu wrote: > > Greetings to all, > > I have a simple question for those expereinced in > molecular modeling: > > I have a pdb file for a right-handed beta-helix, now > for some reason I want to see how its left-handed > counterpart looks like. Is that any easy way to convert > the pdb file into another file for the left-handed one? > Specifically, what kind of software, if any, could > I use to do that? > > Thank you all in advance! I think all you have to do is change the signs of the either all the z-coordinates or all the y-coordinates or all the x-coordinates. Since PDB uses a fixed record format, the best way is probably to write a small Fortran or C program to change the appropriate fields of the ATOM records. All the best David -- 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 Mon Mar 17 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: antonio@risc1.lrm.fi.cnr.it (Antonio Rosato) Newsgroups: bionet.structural-nmr Subject: Course on Computing in NMR Date: 18 Mar 1997 14:28:21 -0000 Lines: 65 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5gm8q5$qkn@mserv1.dl.ac.uk> X-Sender: antonio@risc1.lrm.fi.cnr.it (Unverified) Original-To: str-nmr@dl.ac.uk FIRST ANNOUNCEMENT!!!!! EUROPEAN INITIATIVE FOR TRAINING IN NMR Practical Training Course Advanced Computing in NMR Spectroscopy Florence, September 20-27, 1997 Organizer: Lucia Banci, Department of Chemistry, University of Florence Location: Lectures: Aula Ugo Schiff, Department of Chemistry, University of Florence Practicals: NMR laboratory, Department of Chemistry, University of Florence Speakers: Lucia Banci (Florence) Rolf Boelens (Utrecht) Peter G=FCntert (Z=FCrich) Ernest D. Laue (Cambridge) Dominique Marion (Grenoble) Gottfried Otting (Stockholm) Ruud M. Scheek (Groeningen) J=FCrgen Schmidt (Frankfurt am Main) Gert Vriend (Heidelberg) Topics: - Processing and analysis of NMR data - Simulation of NMR spectra - Automated assignment of NMR spectra - Introduction to molecular dynamics simulation - Computational methods for solution structure determination of macromolecules - Methods for the refinement of structural models - Investigation and analysis of molecular dynamics in solution =20 Contact: Prof. Lucia Banci Dept. of Chemistry - University of Florence Via Gino Capponi 7 50121, Firenze - Italy Tel.: +39 55 2757550 Fax: +39 55 2757555 E-mail: lucia@risc1.lrm.fi.cnr.it The number of participants will be limited to 20. A registration fee of 800'000 italian lire is asked for participation. A limited number of grants to cover accomodation expenses and/or the registration fee is available (for participants with EC citizenship only). WWW: http://risc3.lrm.fi.cnr.it/antonio/adcnmr.html From owner-structural-nmr@net.bio.net Mon Mar 17 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!csulb.edu!hammer.uoregon.edu!news-xfer.netaxs.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!news.imag.fr!ciril.fr!u-strasbg.fr!news From: Kieffer Bruno Newsgroups: bionet.structural-nmr Subject: HSQC Date: Tue, 18 Mar 1997 09:25:38 +0100 Organization: CRC - Universite Louis Pasteur - Strasbourg France Lines: 19 Message-ID: <332E5182.167E@bali.u-strasbg.fr> NNTP-Posting-Host: moa.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.3 IP22) Dear Spectroscopists, I'm looking for an experiement which allows to spot cross peaks originating from glycines in a 1H-15N heteronuclear spectrum (HSQC for instance). Has someone already done this or is it totally hopeless ? PS: the sample is 15N labeled, not 13C. Many thanks, -- _____________________________________________________________________ Bruno KIEFFER ECOLE SUPERIEURE DE BIOTECHNOLOGIE DE STRASBOURG Boulevard Sebastien Brant, Pole API 67400 STRASBOURG-ILLKIRCH FRANCE Fax : (33) 03.88.65.52.62 Voice : (33) 03.88.65.52.71 From owner-structural-nmr@net.bio.net Wed Mar 19 22:00:00 1997 Path: biosci!NMR.UTMB.EDU!david From: david@NMR.UTMB.EDU (David Gorenstein) Newsgroups: bionet.structural-nmr Subject: NMR Spectroscopist Positions Date: 20 Mar 1997 15:30:49 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 98 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Announcement: NMR Spectroscopist Positions University of Texas Medical Branch at Galveston Positions in Virology and Structural Biology Postdoctoral and research technician positions are available to carry out structure-based design of antiviral agents directed against cell attachment and replication of alphaviruses, flaviviruses and arenaviruses. This project, funded by the Defense Advanced Research Projects Agency (DARPA; see Science, 275, pp- 744-746), provides unique opportunities to participate in a highly focused interdisciplinary approach bringing together internationally recognized structural biologists from the Sealy Center for Structural Biology and virologists from the World Health Organization Collaborating Center for Tropical Diseases. Facilities include state-of-the-art Biosafety level 3 laboratories, automated sequencing and molecular biology imaging equipment. Instrumentation available for structural studies includes Varian UNITYplus 750 (4 channel), 600 and wide-bore 400 MHz spectrometers, Cray J90 supercomputer, SGI multiprocessor computers, MacScience imaging plate detectors and rotating anode X-ray generators, and a Pharmacia DNA synthesizer. Both postdoctoral (Ph.D. degree) and technician (BS or MS degree) candidates are encouraged to apply for positions in the following areas: Structural and Molecular Biology: 1. Expression, purification and X-ray crystallography of viral molecules. 2. Drug development using phage display techniques. 3. Biomolecular NMR spectroscopy (protein and nucleic acid structures), backbone modified aptamer oligonucleotide synthesis, molecular biology, combinatorial chemistry, computational biology and computer-aided drug design. 4. Production, purification and testing of recombinant NFkB proteins, and testing of decoy oligonucleotides using recombinant NFkB proteins in vitro and in cell culture systems Structural Biology Faculty: David G. Gorenstein Robert O. Fox Bruce A. Luxon Stanley J. Watowich Virology: 1. Assay development and testing of decoy oligonucleotides in animal systems. Experience in tissue and virus culture, animal infections, cytokine bioassays and immunoasssays is required. 2. Mapping of RNA packaging signals and other conserved sequence elements in alphavirus genomes; testing of decoy oligonucleotides in cell culture and animal models. Experience in molecular virology and animal infections is required. Virology Faculty: Judy F. Aronson Alan D. T. Barrett Norbert K. Herzog Robert E. Shope Scott C. Weaver Send CV, statement of research interests and career goals, and the names, addresses and telephone numbers of three references to: Dr. Robert E. Shope, Department of Pathology, University of Texas Medical Branch, Galveston, Texas 77555-0609; FAX (409) 747-2429; Email: robert.shope@utmb.edu. If you will be attending the ENC, please leave a message on the message board to Bruce Luxon who will be able to further explain this multidisciplinary project involving NMR structure of proteins, nucleic acid aptamers and structure-based design of anti-viral agents. Further information can also be obtained by contacting me or any of the faculty listed above. Please post this announcement. Thank you, ----------------------------------------------------------- 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 Wed Mar 19 22:00:00 1997 Path: biosci!agate!howland.erols.net!worldnet.att.net!news.sprintlink.net!news-peer.sprintlink.net!news.enteract.com!news.inetnebr.com!netserv.unmc.edu!news From: Weixing Zhang Newsgroups: bionet.structural-nmr Subject: Re: HSQC Date: Thu, 20 Mar 1997 07:48:54 -0600 Organization: Eppley Institute, University of Nebraska MC Lines: 27 Message-ID: <33314046.78A9@unmc.edu> References: <332E5182.167E@bali.u-strasbg.fr> NNTP-Posting-Host: 137.197.152.15 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; SunOS 5.5 sun4m) Kieffer Bruno wrote: > > Dear Spectroscopists, > > I'm looking for an experiement which allows to spot cross peaks > originating from glycines in a 1H-15N heteronuclear spectrum (HSQC for > instance). Has someone already done this or is it totally hopeless ? > > PS: the sample is 15N labeled, not 13C. > > If you are willing to run a 3D experiment, most of the glycine residues can be identified. The 3D HNHA expeiment (Vuister and Bax, JACS, 115, 7772-7777 (1993)) is commonly used for measuring J[HN-HA] coupling constant. In most situations, two cross peaks can be seen for glycine. If the chemical shifts of the two alpha protons are the same or the coupling constant is two small for one of the two alpha protons, then only one peak is seen, like the rest residues. Good luck, Weixing Zhang Eppley Cancer Institute University of Nebraska Medical Center Omaha, NE 68198-6805 USA From owner-structural-nmr@net.bio.net Thu Mar 20 22:00:00 1997 Path: biosci!ggr.co.uk!rhf23484 From: rhf23484@ggr.co.uk (Dr R H Fogh) Newsgroups: bionet.structural-nmr Subject: Helix handedness conversion Date: 21 Mar 1997 05:27:06 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <14626.199703211326@mailhub.ggr.co.uk> NNTP-Posting-Host: net.bio.net Dr. David Stephenson proposed (in answer to the original queston by Feng Xu) to convert a righthanded beta-helix to a lefthanded one by inverting the sign of one of the coordinates. Doing this you invert the handedness of the amino acids too, and in general get the exact mirror image of the original structure. Is the idea not to invert the structure without inverting the amino acids? (which would require a different approach?). Yours, somewhat puzzled, Rasmus Rasmus Fogh, Senior Research Scientist Glaxo Wellcome Medicines Research Center, Via A. Fleming 4, 37135 Verona, Italy rhf23484@ggr.co.uk Opinions expressed in this message do not necessarily reflect those of Glaxo Wellcome. From owner-structural-nmr@net.bio.net Thu Mar 20 22:00:00 1997 Path: biosci!ATC.ATCCU.CHULA.AC.TH!porn From: porn@ATC.ATCCU.CHULA.AC.TH (Pornthep Sompornpisut) Newsgroups: bionet.structural-nmr Subject: Funding, Programme for Thailand Tropical Diseases Research, a , self-help model. Date: 20 Mar 1997 19:07:53 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 60 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear str-nmr members, I was asked to forward this announement to scientists who are interested in our research. We are looking forward to hear from you. Thep ---------- Forwarded message ---------- Date: Tue, 18 Mar 1997 10:33:57 +0000 From: Yongyuth Yuthavong To: emarshal@aaas.org Cc: scytr@mahidol.ac.th, vicharn@nwg.nectec.or.th Subject: Thailand Tropical Diseases Research, a self-help model. Dear all I read newspiece on malaria in Africa (Science 275, 299(1997)) with great interest. It may be of interest to your readers that two research funding agencies in Thailand, NSTDA, through its Thailand National Centre for Genetic Engineering and Biotechnology (also a research agency), and Thailand Research Fund, are teaming up with WHO/TDR to launch the "Thailand Tropical Diseases Research " Programme (T-2 for short), to be funded jointly by the three agencies at a ratio of 40%:40%:20%. The scale of the funding is about $2.5 million per year for at least five years. This is the first major attempt by Thailand to fund its own international-level research mainly by itself. The scope will include malaria, Dengue, diarrhoeal diseases, helminthic diseases (liver fluke, elephantiasis, etc.), hepatitis and TB, all with emphasis on those prevalent in Thailand. It will involve both research funding, product development, and technology transfer and training. The funding will be open to the international community, provided that the work is done in Thailand or has significant Thai researchers input. An international advisory board has been set up, and will hold its first meeting in Bangkok next month (11-12 April), which can be considered as the launch date. We think that this Programme will help Thailand help itself overcome the difficult problems of tropical diseases, as well as demonstrate to the world that something can be done initiated by the endemic developing country itself, provided the world also helps. If you would like more detail, please contact Prof Yodhathai Thebtaranonth, Director of the T-2 Programme at scytr@mahidol.ac.th. Sincerely Yongyuth Yuthavong -- ====== Please take note of our new Internet Address ====== Prof. Dr. Yongyuth Yuthavong, Director, National Science & Technology Development Agency (NSTDA), Yothee Research Building, 73/1, Rama VI Rd., Rajdhevee, Bangkok 10400, THAILAND Tel: 662 6448002; 662 6448150-99 Fax: 662 6448020; 662 6448027-9 E-mail: yongyuth@nstda.or.th WWW: http://www.nstda.or.th ========================================================== NSTDA: THE MAIN DRIVING FORCE FOR RAPID S&T DEVELOPMENT ========================================================== From owner-structural-nmr@net.bio.net Fri Mar 21 22:00:00 1997 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.structural-nmr Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 22 Mar 1997 02:00:08 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 239 Sender: daemon@net.bio.net Distribution: world Message-ID: <199703221000.CAA02928@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 Wed Mar 26 22:00:00 1997 Newsgroups: bionet.structural-nmr Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news.maxwell.syr.edu!ais.net!news.stealth.net!news.ibm.net.il!news.ibm.net!news.biu.ac.il!discus.technion.ac.il!news From: Ariel Subject: quantitative microscopic tissue morphology and microanatomy of the brain tissue Content-Type: text/plain; charset=us-ascii Reply-To: bmesver@tx.technion.ac.il Organization: Technion, Israel Institute of Technology Date: Thu, 27 Mar 1997 17:45:05 GMT Message-ID: <333AB221.6D@tx.technion.ac.il> X-Mailer: Mozilla 3.01Gold (WinNT; I) Mime-Version: 1.0 X-Nntp-Posting-Host: 132.68.176.145 Content-Transfer-Encoding: 7bit Sender: news@discus.technion.ac.il (News system) Lines: 21 Hello I am trying to form a mathematical microstructural mechanical model of the brain tissue. To this end I am searching for data on quantitative microscopic tissue morphology and microanatomy of the brain tissue: fibers orientation, partial volume (of each tissue), capillary count, etc. I am also looking for data on the mechanical properties of the different "building blocks" of the tissue: Nerve fibres, Glia cells, Blood vessels, etc. Therefor I will be very grateful to get any kind of direction to information on these topics (even very old ones). Thanks in advance for the help. Ariel Sverdlik Please answer directly to the e-mail address below: E-mail: bmesver@tx.technion.ac.il Fax : 972-4-8234131 From owner-structural-nmr@net.bio.net Sat Mar 29 22:00:00 1997 Path: biosci!INDIGO1.BIOMOL.UCI.EDU!raman From: raman@INDIGO1.BIOMOL.UCI.EDU (CS Raman) Newsgroups: bionet.structural-nmr Subject: Newsgroup moderation update Date: 30 Mar 1997 08:31:43 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 29 Sender: daemon@net.bio.net Distribution: world Message-ID: <199703301632.QAA02721@indigo1.biomol.uci.edu> NNTP-Posting-Host: net.bio.net Thanks to everyone who has written to me regarding moderation of the BIONET STR-NMR newsgroup. I had brought up this issue about a year ago and at that time despite tremendous support from the readership for pro-moderation, I was hoping that these junk mails would go away. It appears that the only way we can protect ourselves from such spams is to to moderate the newsgroup and your recent surge of support for the same has convinced me to go ahead with it. Considering the traffic on this newsgoup moderation should not pose a serious time constraint for me. I hope we can prevent this intrusion in the future and devote more time to thinking and discussing about STR-NMR issues. Please bear with me while we switch from unmoderated to moderated status. I am hoping this will happen real soon. Cheers -raman ___________________________________________________________________ C.S.Raman Tel: (714) 824-4322 University of California Fax: (714) 824-8540 Dept. MB & B email: raman@indigo1.biomol.uci.edu 3205 Bio Sci II Irvine, CA 92697-3900 ------------------------------------------------------------------- The real problem in speech is not precise language. The problem is clear language. --Richard Feynman ___________________________________________________________________ From owner-structural-nmr@net.bio.net Mon Mar 31 23:00:00 1997 Path: biosci!OPAL.TUFTS.EDU!akuliopu From: akuliopu@OPAL.TUFTS.EDU (Athan Kuliopulos) Newsgroups: bionet.structural-nmr Subject: NMR-Signal Transduction Postdoc Avail in Boston Date: 1 Apr 1997 08:47:04 -0800 Organization: Tufts-NEMC Lines: 50 Sender: daemon@net.bio.net Distribution: world Message-ID: <33414FFE.52FA@opal.tufts.edu> Reply-To: Department@nemc.org, of@nemc.org, Medicine@nemc.org, Box@nemc.org, 832@nemc.org, 750@nemc.org, Washington@nemc.org, St.@nemc.org, Boston@nemc.org, MA@nemc.org, 02111@nemc.org NNTP-Posting-Host: net.bio.net Postdoctoral Position Available Center of Hemostasis and Thrombosis Research Tufts University School of Medicine-NEMC Boston, MA We have an immediate opening for a Postdoctoral Fellow to work in the field of molecular signaling and peptide-protein recognition. The project focuses on the human thrombin receptor. The thrombin receptor is activated by thrombin cleavage of the receptor exodomain and exposure of an N-terminal tethered ligand that binds to the body of the receptor. Receptor activation precipitates complex signaling events culminating in platelet aggregation, wound healing, and cellular proliferation. Since chronic activation of the receptor may lead to coronary artery disease, stroke, and other vascular diseases, preventing thrombin receptor activation is of pharmacologic interest. NMR structural studies of the thrombin receptor exodomain in activated and resting forms are currently in progress and a preliminary structure has been generated for the activated exodomain. Future projects include solving the structure of the exodomain complexed with extracellular loops and the mechanism of substrate-assisted domain cleavage by thrombin. Insight into the molecular interactions between the exodomain and the body of the receptor should provide leads for the development of novel anti-thrombotic agents. The laboratory is located within the Center of Hemostasis and Thrombosis Research, a modern, state-of-the-art facility with a staff of 20 investigators including technical support. The NMR facility is located in the Medical School Biochemistry Department and current instrumentation include Bruker AMX 500 MHz and 400 MHz magnets along with several SGI workstations. A new 600 MHz magnet will be added to the NMR facility in the next 6 months. Our lab has a close collaboration with NMR spectroscopist, Dr. James Baleja, who provides additional technical expertise. Qualifications for this position are a Ph.D. degree and US citizenship or permanent residency. Candidates with training in NMR who would like to acquire expertise in molecular biology are encouraged to apply. Interested candidates should e-mail a description of their research interests, a CV, and names of three references to: Athan Kuliopulos, MD., Ph.D. Assistant Professor Departments of Medicine and Biochemistry Tufts-NEMC Box 832 750 Washington Street Boston, MA 02111 617-636-5650 617-636-4833 (fax) akuliopu@opal.tufts.edu From owner-structural-nmr@net.bio.net Mon Mar 31 23:00:00 1997 Path: biosci!COSY.UTMB.EDU!bruce From: bruce@COSY.UTMB.EDU ("Bruce A. Luxon") Newsgroups: bionet.structural-nmr Subject: Model-free Software Date: 1 Apr 1997 10:58:11 -0800 Organization: Sealy Center for Structural Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <9704011259.ZM7178@cosy.utmb.edu> Reply-To: bruce@nmr.utmb.edu NNTP-Posting-Host: net.bio.net Can someone point to a URL or two where I can look up some software utilizing the model-free formalism (per Lipari & Szabo) for the analysis of NMR relaxation rates? All help much appreciated, Bruce -- *=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-* * Bruce A. Luxon, Ph.D * * Assistant Professor * * Sealy Center for Structural Biology U * Dept. of Human Biological Chemistry & Genetics T * University of Texas Medical Branch M * Galveston, TX 77555-1157 B * * * (409)747-6802; Fax (409)747-6850 http://www.hbcg.utmb.edu/ * * bruce@nmr.utmb.edu http://www.nmr.utmb.edu/ * *=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-*