From owner-structural-nmr@net.bio.net Thu Sep 01 23:00:00 1994 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: pulse widths in different samples? Date: 2 Sep 1994 16:46:07 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 63 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <347n9o$n70@news.umu.se> NNTP-Posting-Host: net.bio.net On 2 Sep 1994, Peter Lundberg wrote: > Dear audience, > > * Suppose I am find that the pulse width of H1 (H2O) is 10 us, and that > of C13 is 20 us with a particular sample and probe). > > If I find that the H1 pulse width (H2O) is 15 us with ANOTHER sample > (e.g., a 'salty' solution), what is the pulse width of C13 in that > sample? > > Is it reasonably to use a pulse width of 20*15/10=30 for C13 with that > sample? Suppose that the C13 concentration is so low in sample 2 that > it is not feasible to measure it directly (that's of course why I am > asking). Considering that you may have difficulties in measuring 13C pulses directly I think it would be an acceptable approximation. However, make it sure that tuning of each channel are as close as possible to the optimum each case. > > * Besides are there any obvious DISadvantages in using 360 degree > pulses for measuring pulse widths, instead of 180 degree pulses? Just > curious... > Actually 360 is better to check than the 180 in my opinion. It usually shows a quite clean zero transition, and you will not have to worry about relaxation delays as much (provided you're scanning in the neighborhood of the 360). > Comments? > > 73, Peter > > ================================== > Peter Lundberg > Email: peterl@umdix.umdc.umu.se > ============761.91141============= > > Good luck, Istvan ------------------------------- Istvan Pelczer, Ph.D. Res. Assist. Professor Chemistry Department, CST Bldg. Syracuse University Syracuse, NY 13244-4100 ph# 315 443 1023 fax# x-4070 ------------------------------- From owner-structural-nmr@net.bio.net Thu Sep 01 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!umdac!Peter.Lundberg From: peterl@umdix.umdc.umu.se (Peter Lundberg) Newsgroups: bionet.structural-nmr Subject: pulse widths in different samples? Date: 2 Sep 1994 17:27:20 GMT Organization: Phys Chem, University of Umea, Sweden Lines: 26 Sender: -Not-Authenticated-[2976] Message-ID: <347n9o$n70@news.umu.se> NNTP-Posting-Host: plgmac.chem.umu.se X-Posted-From: InterNews 1.0@news.umu.se. Xdisclaimer: No attempt was made to authenticate the sender's name. Dear audience, * Suppose I am find that the pulse width of H1 (H2O) is 10 us, and that of C13 is 20 us with a particular sample and probe). If I find that the H1 pulse width (H2O) is 15 us with ANOTHER sample (e.g., a 'salty' solution), what is the pulse width of C13 in that sample? Is it reasonably to use a pulse width of 20*15/10=30 for C13 with that sample? Suppose that the C13 concentration is so low in sample 2 that it is not feasible to measure it directly (that's of course why I am asking). * Besides are there any obvious DISadvantages in using 360 degree pulses for measuring pulse widths, instead of 180 degree pulses? Just curious... Comments? 73, Peter ================================== Peter Lundberg Email: peterl@umdix.umdc.umu.se ============761.91141============= From owner-structural-nmr@net.bio.net Thu Sep 01 23:00:00 1994 Path: biosci!DELPHI.COM!CAMBISOTOPE From: CAMBISOTOPE@DELPHI.COM Newsgroups: bionet.structural-nmr Subject: 20%13C 98%15N substrates Date: 2 Sep 1994 08:33:25 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HGMVB955NE939LR7@delphi.com> NNTP-Posting-Host: net.bio.net I am Ron Trolard with Cambridge Isotopes. This is my first posting. I am interested in 3d dynamic experiments which may require 13C 20% ,15N 98% enriched substrates/precursors. Thses would yield proteins that would have 20% of the possible C sites labeled with 13C NOT 20% of the proteins uniformly labeled with 13C. This would reduce the # of carbons 13C in the molecule that have another 13C as nearest neighbor and should simplify the math used to intrepret the dynamics. The substrates we are considering are amino acids, nucleosides and growth media if these would be useful let me know which ones and the enrichment levels. thanks From owner-structural-nmr@net.bio.net Thu Sep 01 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: " (Ton Rullmann)" Newsgroups: bionet.structural-nmr Subject: Re: xplor pdb format Date: 2 Sep 1994 10:11:35 +0100 Lines: 16 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <346q87$98k@mserv1.dl.ac.uk> Reply-To: rull@ruuci9.chem.ruu.nl Original-To: str-nmr@dl.ac.uk Mogens Kjaer writes: > Does anyone know, what PDB uses the convert/check atom names? Are these > programs publicly available? > I think they use Janet Thornton's PROCHECK - at least for geometry checking. This program starts with a cleanup of the coordinate files. Info about PROCHECK is somewhere on the PDB gopher server. -- | Ton Rullmann NMR Spectroscopy | | Bijvoet Center for Biomolecular Research | Tel. : int+31.30.533641 | | Utrecht University, Padualaan 8, | Fax : int+31.30.537623 | | 3584 CH Utrecht, The Netherlands | Email: rull@nmr.chem.ruu.nl | From owner-structural-nmr@net.bio.net Fri Sep 02 23:00:00 1994 Path: biosci!OTTER.BIOCHEM.UBC.CA!mcintosh From: mcintosh@OTTER.BIOCHEM.UBC.CA (Lawrence McIntosh) Newsgroups: bionet.structural-nmr Subject: Re: pulse widths in different samples? Date: 2 Sep 1994 19:09:22 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 51 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <347n9o$n70@news.umu.se> NNTP-Posting-Host: net.bio.net I think that the answer to your question depends upon the type of probe. If it is an inverse or triple resonance probe, then the 13C tuning is usually much LESS SENSITIVE to the sample conditions than the 1H coil (the 13C coil is outside the 1H coil in these probes). We find little change in the 13C or 15N pulse lengths between samples of 0 - 500 mM NaCl with a Varian 5 mm triple resonance probe. Therefore, you are probably better off not changing the 13C pulse lenghts, despite what happens with 1H. Good luck, Lawrence McIntosh UBC, Vancouver. On 2 Sep 1994, Peter Lundberg wrote: > Dear audience, > > * Suppose I am find that the pulse width of H1 (H2O) is 10 us, and that > of C13 is 20 us with a particular sample and probe). > > If I find that the H1 pulse width (H2O) is 15 us with ANOTHER sample > (e.g., a 'salty' solution), what is the pulse width of C13 in that > sample? > > Is it reasonably to use a pulse width of 20*15/10=30 for C13 with that > sample? Suppose that the C13 concentration is so low in sample 2 that > it is not feasible to measure it directly (that's of course why I am > asking). > > * Besides are there any obvious DISadvantages in using 360 degree > pulses for measuring pulse widths, instead of 180 degree pulses? Just > curious... > > Comments? > > 73, Peter > > ================================== > Peter Lundberg > Email: peterl@umdix.umdc.umu.se > ============761.91141============= From owner-structural-nmr@net.bio.net Sun Sep 04 23:00:00 1994 Path: biosci!newshost.lanl.gov!transposon.lanl.gov!pxc From: pxc@transposon.lanl.gov (Paolo Catasti) Newsgroups: bionet.structural-nmr Subject: Re: pulse widths in different samples? Date: 5 Sep 1994 15:25:18 GMT Organization: Los Alamos National Laboratory, T-10 Lines: 17 Distribution: world Message-ID: <34fd8u$517@newshost.lanl.gov> References: <347n9o$n70@news.umu.se> NNTP-Posting-Host: transposon.lanl.gov In article <347n9o$n70@news.umu.se> peterl@umdix.umdc.umu.se (Peter Lundberg) writes: >* Besides are there any obvious DISadvantages in using 360 degree >pulses for measuring pulse widths, instead of 180 degree pulses? Just >curious... If you measure the 90 pulse width through a 360 you'll get a shorter value than doing it through a 180. The reason is that relaxation starts after you begin irradiating your sample with your first pulse, and not at the end of it. To me the best 90 pulse is extrapolating the correction due to the relaxation measuring both 360 and 180 pulses. This is especially true for longer 90 pulses i.e. 13C pulses. Cheers, Paolo Catasti From owner-structural-nmr@net.bio.net Tue Sep 06 23:00:00 1994 Path: biosci!DELPHI.COM!CAMBISOTOPE From: CAMBISOTOPE@DELPHI.COM Newsgroups: bionet.structural-nmr Subject: deuterated buffers Date: 7 Sep 1994 14:06:42 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HGU6LZDNSAA8DZ4J@delphi.com> NNTP-Posting-Host: net.bio.net We are interested in your requirements for deuterated buffers. We have the following currently available: Tris (hydroxymethyl)methylamine dodecylphosphocholine (DPC) N-tris(hydroxymethyl)methyl)glycine (tricine) We have been requested to make these and would like to have a consensus on their utility since they do take time and effort to synthesize. MES, HEPES, CHAPS, KHP, Sarcosine. Thanks for your input, Ron Trolard Cambridge Isotopes CAMBISOTOPES@delphi.com From owner-structural-nmr@net.bio.net Tue Sep 06 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!newsfeed.ksu.ksu.edu!moe.ksu.ksu.edu!kuhub.cc.ukans.edu!falcon.cc.ukans.edu!jalluri Newsgroups: bionet.structural-nmr Subject: Need info on PSEUDOROT Message-ID: <1994Sep6.152410.72065@kuhub.cc.ukans.edu> From: jalluri@falcon.cc.ukans.edu (jalluri ravi) Date: 6 Sep 94 15:24:09 CDT Nntp-Posting-Host: falcon.cc.ukans.edu X-Newsreader: TIN [version 1.2 PL2] Lines: 15 I am looking for information about the program PSEUDOROT. We would like to know the address from where we can get this program. Any suggestions about similar programs. Thanks -- ***************************************************************************** RAVI K. JALLURI jalluri@falcon.cc.ukans.edu jalluri@kuhub.cc.ukans.edu ***************************************************************************** From owner-structural-nmr@net.bio.net Wed Sep 07 23:00:00 1994 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: contact Date: 8 Sep 1994 04:22:55 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net I'd like to contact Marc Delsuc in France, also Bruce Johnson here in the US at Merck by Email. Could anybody help me? Thanks, Istvan ------------------------------- Istvan Pelczer, Ph.D. Res. Assist. Professor Chemistry Department, CST Bldg. Syracuse University Syracuse, NY 13244-4100 ph# 315 443 1023 fax# x-4070 ------------------------------- From owner-structural-nmr@net.bio.net Wed Sep 07 23:00:00 1994 Path: biosci!BIOC01.UTHSCSA.EDU!raman From: raman@BIOC01.UTHSCSA.EDU (C.S.RAMAN) Newsgroups: bionet.structural-nmr Subject: Re: contact Date: 8 Sep 1994 05:47:28 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 27 Sender: daemon@net.bio.net Distribution: world Message-ID: <9409081247.AA00232@bioc01.uthscsa.edu> References: NNTP-Posting-Host: net.bio.net Istvan: > I'd like to contact Marc Delsuc in France, also Bruce Johnson here in the > US at Merck by Email. Could anybody help me? > Thanks, My mail to you kept bouncing and hence am directly posting this to the net. You can get Marc's email address from a colleague of mine who works in his lab at Montpellier. kamna@bresse.cbs.univ-montp1.fr Hope this helps Cheers -raman -- C.S.Raman UNIX Programming & Administration SPARC & SGI Systems raman@bioc01.uthscsa.edu - INTERNET Department of Biochemistry raman@mintaka.chpc.utexas.edu - CHPC UTHSCSA c.raman@launchpad.unc.edu 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From owner-structural-nmr@net.bio.net Wed Sep 07 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: BOLIS%IMICLVX.earn@earn-relay.ac.uk Newsgroups: bionet.structural-nmr Subject: Pharmaceutical NMR vs GLP & SOP Date: 8 Sep 1994 09:28:36 +0100 Lines: 46 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <34mhvk$jma@mserv1.dl.ac.uk> Original-To: str-nmr@dl.AC.UK Dear Netters: particularly to INDUSTRIAL NMR USERS on behalf of the A.F.I.-NMR Group (Italian Pharmaceutical-chemists Association NMR Group) REQUEST OF INFORMATION, GUIDELINES, REFERENCES & COMMENTS ON INDUSTRIAL NMR & GLP/SOP (in PHARMACEUTICALS and CHEMICALS) We are trying to setup some common guidelines in our labs about Good Laboratory Practice & Standard Operating Procedure, with special concern about FDA & other Governamental Boards inspections: Quality has arrived in Italy !!! We would like to receive any info about accepted procedures for testing & calibrations of spectrometers, data storage & retrieval istrument manteinance (regular & registerd controls), etc. Please FORWARD this message to anybody could give infos (any Bruker Users Network ?!). I'll collect all the answers and post the summary on the network THANKS in advance for your collaboration for A.F.I.-NMR Group M.Tato' Marco Tato' e-mail bolis@icil64.cilea.it PHARMACIA-Italy Bioscience Center, NMR lab via Giovanni XXIII n.23 20014 Nerviano (MI), Italy tel. xx39-331-583147,6,5 fax xx39-331-583100 ******************************************************************** Reading this stuff can affect the dimensionality of your experiments, change the cross-relaxation rate of your spins, cause the growth of artifacts on your spectra, and make a difference in the outcome of your favorite pulse sequence. ********************************************************************* From owner-structural-nmr@net.bio.net Mon Sep 12 23:00:00 1994 Path: biosci!RISC1.LRM.FI.CNR.IT!thep From: thep@RISC1.LRM.FI.CNR.IT (Pornthep Sompornpisut) Newsgroups: bionet.structural-nmr Subject: how to add HEME to the library as a additional residue type Date: 13 Sep 1994 12:20:52 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: <9409131922.AA15828@risc1.lrm.fi.cnr.it> NNTP-Posting-Host: net.bio.net Dear Do anyone know how to declare the atom types, the nomenclature, the dihedral angle definitions and the standard geometry of HEME in the residue library input file. I will appreciate for any responses Thanks Thep From owner-structural-nmr@net.bio.net Tue Sep 13 23:00:00 1994 Newsgroups: bionet.structural-nmr Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!wupost!monsanto.com!alex.monsanto.com!wchutt From: wchutt@alex.monsanto.com (Bill C Hutton) Subject: NMR Position Open at Monsanto Message-ID: <1994Sep14.141422.4068@tin.monsanto.com> Sender: news@tin.monsanto.com (USENET News System) Organization: Monsanto Company X-Newsreader: TIN [version 1.2 PL0] Date: Wed, 14 Sep 1994 14:14:22 GMT Lines: 69 Please be kind enough to bring this position to the attention of potential applicants. ************************************************************************ MONSANTO CORPORATE RESEARCH NMR Laboratory Technical Support Monsanto Corporate Research is looking for a talented individual to join a corporate-wide NMR Consortium. The Consortium is responsible for twelve superconducting NMR spectrometers housed in four laboratories throughout Monsanto's St. Louis area research campuses. The successful applicant will have a B.S. or B.A. in the physical sciences, preferably chemistry, or equivalent degree level in electronics or computer science. This position requires excellent verbal and written communication skills Those with experience in any (but not necessarily all) of the following areas are encouraged to apply: 1) significant experience in the operation/general maintenance of high-resolution NMR spectrometers 2) structure elucidation of organic molecules, including a working knowledge of contemporary NMR methods (2D, selective excitation, etc.) 3) significant experience in a UNIX computing environment 4) significant experience in the repair, maintenance and modification of modern NMR spectrometers, probes and simple UNIX workstation hardware repairs (initial diagnostics, board swaps) Responsibilities will be in the area of technical support for NMR laboratories at Monsanto's research campuses and will - depending on the interest and skill base of the applicant - include some of the following: 1) spectrometer maintenance, including cryogen refills 2) act as a focal point for administrative support and operational issues 3) train and assist users 4) consult with chemists to optimize the impact of NMR 5) spectrometer Good Laboratory Practice 6) test/evaluate software 7) repair and improvement of a CP/MAS NMR spectrometer, repair and maintaining high-resolution NMR spectrometers, repair of UNIX workstations, construction of new probes/hardware for solids and/or MRI efforts Monsanto offers a highly competitive salary and a generous benefits plan. For consideration, send a CV with three references to Rodina Rich WH-1; Monsanto Company; 800 North Lindbergh Blvd., O2H; St. Louis, MO 63167. Monsanto is an Equal Opportunity Employer M/F/D/V. From owner-structural-nmr@net.bio.net Tue Sep 13 23:00:00 1994 Path: biosci!GIBBS.OIT.UNC.EDU!vaisman From: vaisman@GIBBS.OIT.UNC.EDU (Iosif Vaisman) Newsgroups: bionet.structural-nmr Subject: Molecular Modeling Conference 1994 Date: 14 Sep 1994 10:21:23 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 112 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Molecular Modeling Conference 1994 Fundamentals and Applications for the Pharmaceutical Industry 2-4 October 1994 Brunswick Hilton and Towers, East Brunswick, New Jersey Molecular Modeling Conference 1994 is organized by Advanstar Communications, the publishers of Pharmaceutical Technology, BioPharm, LC-GC, and Spectroscopy magazines. * A limited number of discounted registrations are available for * full-time university students and faculty. Conference Moderators: Alexander MacKerell, Assistant Professor, Department of Pharmaceutical Sciences, University of Maryland at Baltimore Alexander Tropsha, Assistant Professor, Director, Laboratory for Molecular Modeling, University of North Carolina at Chapel Hill Herschel J.R. Weintraub, Assistant Director, Medicinal Chemistry, R.W. Johnson Pharmaceutical Research Institute Sunday, 2 October 1994 Afternoon Session: Optional Introductory Workshop - Molecular Modeling Basics Instructors: Warren J. Hehre, Wavefunction, Inc., and University of California, Irvine Alexander Tropsha (Session Organizer), University of North Carolina, Chapel Hill Herschel J.R. Weintraub, R.W. Johnson Pharmaceutical Research Institute Monday, 3 October 1994 Plenary Lecture: Molecular Modeling - For Better, For Worse. For Richer, For Poorer. Peter Goodford, University of Oxford, UK On the Effect of Long-range Interactions on Protein Structure, Specificity, & Ligand Binding Free Energies Arnie Hagler, Biosym Technologies, Inc. Modeling Selectivity in Organic Reactions Warren J. Hehre, Wavefunction, Inc. and University of California, Irvine General Representation and Solution of the QSAR Problem Based Upon Tensor Analysis A. J. Hopfinger, University of Illinois at Chicago Rapid Prediction of Binding Energies Using Continuum Methods Barry Honig, Columbia University Pharmacophore Determination: The Critical Decision in Ligand-Based Design Richard D. Cramer, Tripos, Inc. Overview of 3D-Searching: A Powerful Technique for Computer-Assisted Molecular Design Robert S. Pearlman, University of Texas, Austin Tuesday, 4 October 1994 X-ray Crystallographic Analysis of Macromolecular Structures Wayne A. Hendrickson, Columbia University Free Energy Modeling Monte Pettitt, University of Houston Multidimensional Heteronuclear NMR of Proteins Angela M. Gronenborn, NIDDK, National Institutes of Health Models of G Protein-Linked Receptors: How Do We Get Them and What Can We Do With Them? Charles Hutchins, Abbott Laboratories Comparative Homology Modeling: What Is It Good For and How Well Does It Work? Jonathan Greer, Abbott Laboratories De Novo Predications of Quaternary Protein Structure: Applications to Coiled Coils Jeffrey Skolnick, Scripps Research Institute Computer Assisted Ligand Design I.D. Kuntz, University of California, San Francisco Retrospective and Prospective Successes of Molecular Modeling in the Pharmaceutical Industry Peter Gund, Molecular Simulations Inc. Registration Information To register or to receive a copy of the conference program brochure, please call the Molecular Modeling Conference Registrar at (800) 343-3423 or (503) 343-1200. Fees for Molecular Modeling Conference include all course materials, a copy of the conference proceedings, admission to the Technology Demonstration Room, the Optional Introductory Workshop, and refreshment breaks. Fees Regular (postmarked after 19 August 1994): $645.00 On-Site: $695.00 For more information, contact: Molecular Modeling Conference 1994 859 Willamette Street Eugene, OR 97401-6806 Phone: (800) 343-3423 or (503) 343-1200 Fax: (503) 343-7024 From owner-structural-nmr@net.bio.net Tue Sep 13 23:00:00 1994 Path: biosci!RISC1.LRM.FI.CNR.IT!thep From: thep@RISC1.LRM.FI.CNR.IT (Pornthep Sompornpisut) Newsgroups: bionet.structural-nmr Subject: how to add HEME in DIANA (DG) library Date: 14 Sep 1994 01:51:37 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <9409140853.AA15364@risc1.lrm.fi.cnr.it> References: <9409132034.AA27113@lanczos.Scripps.EDU> NNTP-Posting-Host: net.bio.net I appologize for an unclearly previous message. I wrote: > > > > > Do anyone know how to declare the atom types, the nomenclature, > > the dihedral angle definitions and the standard geometry of > > HEME in the residue library input file. > > > In order to perform Distance Geometry (DG) calculation, DIANA, with cytochrome, the program needs Non-standard amino acid, HEME, in the library. In anycase, I would appreciate for any suggestion. Thanks Thep From owner-structural-nmr@net.bio.net Thu Sep 15 23:00:00 1994 Path: biosci!RISC1.LRM.FI.CNR.IT!thep From: thep@RISC1.LRM.FI.CNR.IT (Pornthep Sompornpisut) Newsgroups: bionet.structural-nmr Subject: Need information about XPLOR Date: 16 Sep 1994 00:58:01 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <9409160759.AA53234@risc1.lrm.fi.cnr.it> References: <9409151842.AA24560@spasm.niddk.nih.gov> NNTP-Posting-Host: net.bio.net Dear Sir, I have heard about XPLOR program but I've never used it. Is there a possibility to calculate solution structures using the structural infomation (NOESY) of NMR experiments as an input? This would be great if you can give general information and how to get the program. Thanks for your consideration Thep From owner-structural-nmr@net.bio.net Thu Sep 15 23:00:00 1994 Path: biosci!agate!spool.mu.edu!howland.reston.ans.net!pipex!warwick!doc.ic.ac.uk!dundee.ac.uk!dundee.ac.uk!not-for-mail From: mjmilton@dux.dundee.ac.uk (M.J. Milton Biochemistry) Newsgroups: bionet.structural-nmr Subject: XPLOR/DISCOVER Date: 7 Sep 1994 15:18:46 +0100 Organization: The University, Dundee, DD1 4HN, Scotland, UK. Lines: 11 Message-ID: <34ki46$i3c@dux.dundee.ac.uk> NNTP-Posting-Host: dux.dundee.ac.uk X-Newsreader: TIN [version 1.2 PL1] Has any one out their in internet land used the time averaged constraints function in XPLOR. I've tried several MD runs changing different parameters. Howver, all of my dynaics simulations appear to be exactly the same regard less of the value of TAU etc. Somebody please send me an example input file. This problem is slowly driving me spare!!!. Thanks Mark From owner-structural-nmr@net.bio.net Fri Sep 16 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!uunet!panix!zip.eecs.umich.edu!newsxfer.itd.umich.edu!nntp.cs.ubc.ca!unixg.ubc.ca!news.bc.net!news.mic.ucla.edu!hodgkin.mbi.ucla.edu!arne From: arne@hodgkin.mbi.ucla.edu (Arne Elofsson) Newsgroups: bionet.structural-nmr Subject: Re: Need information about XPLOR Date: 16 Sep 1994 17:54:03 GMT Organization: OrgFreeware Lines: 34 Distribution: world Message-ID: <35cm3r$d72@news.mic.ucla.edu> References: <9409151842.AA24560@spasm.niddk.nih.gov> <9409160759.AA53234@risc1.lrm.fi.cnr.it> Reply-To: arne@hodgkin.mbi.ucla.edu (Arne Elofsson) NNTP-Posting-Host: hodgkin.mbi.ucla.edu XPLOR is it. Xplor (developed by Axel Brunger, Yale from the CHARMM molecular mechanics package (brooks, et al)) is a molecular mechanics (dynamics minimisation...) package for biological macromolecules. Besides the standard MM thngs it can do it has been developed for refinement od structures (from X-ray and NMR) It has become the de Facto standard for X-ray crysallographic refinements, but is not that videly used by NMR people. However it has everything in it that you aver need (I think so but I've not really used it). It has distance geometry methods as well as MD-refinement protocols. It has backcalculation possibilities (of NOE intensities) I guess you could do something like DIANA in it to. It is availabale as a commercial prodoct from MSI (hotline@msi.com) and as an academic package from Brunger (brunger@newton.biology.yale.edu) arne -- ****************************************************************************** ** From: Arne Elofsson ** ** Fax: +1-(310)-206-3914 or Fax: +1-(310)-206-7286 ** ** Tel: +1-(310)-825-1402 ** ** ** ** Email: arne@hodgkin.mbi.ucla.edu (arne@uclaue.mbi.ucla.edu) ** ** ** ** Adress: Molecular Biology Institute Home: 1370 Veteran #311 ** ** 405 Hilgard Avenue, UCLA Los Angeles ** ** Los Angeles CA 90024 ** ** 90024-1570 California USA ** ** USA Tel: +1-(310)-268-8006 ** ****************************************************************************** From owner-structural-nmr@net.bio.net Wed Sep 21 23:00:00 1994 Path: biosci!UICBAL.PMMP.UIC.EDU!KAR From: KAR@UICBAL.PMMP.UIC.EDU ("Leela Kar") Newsgroups: bionet.structural-nmr Subject: HOHAHA on a `GE' Omega-500 spectrometer Date: 22 Sep 1994 10:27:21 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <199409221727.KAA06490@net.bio.net> NNTP-Posting-Host: net.bio.net This is addressed to anyone out there still using a GE-Omega 500. Our spectrometer has the original GE-console, and we use a GE high resolution proton probe (5MARKII) for homonuclear spectroscopy. After more than five years of reasonably successful (but not trouble-free) data collecting, our probe has developed an arcing problem which occurs only when the proton decoupler channel (f2) is used as the XMTR (as in spin-lock experiments, or simply the `f2puls' experiment). We were told that the power (dlev and slev) we used in hohahaphy experiments was too high. So we would appreciate some feed-back from other groups doing protein nmr with a similar setup. What are `typical' gamma*H2 values used for hohaha and roesy experiments - and how is gamma*H2 related to the spectral width (sw) in each case? We've been using gamma*H2 values of about 2sw for hohaha and sw for roesy. Any relevant references would be helpful. Thanks. Leela Kar (KAR@UICBAL.PMMP.UIC.EDU) From owner-structural-nmr@net.bio.net Sun Sep 25 23:00:00 1994 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.structural-nmr Subject: UNSUBSCRIBING, BIOSCI ARCHIVES, ADDRESS DATABASE & BIOSCI FAQ Date: 26 Sep 1994 02:00:10 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 322 Sender: daemon@net.bio.net Distribution: world Message-ID: <199409260900.CAA25071@net.bio.net> NNTP-Posting-Host: net.bio.net Four important items follow: How to cancel e-mail subscriptions to BIOSCI newsgroups, BIOSCI archive searching, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our BIOSCI user directory, please take a few minutes to complete and return the form below. If your personal information has changed since you listed yourself, please send us a complete new updated form. We can not make manual revisions to existing entries. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net **** How to cancel a BIOSCI e-mail subscription **** If you want to cancel your e-mail subscription to this group, PLEASE DO NOT POST YOUR UNSUBSCRIBE REQUEST TO THE NEWSGROUP ADDRESS (NOR REPLY TO A MESSAGE POSTED TO THE NEWSGROUP)!!! This would send your request to all of the readers of the newsgroup, but it might still not be seen by the BIOSCI staff - thus you would annoy many people and possibly not accomplish your goal anyway. IF YOU ARE LOCATED IN THE AMERICAS OR PACIFIC RIM COUNTRIES, please send a message to biosci@net.bio.net Instructions will be returned automatically, so the contents of your message do not matter. IF YOU ARE LOCATED IN EUROPE, AFRICA OR CENTRAL ASIA, please send a message to MXT@dl.ac.uk containing the word help in the body of the message to retrieve e-mail server instructions. 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Thanks again for your cooperation! --------------- please cut here and return portion below --------------- New information or Update to old record (enter N or U): date (DD-MM-YY): first name: middle initial: family name: job title: e-mail address: e-mail network: phone number: FAX number: institution: address1: address2: address3: city: state/province: country: postal code: research interest: research interest: comment: comment: comment: comment: comment: From owner-structural-nmr@net.bio.net Tue Sep 27 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!swrinde!sgiblab!sgigate.sgi.com!rutgers!csn!yuma!purdue!mozo.cc.purdue.edu!sonata.cc.purdue.edu!(null pointer) From: (null pointer)@sonata.cc.purdue.edu () Newsgroups: bionet.structural-nmr Subject: Retrieving chemical exchange rates using NOESY data? Date: 28 Sep 1994 16:34:04 GMT Organization: Purdue University Lines: 31 Distribution: world Message-ID: <36c5ts$ei@mozo.cc.purdue.edu> NNTP-Posting-Host: sonata.cc.purdue.edu I am posting the following for a friend who does not have access to internet. ---------------------------------------------------------------------------- The system is a mixture of two phosphene-nickel compounds. (Structres not necessarily the exact ones he has.) ___/ ____/ / \ / \ P1 P2 P1 P2 \ / \ / Ni Ni / \ / \ P3 P4 P5 P6 \____/ \____/ / \ There is ligand exchange between, e.g., P3-P4 and P5-P6. He has got the NOESY volumes from a P31-NOESY experiment. Now the questions: Does anybody out there has any experience in analysing this kind of chemical exchange systems using NOESY data? (He wants to get the exchange rates.) Are there any programs available to do so? Thanks in advance. ----------------------------- David Donne Department of Chemistry Purdue University ddonne@sonata.cc.purdue.edu From owner-structural-nmr@net.bio.net Wed Sep 28 23:00:00 1994 Path: biosci!ksc-bg.murmansk.su!katya From: katya@ksc-bg.murmansk.su ("E. D. Balaganskaya") Newsgroups: bionet.structural-nmr Subject: Soil Organic Matter Date: 29 Sep 1994 08:24:31 -0700 Organization: Polar-Alpine Botanical Garden-Institute Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net I'm newcommer in NMR. My main issue is The influence of heavy metal and sulphur pollution on transformation of soil organic matter (SOM). I'm going to study SOM transformation by NMR-spectrometry. Are anybody deal with the same problem? --------------------- Katya Balaganskaya, Polar-Alpine Botanical Garden-Institute Kola Science Centre RAS Apatity, Russia katya@ksc-bg.murmansk.su From owner-structural-nmr@net.bio.net Thu Sep 29 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!sunic!ugle.unit.no!marvin!drablos From: drablos@marvin.mr.sintef.no (Finn Drablos) Newsgroups: bionet.structural-nmr Subject: Carbohydrate Bioengineering Meeting Date: 30 Sep 94 13:59:18 GMT Organization: University of Trondheim, Norway Lines: 32 Message-ID: NNTP-Posting-Host: marvin.mr.sintef.no Summary: Meeting on carbohydrates and carbohydrate active enzymes Keywords: carbohydrate,protein,enzyme CARBOHYDRATE BIOENGINEERING MEETING Organized together with The Working Party on Applied Biocatalysis of the European Federation of Biotechnology April 23-26, 1995 Elsinore, Denmark Sessions: Structure of Carbohydrates Structure and function of Carbohydrate active enzymes Applications of Protein Engineering Carbohydrates for medical use Carbohydrates for food/feed applications Carbohydrates as raw materials for chemical synthesis The Organizing Committee: Sven Pedersen, Novo Nordisk, Denmark Birte Svensson, Carlsberg Laboratory, Denmark Steffen B. Petersen, SINTEF UNIMED, MR-Center, Norway For further information, please contact: Mona K. Eidem SINTEF UNIMED, MR-Center N-7034 Trondheim, Norway tel +47 73 99 77 00 fax +47 73 99 77 08 or Steffen B. Petersen email sbp@marvin.mr.sintef.no From owner-structural-nmr@net.bio.net Thu Sep 29 23:00:00 1994 Path: biosci!OTTER.BIOCHEM.UBC.CA!mcintosh From: mcintosh@OTTER.BIOCHEM.UBC.CA (Lawrence McIntosh) Newsgroups: bionet.structural-nmr Subject: (none) Date: 29 Sep 1994 20:59:06 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hello: I am looking for the names of manufactures of good plastic atomic model parts, specifcally to build DNA and protein models for teaching and hands-on molecular graphics. Any advice? Thanks, Lawrence McIntosh UBC, Vancouver From owner-structural-nmr@net.bio.net Thu Sep 29 23:00:00 1994 Path: biosci!BIOC01.UTHSCSA.EDU!raman From: raman@BIOC01.UTHSCSA.EDU (C.S.RAMAN) Newsgroups: bionet.structural-nmr Subject: Re: molecular models Date: 30 Sep 1994 07:17:28 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 46 Sender: daemon@net.bio.net Distribution: world Message-ID: <9409301417.AA16695@bioc01.uthscsa.edu> References: NNTP-Posting-Host: net.bio.net Lawrence: > I am looking for the names of manufactures of good plastic atomic model > parts, specifcally to build DNA and protein models for teaching and > hands-on molecular graphics. Your best bet is to contact the following maufacturers. Aldrich Chemical 800-558-9160 Brinkman Instruments 800-645-3050 Cache Scientific 503-627-3737 Curtin Matheson Scientific Inc. 713-878-2349 Harvard Apparatus Inc. 800-272-2775 Inamco chemicals 718-969-0926 MOLECULAR MODELS CO. 608-884-9877 SIGMA Chemical Co. 800-325-3010 Hope this helps Cheers -raman -- C.S.Raman UNIX Programming & Administration SPARC & SGI Systems raman@bioc01.uthscsa.edu - INTERNET Department of Biochemistry raman@mintaka.chpc.utexas.edu - CHPC UTHSCSA c.raman@launchpad.unc.edu 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** -- C.S.Raman UNIX Programming & Administration SPARC & SGI Systems raman@bioc01.uthscsa.edu - INTERNET Department of Biochemistry raman@mintaka.chpc.utexas.edu - CHPC UTHSCSA c.raman@launchpad.unc.edu 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From owner-structural-nmr@net.bio.net Fri Sep 30 23:00:00 1994 Path: biosci!OTTER.BIOCHEM.UBC.CA!mcintosh From: mcintosh@OTTER.BIOCHEM.UBC.CA (Lawrence McIntosh) Newsgroups: bionet.structural-nmr Subject: (none) Date: 1 Oct 1994 09:44:20 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 35 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Some suggestions that I received for molecular models are: (thanks!) Maruzen Co. LTD. 3-10 Nihonbashi 2-Chome Chuo-ku P.O.Box 5050 Tokyo 103 Japan phone TOKYO (03) 3278-9223 fax TOKYO (03) 3274-2270 Maruzen Int co ltd suite 1780 1251 avenue of the amerias New York, NY 10020 Aldrich Chemical 800-558-9160 Brinkman Instruments 800-645-3050 Cache Scientific 503-627-3737 Curtin Matheson Scientific Inc. 713-878-2349 Harvard Apparatus Inc. 800-272-2775 Inamco chemicals 718-969-0926 SIGMA Chemical Co. 800-325-3010 L McIntosh UBC From owner-structural-nmr@net.bio.net Fri Sep 30 23:00:00 1994 Path: biosci!biosci!not-for-mail From: drablos@marvin.mr.sintef.no (Finn Drablos) Newsgroups: bionet.announce,bionet.general,bionet.structural-nmr,bionet.xtallography,sci.bio,sci.chem,sci.bio.technology Subject: Carbohydrate Bioengineering Meeting Date: 1 Oct 1994 13:42:26 -0700 Organization: University of Trondheim, Norway Lines: 29 Sender: kristoff@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Summary: Meeting on carbohydrates and carbohydrate active enzymes Keywords: carbohydrate,protein,enzyme,synthesis Xref: biosci bionet.announce:1451 bionet.general:11371 bionet.structural-nmr:261 bionet.xtallography:1200 sci.bio:11128 sci.chem:17304 sci.bio.technology:1699 CARBOHYDRATE BIOENGINEERING MEETING Organized together with The Working Party on Applied Biocatalysis of the European Federation of Biotechnology April 23-26, 1995 Elsinore, Denmark Sessions: Structure of Carbohydrates Structure and function of Carbohydrate active enzymes Applications of Protein Engineering Carbohydrates for medical use Carbohydrates for food/feed applications Carbohydrates as raw materials for chemical synthesis The Organizing Committee: Sven Pedersen, Novo Nordisk, Denmark Birte Svensson, Carlsberg Laboratory, Denmark Steffen B. Petersen, SINTEF UNIMED, MR-Center, Norway For further information, please contact: Mona K. Eidem SINTEF UNIMED, MR-Center, N-7034 Trondheim, Norway tel +47 73 99 77 00 fax +47 73 99 77 08 or Steffen B. Petersen email sbp@marvin.mr.sintef.no