From owner-structural-nmr@net.bio.net Mon Apr 01 23:00:00 1996 Path: biosci!daresbury!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!news.ox.ac.uk!news From: "Simon M. Brocklehurst" Newsgroups: bionet.molec-model,bionet.structural-nmr,bionet.xtallography Subject: Re: CONECT records in pdb files? Date: Tue, 02 Apr 1996 12:58:18 +0100 Organization: University of Oxford Lines: 35 Message-ID: <3161165A.41C67EA6@bioch.ox.ac.uk> References: <4jpo94$8ei@nntp.ucs.ubc.ca> 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 2.01 (X11; I; SunOS 4.1.3_U1 sun4m) Xref: biosci bionet.molec-model:887 bionet.structural-nmr:1183 bionet.xtallography:2482 Dr Sue Brown wrote: > > I have a PDB file of a protein structure, and I need to generate a > complete set of CONECT records from the coordinates, including the > backbone connectivities. > Are there any program utilities available to do this? > If not, any other suggestions? > > Any help appreciated, > > Sue > > Dr Sue Brown > email: sebrown@laue.biochem.ubc.ca > Dept of Biochemistry, University of British Columbia > Vancouver, Canada, V6T 1Z3 You can do this easily with NAOMI by using input commands: read pdb my_pdb_file.pdb use covalent_bonds table conect_records More info at the Web site: http://www.ocms.ox.ac.uk/~smb/Software/N_details/naomi.html _____________________________________________________________________________ | | ,_ o Simon M. Brocklehurst, | / //\, Oxford Centre for Molecular Sciences, Department of Biochemistry, | \>> | University of Oxford, Oxford, UK. | \\, E-mail: smb@bioch.ox.ac.uk | WWW: http://www.ocms.ox.ac.uk/~smb/ |____________________________________________________________________________ From owner-structural-nmr@net.bio.net Mon Apr 01 23:00:00 1996 Path: biosci!RUUCI9.CHEM.RUU.NL!frederic From: frederic@RUUCI9.CHEM.RUU.NL (Frederic Bellier) Newsgroups: bionet.structural-nmr Subject: Re: 3D NMR data processing Date: 2 Apr 1996 03:56:52 -0800 Organization: Bijvoet Center NMR Department Lines: 37 Sender: daemon@net.bio.net Distribution: world Message-ID: <31613172.41C6@nmr.chem.ruu.nl> NNTP-Posting-Host: net.bio.net -- Hello, I am quite disagree with Christoph Weber who wrote about the ND processing module of felix95: > The macro language - easy to understand, versatile and forgiving >- is the real power of FELIX and should be a mainstay of any demanding >user (in my opinion). I would recommend FELIX to anyone contemplating >serious ND work. I personally don't like the processing part of felix (even 95). And I think I do serious ND work... Did you ever try to reshufle data from 3D spectra recorded with gradients? The macro language is not so easy to understand. I should say than some algorithm from felix give good results. And that the 2 others modules "assign" and "model" are more than interesting. Nevertheless I would suggest to people who want to process spectra from 1 to 4D to use a very good software (in my opinion) which is Pipe. Moreover Pipe is free of charge for university, is very easy to use, and powerfull for multidimensional NMR data. Kind regards. Frederic. ________________________________________________________________________ M. Mr. BELLIER Frederic UTRECHT, University of BIJVOET CENTER FOR BIOMOLECULAR RESEARCH Padualaan 8, 3584 CH Utrecht DEPARTMENT OF NMR SPECTROSCOPY THE NETHERLANDS. http://www-nmr.chem.ruu.nl/ ________________________________________________________________________ _/ _/ _/ _/ _/_/_/ _/_/ _/ _/_/ _/_/ _/ _/ FAX : int-(31)-302-537-623 _/ _/ _/ _/ _/ _/ _/_/_/ PHONE : int-(31)-302-532-875 _/ _/_/ _/ _/ _/ _/ EMAIL :frederic@nmr.chem.ruu.nl _/ _/ _/ _/ _/ _/ ________________________________________________________________________ From owner-structural-nmr@net.bio.net Mon Apr 01 23:00:00 1996 Path: biosci!MRR.COM!jon From: jon@MRR.COM (Jon Webb) Newsgroups: bionet.structural-nmr Subject: change of email address Date: 2 Apr 1996 07:59:05 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <199604021355.IAA01610@mrr.com> NNTP-Posting-Host: net.bio.net Please note a change in my Email address and have these newsgroup postings sent to it. jon@mrr.com Best regards, 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 Apr 01 23:00:00 1996 Path: biosci!ns1.faseb.org!lamarck.sura.net!ra.nrl.navy.mil!news.math.psu.edu!chi-news.cic.net!news.nd.edu!spool.mu.edu!howland.reston.ans.net!torn!hone!informer1.cis.McMaster.CA!mcmail.CIS.McMaster.CA!not-for-mail From: g9026772@mcmail.cis.McMaster.CA (Andre Saint-Jean) Newsgroups: bionet.structural-nmr Subject: Searching for post-doctoral position Date: 2 Apr 1996 10:43:14 -0500 Organization: McMaster University, Hamilton, Ontario, Canada. Lines: 26 Message-ID: <4jrhui$f5n@mcmail.CIS.McMaster.CA> NNTP-Posting-Host: mcmail.cis.mcmaster.ca Hello, I will have completed my Ph.D. in chemistry at McMaster University as of April 1996. My thesis concerned biomolecular conformational analysis by NMR and molecular dynamics of peptides and their interaction with calcium in a nonpolar solvent and in a lipid media. I also have experience with CD, fluorescence spectroscopy, FTIR, peptide purification, electron microscopy, solid state NMR, molecular modeling (Biograf and Discover) and to a lesser extent x-ray fluorescence and diffraction. As my Ph.D.is near completion I am now looking for the opportunity to further pursue the characterization and biophysical studies of more challenging and complex biomolecules by NMR spectroscopy. Thank you for your interest, Andre Saint-Jean Department of Biochemistry, Mc Master University, Hamilton, Ontario, Canada L8N 3Z5 Tel.:(905) 525 9140 ext. 22864 Fax: (905) 522 9033 E-mail: g9026772@McMaster.CA From owner-structural-nmr@net.bio.net Tue Apr 02 23:00:00 1996 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!howland.reston.ans.net!newsfeed.internetmci.com!news1.erols.com!news2.cais.net!news.cais.net!nntp.uio.no!nntp.uib.no!nntp-bergen.UNINETT.no!nntp-trd.UNINETT.no!daresbury!not-for-mail From: "Lennart Nilsson (Karolinska institutet)" Newsgroups: bionet.structural-nmr Subject: ANNOUNCEMENT: Understanding Protein Structure Determination Date: 3 Apr 1996 12:19:27 +0100 Lines: 28 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4jtmrv$hqo@mserv1.dl.ac.uk> X-Mts: smtp 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 Posted-Date: Wed, 03 Apr 96 13:18:43 +0200 The Karolinska Institute's Center for Structural Biochemistry will hold its 6th summer school, entitled "Understanding Protein Structure Determination" on September 1-6, 1996. This is one of a series of short graduate courses organized each summer by the Summer University of Southern Stockholm at NOVUM Research Park, located about 15 km south of Stockholm. As usual we are aiming for an informal format with students on the graduate and postdoc levels. A fair amount of time will be set aside for discussions and social activities. The topic of the 1996 summer school is intended to cover the two major protein structure determination techniques: X-ray crystallography and NMR spectroscopy. Topics such as the physical basis, experimental aspects, computational and software aspects, quality assessment of determined structures, and effects of structural heterogeneity and dynamics will be addressed. Emphasis will be put on the complementarity of the two techniques. Course fee: SEK 2500 (academic), SEK 5000 (non academic) Deadlines: Application June 14, 1996; poster abstract August 2, 1996. For further information/application forms please contact Ms. Aila Holappa at FAX +46-8-608 9290 or e-mail Aila.Holappa@cbt.ki.se More information is available at http://www.csb.ki.se/events/summer96.html Organizing committee: Hans Hebert, Torleif Hard, Rudolf Ladenstein, Lennart Nilsson From owner-structural-nmr@net.bio.net Wed Apr 03 23:00:00 1996 Path: biosci!POUND.MED.UTORONTO.CA!ouwen From: ouwen@POUND.MED.UTORONTO.CA (Ouwen Zhang) Newsgroups: bionet.structural-nmr Subject: unfolded proteins in biomolecular recognition Date: 4 Apr 1996 09:29:33 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: <9604042031.AA28155@pound.med.utoronto.ca> NNTP-Posting-Host: net.bio.net Hello, It is generally believed that proteins must be able to recognize and bind other molecules specifically in order to fulfil their functional roles. And it have been observed often by NMR that some proteins exist in unfolded or only partially folded if they are free in solution, for example some DNA or RNA binding proteins (easily tell from HSQC spectra). However they behave like folded protein when ligands added in (HSQC spetra become so much better). I am wondering whther there is review in the literature talking the potential roles of unfoled states in biomolecular recognition. Just as in the protein folding, residual structure in a unfolded state may direct a protein folding pathway. Any hint or help will be appreciated. Ouwen Zhang University of Toronto From owner-structural-nmr@net.bio.net Wed Apr 03 23:00:00 1996 Path: biosci!UCDAVIS.EDU!jsderopp From: jsderopp@UCDAVIS.EDU (Jeffrey Deropp) Newsgroups: bionet.structural-nmr Subject: subscribe Date: 3 Apr 1996 17:03:39 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net subscribe Jeff de Ropp Jeff de Ropp UCD NMR Facility jsderopp@ucdavis.edu Phone: 916-752-7677 FAX: 916-752-3516 NMR Facility URL http://www.nmr.ucdavis.edu From owner-structural-nmr@net.bio.net Wed Apr 03 23:00:00 1996 Path: biosci!MRR.COM!bobbie From: bobbie@MRR.COM (Bobbie DeCato) Newsgroups: bionet.structural-nmr Subject: Employment Opportunities Date: 4 Apr 1996 10:07:47 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 48 Sender: daemon@net.bio.net Distribution: world Message-ID: <199604041651.LAA10076@mrr.com> NNTP-Posting-Host: net.bio.net Employment Opportunities MR Resources is currently seeking seasoned NMR System Engineers for full time employment. Work will be performed at our Gardner, MA headquarters as well as various customer locations around the country on most makes and models of NMR systems and components by Varian, Bruker, JEOL, GE, Nicolet and Oxford. Required qualifications include in-depth hands on experience in one or more of the following areas: 1. Magnet assembly and commissioning 2. Complete NMR system installation 3. NMR system maintenance, repair and troubleshooting to board and component level. 4. Magnet cryogen filling 5. NMR system deinstallation, magnet decommissioning and packing 6. Probe repair and modification MR Resources, now in our eleventh year of operation, is the recognized leader in providing high quality remanufactured instrumentation, parts and services to the NMR Community. In addition to our generous compensation and benefit package, we offer a progressive, team oriented company culture that affords each team player a unique opportunity for personal growth. If you are a qualified, self motivated individual with comprehensive NMR hardware engineering skills and are interested in making a positive career change, please contact: Bobbie Decato, Operations Manager MR Resources, Inc. Sincerely, Bobbie Decato Operations Manager MR Resources, Inc. Remanufactured NMR & MRI Systems, Parts and Services 158R Main Street P.O. Box 880 Gardner, MA 01440 Voice: 508-632-7000 Fax: 508-630-2509 Email: Bobbie@mrr.com Web Site: http://www.mrr.com From owner-structural-nmr@net.bio.net Thu Apr 04 23:00:00 1996 Path: biosci!rutgers!gatech!newsfeed.internetmci.com!in1.uu.net!news.ner.bbnplanet.net!news3.near.net!yale!news-mail-gateway!daemon From: tree@afn.org (David T. Gray) Newsgroups: bionet.structural-nmr Subject: DownLoad - ~Net/DownLoad Manager (Latest Version) Date: 5 Apr 1996 08:37:53 -0500 Organization: Yale CS Mail/News Gateway Lines: 27 Sender: daemon@cs.yale.edu Message-ID: <199604051319.HAA09936@phoenix.phoenix.net> NNTP-Posting-Host: babyblue.cs.yale.edu Version "B" is available on the Net at: http://www.phoenix.net/~aquarian/davids/net.html or http://www.afn.org/~tree/net.html The search engine is an offline interrogator of large disorganized text files supporting multiple searches on single files or whole directories for up-to four key words or phrases, simulating hyper-text associations. Hope you enjoy the new version... David ~~~~~~~~~~~~~~~~~~~~~ VISIT MY WEB SITES ~~~~~~~~~~~~~~~~~~~~~ WEB SITES: http://www.phoenix.net/~aquarian/davids/tree.html http://www.afn.org/~tree/tree.html TOPICS: Weighted Asset Model of Real Estate Appraisal Real Estate Investment Software, Reinvest (shareware) My special fondness for the I.R.S. ~Net/DownLoad Manager, shareware Legal Searcher, shareware David's Secrets of Yo-Yo's 477-LIVE, Homes for Rent in Austin, TX Locating lost family members (Adoption Registry) The Transformational Portal ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ David T. Gray at tree@afn.org From owner-structural-nmr@net.bio.net Thu Apr 04 23:00:00 1996 Path: biosci!bloom-beacon.mit.edu!senator-bedfellow.mit.edu!bluebox-18.mit.edu!user From: dcoufal@mit.edu (David Coufal) Newsgroups: bionet.molec-model,bionet.structural-nmr,bionet.xtallography Subject: Re: CONECT records in pdb files? Date: Thu, 04 Apr 1996 21:07:02 -0500 Organization: MIT Lines: 17 Message-ID: References: <4jpo94$8ei@nntp.ucs.ubc.ca> NNTP-Posting-Host: bluebox-18.mit.edu X-Newsreader: Yet Another NewsWatcher 2.1.8 Xref: biosci bionet.molec-model:891 bionet.structural-nmr:1190 bionet.xtallography:2486 In article <4jpo94$8ei@nntp.ucs.ubc.ca>, sebrown@laue.biochem.ubc.ca (Dr Sue Brown) wrote: > I have a PDB file of a protein structure, and I need to generate a > complete set of CONECT records from the coordinates, including the > backbone connectivities. > Are there any program utilities available to do this? > If not, any other suggestions? I believe BABEL will do this. Do a Alta Vista (http://alta-vista.digital.com) search on BABEL to find a copy. -- David Coufal dcoufal@mit.edu http://www.mit.edu:8001/people/dcoufal/ "I came here to eat sushi and kick butt. And I'm all outta sushi." From owner-structural-nmr@net.bio.net Thu Apr 04 23:00:00 1996 Path: biosci!galaxy.ucr.edu!library.ucla.edu!info.ucla.edu!agate!howland.reston.ans.net!newsfeed.internetmci.com!in1.uu.net!newsfeed.ACO.net!mail.boku.ac.at!news From: Iain Wilson Newsgroups: bionet.structural-nmr,sci.techniques.mag-resonance Subject: Second Electronic Glycoscience Conference: Announcement and Call for Papers Date: Fri, 05 Apr 1996 13:47:41 -0800 Organization: Universität für Bodenkultur Wien Lines: 285 Message-ID: <316594FD.5EDF@bellatrix.pcl.ox.ac.uk> NNTP-Posting-Host: 141.244.58.101 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Win16; I) Xref: biosci bionet.structural-nmr:1191 sci.techniques.mag-resonance:1566 Readers of the sci.techniques.mag-resonance and newsgroups may be interested in the following announcement since EGC-2 features 'NMR' and 'Molecular Modelling' sections. SECOND ELECTRONIC GLYCOSCIENCE CONFERENCE ***************************************** The Second Electronic Glycoscience Conference (EGC-2) will be held on the Internet (the Net) and World Wide Web (the Web) from Sept 9 - 20, 1996 and will follow the same pattern as the first such conference, EGC-1, held in 1995. The conference is sponsored by Chapman & Hall, Eurocarb and Oxford Glycosystems. EGC-2 will be a fully international event open to all members of our scientific community and will cover a broad range of disciplines related to carbohydrate and glycoconjugate molecules including chemical, physical, biological and medical areas using theoretical, experimental and computational approaches. Conference subject areas are: Biological Function of Protein-Linked Glycans; Carbohydrate Biotechnology; Crystallography; General Glycobiology; Glycanalysis; Glycoimmunology; Glycolipids; Glycomedicine; Glycosynthesis; Glycosyltransferases; Lectins; Mass Spectrometry; Molecular Modelling, Design & Informatics; NMR; Polysaccharides and Cellulose; Proteoglycans and Glycosaminoglycans; and Perspectives in the Glycosciences. Each subject area has a section convener who will screen abstracts sent by authors for suitability. Authors can opt to have their presentation in the following categories: - non-permanent presentation like a normal conference poster - refereed presentation which will be considered for publication as a Letter to the Editor in a special issue of Glycoconjugate Journal in 1997. - refereed presentation which will be considered for publication as a full paper in a special issue of Glycoconjugate Journal. Referees will be appointed by the section conveners and the reports will be handled via a Special Editor for Glycoconjugate Journal, in consultation with Harry Schachter and Graham Turner, editors of Glycoconjugate Journal. Presentations must be prepared in Hypertext Markup Language (HTML) with figures in GIF, Rasmol or other Web-compatible formats so that participants can view the papers via the World Wide Web. Aid and consultation will be provided to participants during summer 1996 to help them with their presentation. Further details will be given in the authors' guide accessible via the URL: http://bellatrix.pcl.ox.ac.uk/egc2/ During the conference discussions will take place via the Internet in real-time using a virtual conference centre based on a MOO (multiple-user domain, object oriented) and via Internet-accessible electronic mailing lists. Trial sessions for those not familiar with MOO will be held before the conference. During the conference, a timetable for MOO discussion sessions of each section will be posted. Since these realtime discussions are an integral part of the conference, authors will be expected to attend one for their subject; the right is reserved not to referee submissions by authors who do not attend one of these sessions. The Conference will feature a Virtual Trade Center where commercial vendors, consultants, manufacturers, and contractors will be able to display their goods and services in return for exhibition fees to support conference activities. Any potential advertisers should contact the conference organisers. ******************* DEADLINES AND DATES 1) DO NOW - The Glycoscience Network (TGN) mailing list Conference-related news and announcements will be posted regularly to the TGN mailing list (http://bellatrix.pcl.ox.ac.uk/hypermail/TGN/) and the bionet.glycosci newsgroup (news:bionet.glycosci or http://www.bio.net:80/hypermail/GLYCOSCI/) If you wish to subscribe to the TGN list send the following one line message to majordomo@bellatrix.pcl.ox.ac.uk: subscribe tgn@bellatrix.pcl.ox.ac.uk your_email@address your_name 2) Registration The deadline for registration is Sept 1 1996. Early registration is strongly encouraged to aid the efficient operation of the conference including the establishment of timely access to the conference. If you intend to participate in EGC-2 please use the special registration form accessible via http://bellatrix.pcl.ox.ac.uk/egc2/ which will be available for registration starting April 22. The electronic registration will be used to construct a registrant database for the conference which will generate the conference mailing list and handle assignment of userids and passwords. In addition it is necessary to pay for registration via ordinary means: The conference fee will be 35 pounds sterling (50 US dollars) with a special rate for students of 20 pounds sterling (30 US dollars). A copy of a suitable student identification or a letter from the supervisor will be required to be charged at the lower rate. Cheques or bank orders in pounds or dollars should be made out to Greenlea Communications and mailed to: Dr. Barry Hardy, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK Please include your full name, address, phone and fax numbers, and email address in your correspondence. Your conference userid and password will be emailed to you. It is hoped to establish a credit card clearing service by May and information will be provided in due course. Academic registrants from economically-disadvantaged countries can write to Barry Hardy requesting an exemption to the registration fee. Exemptions will be made on a discretionary basis taking into account the reasons given for the request and will be dependent on suitable funds being available. We will consider economically disadvantaged countries to include those of Eastern Europe, Africa, Central and South America, Indian sub-continent, etc. 3) DEADLINE for receipt of ABSTRACT. The deadline for receipt of presentation abstracts is June 15. Email your abstract directly to the appropriate section convener listed below. Fuller details of the scope of each section will be given in the authors' guide accessible via http://bellatrix.pcl.ox.ac.uk/egc2/ Your abstract should be no longer than 300 words. And remember to state which category of presentation (non-permanent, refereed as letter, refereed as full paper) you wish. If you are unsure as to which section your abstract is suitable for, please e-mail a possible section convener or Iain Wilson (wilson@edv1.boku.ac.at). Section conveners do have the discretion to reject abstracts, ask for revisions to an abstract or to send the abstract to the convener of a more suitable section. 4) DEADLINE for receipt of PRESENTATION The deadline for receipt of papers and posters is August 15. You must deposit your text and graphics files at the conference ftp site. 5) Refereeing Period The refereeing period will commence upon completion of the conference. If you have a presentation at EGC-2 you may be requested to contribute a refereeing evaluation on another conference presentation. Referee reports will be due November 1. After that time, conveners make overall recommendations to be forwarded to a Special Editor of Glycoconjugate Journal. Only presentations will be refereed for which one of the two publication categories has been requested. ******************* SECTIONS AND SECTION CONVENERS (Please email section conveners with questions related to your particular section and presentation. Fuller details on the sections will be accessible via http://bellatrix.pcl.ox.ac.uk/egc2/) 1. Biological Function of Protein-Linked Glycans Diana Blithe National Institutes of Health, USA Email: BlitheD@cc1.nichd.nih.gov 2. Carbohydrate Biotechnology Liz Hounsell University College London, UK Email: ehounsel@bsm.biochemistry.ucl.ac.uk 3. General Glycobiology Pamela Greenwell University of Westminster, London, UK Email: greenwp@westminster.ac.uk 4. Glycoimmunology Roy Jefferis University of Birmingham, UK Email: R.Jefferis@bham.ac.uk 5. Glycolipids Cara-Lynne Schengrund Penn State University, USA Email: cschengr@cor-mail.biochem.hmc.psu.edu 6. Glycomedicine Graham Turner University of Newcastle, UK Email: G.A.Turner@newcastle.ac.uk 7. Glycosyltransferases Harry Schachter Hospital for Sick Children, Toronto, Canada Email: harry@resunix.ri.sickkids.on.ca 8. Lectins Eric Toone Duke University, USA Email: toone@chem.duke.edu 9. Polysaccharides and Cellulose Angela Savage University College, Galway, Ireland Email: Angela.Savage@ucg.ie 10. Proteoglycans and Glycosaminoglycans Bob Lauder University of Lancaster, UK Email: r.lauder@lancaster.ac.uk 11. Crystallography Bill Winter State University of New York, Syracuse, USA Email: wtwinter@mailbox.syr.edu 12. Glycanalysis Dave Ashford University of York, UK Email: da5@unix.york.ac.uk 13. Mass Spectrometry Vernon Reinhold Boston University Medical School, USA Email: vern@yuki.bu.edu 14. Molecular Modelling, Design and Informatics Andrepeter Heiner State Research Center, Finland Email: Andrepeter.Heiner@vtt.fi 15. NMR Thomas Weimar Medizinische Universitaet zu Luebeck, Germany Email: thio@johann.chemie.mu-luebeck.de 16. Glycosynthesis Tim Gallagher University of Bristol, UK Email: T.Gallagher@bristol.ac.uk with Geert-Jan Boons University of Birmingham, UK 17. Perspectives in the Glycosciences: past, present, future Iain Wilson Universitaet fuer Bodenkultur, Wien, Austria Email: wilson@edv1.boku.ac.at with Kiyoshi Furukawa Tokyo Metropolitan Institute of Gerontology, Japan Email: furukawa@tmig.or.jp CONFERENCE ORGANISERS Barry J. Hardy Physical and Theoretical Chemistry Lab Oxford University, Oxford, OX1 3QZ, U.K. Email: barry@bellatrix.pcl.ox.ac.uk http://bellatrix.pcl.ox.ac.uk/people/barry.html Iain Wilson Institut fuer Chemie der Universitaet fuer Bodenkultur Gregor-Mendelstrasse 33 A-1180, Wien, Austria Email: wilson@edv1.boku.ac.at http://www.boku.ac.at/chemie/bc1/staff/iw/iw.html Any general e-mails (such as registration queries, maillist queries, HTML queries, password queries, timetable queries, general technical advice on browsers and graphics, MOO queries) should be sent to: egc2org@bellatrix.pcl.ox.ac.uk From owner-structural-nmr@net.bio.net Thu Apr 04 23:00:00 1996 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!scripps.edu!obelix!weber From: weber@obelix.scripps (Christoph Weber) Newsgroups: bionet.structural-nmr Subject: Re: 3D NMR data processing Date: 5 Apr 1996 21:29:10 GMT Organization: The Scripps Research Institute Lines: 29 Message-ID: <4k43b6$26p@riscsm.scripps.edu> References: <31613172.41C6@nmr.chem.ruu.nl> NNTP-Posting-Host: obelix.scripps.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I guess I have to respond to this one ;-) > Did you ever try to reshufle data from 3D spectra recorded with > gradients? The macro language is not so easy to understand. Agreed, this is not straightforward in Felix, but doable. Actually, here at Scripps we have written C programs to do this outside of Felix. Ask John Chung (chung@scripps.edu) for a copy. However, why bash the entire package when one functionality that you need is lacking? I still maintain that Felix is well suited for ND work. Witness all the papers that mention it. I can add to this that echo/antiecho-type processing is coming in the next release. Regards, Christoph Disclaimer: I do work part-time for MSI on Felix development. However my statements made here do not reflect the company opinion, nor do I speak as an employee. My opinions were shaped during many years of use of the program. | Christoph Weber Sen. Research Associate | Dept.of Molecular Biology, MB2 619-554-7283 or -8754 (phone) | The Scripps Research Institute 619-554-3757 (FAX) | La Jolla CA 92037 weber@scripps.edu | http://www.scripps.edu/~chazin/people/cw.html From owner-structural-nmr@net.bio.net Mon Apr 08 23:00:00 1996 Path: biosci!rutgers!gatech!newsfeed.internetmci.com!news1.erols.com!newsmaster@erols.com From: devious@erols.com Newsgroups: bionet.structural-nmr Subject: NMR Help needed Date: Tue, 09 Apr 1996 17:16:06 -0700 Organization: Erols Internet Services Lines: 8 Message-ID: <316AFDC6.14D2@erols.com> NNTP-Posting-Host: as21s46.erols.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Win16; U) Requesting help locating the following: "Mr. Brendall, D.M. Dodrell, D.T. Pegg, and W.E. Hull; DEPT, Information brouchere with experimental details, Bruker Analytische Messteschnik, Karlsruhe,1982" I'm trying to help a friend working on a DPX - 300 (300)MHZ NMR using WinNMR. From owner-structural-nmr@net.bio.net Mon Apr 08 23:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news From: "Karen M. Gould" Newsgroups: bionet.structural-nmr Subject: Re: unfolded proteins in biomolecular recognition Date: 9 Apr 1996 12:45:02 GMT Organization: Somewhere in the University of Cambridge Lines: 34 Message-ID: <4kdm4e$5r@lyra.csx.cam.ac.uk> References: <9604042031.AA28155@pound.med.utoronto.ca> NNTP-Posting-Host: hades.bioc.cam.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; IRIX 5.2 IP12) X-URL: news:9604042031.AA28155@pound.med.utoronto.ca ouwen@POUND.MED.UTORONTO.CA (Ouwen Zhang) wrote: >Hello, >It is generally believed that proteins must be able to recognize and bind other >molecules specifically in order to fulfil their functional roles. And it have been >observed often by NMR that some proteins exist in unfolded or only partially folded >if they are free in solution, for example some DNA or RNA binding proteins (easily tell >from HSQC spectra). However they behave like folded protein when ligands added in (HSQC >spetra become so much better). >I am wondering whther there is review in the literature talking the potential roles >of unfoled states in biomolecular recognition. Just as in the protein folding, >residual structure in a unfolded state may direct a protein folding pathway. >Any hint or help will be appreciated. > >Ouwen Zhang >University of Toronto I can confirm it has been observed in a few RNA or DNA binding proteins that they are unfolded/partially-folded in the absence of their ligand, and form structure upon binding/recognition, via NMR and CD analysis. In the case of some oligo nucleotides, the reverse occurs (partially molten structure previous to binding, then static structure in the complex). Although as yet, there is not a review I know of, I suggest you see papers relating to Tat/TAR, by Gariel Varani, and work done on U1A RNA binding to U1A protein (both by x-ray and NMR). ********************************************************************** Karen Gould (Shade) "E lascia pur grattar dov'`e la rognal" kmg@mole.bio.cam.ac.uk Dante ********************************************************************** From owner-structural-nmr@net.bio.net Mon Apr 08 23:00:00 1996 Path: biosci!PILLER.PHARM.UTAH.EDU!durant From: durant@PILLER.PHARM.UTAH.EDU (Phil Durant) Newsgroups: bionet.structural-nmr Subject: Unfolded proteins in biomolecular interactions Date: 9 Apr 1996 09:51:58 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <9604101534.AA16855@piller.pharm.utah.edu> NNTP-Posting-Host: net.bio.net Here is an example of a ligand that potentially loses binding ability after becoming less structured. In Biochem. 34, 7603 1995, nmr results describe the loss of alpha helical structure upon phosphorylation. This protein, phospholamban, inhibits the calcium-ATPase pump in cardiac myocyte sarcoplasmic reticulum. Upon phosphorylation the loss of alpha helical structure (it decreases by about 50%) is thought to cause the protein to dissociate from the pump to allow an increase in pump rate. Phil Durant Dept. of Medicinal Chemistry Univ. of Utah durant@piller.pharm.utah.edu From owner-structural-nmr@net.bio.net Mon Apr 08 23:00:00 1996 Path: biosci!sbphrd.com!Julia_Hubbard-1 From: Julia_Hubbard-1@sbphrd.com (Julia Hubbard-1) Newsgroups: bionet.structural-nmr Subject: subscribe new name Date: 9 Apr 1996 01:12:57 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: <9604091109.AA9864@pho903.sbphrd.com> NNTP-Posting-Host: net.bio.net subscribe From owner-structural-nmr@net.bio.net Mon Apr 08 23:00:00 1996 Path: biosci!sb.com!Julia_Hubbard-1%notes From: Julia_Hubbard-1%notes@sb.com (Julia Hubbard-1) Newsgroups: bionet.structural-nmr Subject: unsubscribe Date: 9 Apr 1996 01:10:27 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: <9604091107.AA2026@pho018.sb.com> NNTP-Posting-Host: net.bio.net unsubscribe From owner-structural-nmr@net.bio.net Mon Apr 08 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!news.cis.okstate.edu!newsfeed.ksu.ksu.edu!news.physics.uiowa.edu!news.uiowa.edu!usenet From: brian-baker@uiowa.edu (Brian M. Baker) Newsgroups: bionet.structural-nmr Subject: unfolded proteins in biomolecular recognition Date: 8 Apr 1996 21:29:07 GMT Organization: University of Iowa, Department of Biochemistry Lines: 47 Distribution: world Message-ID: <4kc0f3$q0c@flood.weeg.uiowa.edu> References: <9604042031.AA28155@pound.med.utoronto.ca> Reply-To: brian-baker@uiowa.edu NNTP-Posting-Host: reaper.biochem.uiowa.edu X-Newsreader: NeoLogic News for OS/2 [version: 4.5 YO Beta] In message <9604042031.AA28155@pound.med.utoronto.ca> - ouwen@POUND.MED.UTORONTO.CA (Ouwen Zhang)4 Apr 1996 09:29:33 -0800 writes: :> :>Hello, :>It is generally believed that proteins must be able to recognize and bind other :>molecules specifically in order to fulfil their functional roles. And it have been :>observed often by NMR that some proteins exist in unfolded or only partially folded :>if they are free in solution, for example some DNA or RNA binding proteins (easily tell :>from HSQC spectra). However they behave like folded protein when ligands added in (HSQC :>spetra become so much better). :>I am wondering whther there is review in the literature talking the potential roles :>of unfoled states in biomolecular recognition. Just as in the protein folding, :>residual structure in a unfolded state may direct a protein folding pathway. :>Any hint or help will be appreciated. :> :>Ouwen Zhang :>University of Toronto Greetings...just some ramblings, I don't really answer the question :) I've heard mumblings about similar ideas here and there, but I can't remember anything specific; a good lit search might bring something up. As far as an -unfolded- protein participating in a binding reaction (excluding chaperones), I would find that hard to believe, but that would depend on what you define as an unfolded state... As far as stabilizing a protein, ligand binding -has- to increase the protein's observable stability through linkage. It is intriguing to imagine a sort of "loose" binding site that "tightens up" upon binding. But then you have to ask what is the native structure of the protein...is it the "loose" form prior to ligand binding, or the "tight" form after...? Brian =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Brian M. Baker brian-baker@uiowa.edu Graduate Student Peon Protein Structural Energetics "I am becalmed and virtured, lost Department of Biochemistry to nothing on a bay of dreams..." University of Iowa -Blue Oyster Cult =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From owner-structural-nmr@net.bio.net Mon Apr 08 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!newsfeed.sunet.se!news01.sunet.se!sunic!news99.sunet.se!news.uni-c.dk!ssv2.dina.kvl.dk!news From: Jesper Broendum Nielsen Newsgroups: bionet.structural-nmr Subject: (no subject) Date: 9 Apr 1996 09:24:18 GMT Organization: Royal Veterinary & Agricultural U., Copenhagen, Denmark Lines: 25 Message-ID: <4kdac2$lhb@ssv2.dina.kvl.dk> NNTP-Posting-Host: newton.foodsci.kvl.dk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; IRIX 5.2 IP22) X-URL: news:bionet.structural-nmr Hi, Being new in the field of nmr spectroscopy I request some help on relevant litterature, etc. More specific I'm interested in low resolution nmr in food analysis. We have just ordered a 25 MHz instrument for large sample sizes from Resonance Instruments and any help (references, contacts, applications etc.) is very welcome (preferable by e-mail). Thanks, Jesper Broendum -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Name: Jesper Broendum Position: M.Sc. Image Analysis Work: Food Technology, Dairy and Food Science Royal Vet. and Agricultural University Rolighedsvej 30, DK - 1958 Frederiksberg C, DK Ph: (+45) 35 28 32 05 Fax: (+45) 35 28 32 45 E-mail: jesper@newton.foodsci.kvl.dk WWW: newton.foodsci.kvl.dk/jesper ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-structural-nmr@net.bio.net Tue Apr 09 23:00:00 1996 Path: biosci!ns1.faseb.org!lamarck.sura.net!newsfeed.internetmci.com!in2.uu.net!EU.net!news.eunet.fi!newsmaster From: piero pollesello Newsgroups: bionet.structural-nmr Subject: Re: Unfolded proteins in biomolecular interactions Date: 10 Apr 1996 12:44:24 GMT Organization: POLYbios, Area Science Park, Trieste, Italy Lines: 11 Message-ID: <4kgaf8$lqi@idefix.eunet.fi> References: <9604101534.AA16855@piller.pharm.utah.edu> NNTP-Posting-Host: protein.orion.fi Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12(Macintosh; I; 68K) To: durant@PILLER.PHARM.UTAH.EDU X-URL: news:9604101534.AA16855@piller.pharm.utah.edu Regarding phospholamban, it is far from proved that its dissociation from calcium-ATPase pump in the sarcoplasmic reticulum of cardiac myocytes is due to unfolding of alpha-helical structure. More probable is that those two vicinal phosphate groups mask the many positive charged aminoacids present near the phosphorylation site. Remamber that SERCA is aspecifically inhibited by spermine and spermidine (do they have a tertiary structure?) Piero From owner-structural-nmr@net.bio.net Wed Apr 10 23:00:00 1996 Path: biosci!daresbury!hgmp.mrc.ac.uk!sunsite.doc.ic.ac.uk!dundee.ac.uk!CHEM11.chem.dundee.ac.uk!fmohdsom From: fmohdsom@its.dundee.ac.uk (FAUZI MOHDSOM) Newsgroups: bionet.structural-nmr Subject: C-13 nmr MODULE Date: Wed, 10 Apr 1996 08:56:30 GMT Organization: University of Dundee Lines: 17 Message-ID: NNTP-Posting-Host: chem11.chem.dundee.ac.uk X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] I recently ordered C13 NMR module by Softshell that only cost US49 inclusive shipping for students. Unfortunately, they have a UK distributor that then charge me for £128 inclusive shipping and VAT because they don't offer student price. When I was doing my master's degree in the US I got paid every month from the university, but in the UK I don't get anything. Seems like UK care less about their students benefit. ===================================== Fauzi Mohd Som University of Dundee Department of Chemistry Rubber Research Institute of Malaysia Technology Centre, Sg. Buloh, Malaysia ===================================== From owner-structural-nmr@net.bio.net Thu Apr 11 23:00:00 1996 Path: biosci!MRR.COM!jon From: jon@MRR.COM (Jon Webb) Newsgroups: bionet.structural-nmr Subject: subscribe Date: 11 Apr 1996 17:03:49 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <199604112031.QAA00203@mrr.com> NNTP-Posting-Host: net.bio.net subscribe Best regards, 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 Sat Apr 13 23:00:00 1996 Path: biosci!PHOENIX.PRINCETON.EDU!ipelczer From: ipelczer@PHOENIX.PRINCETON.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: shield Date: 14 Apr 1996 14:23:23 -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 Dear Netters, I would like to know what mangnetic shields are available for terminals. Please, let me know your experience. Thanks, Istvan wwww,wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww Istvan Pelczer, Ph.D. Email: ipelczer@princeton.edu Senior NMR Spectroscopist Princeton University Department of Chemistry ph# (609) 258 2342 Frick Laboratory fax# (609) 258 6746 Washington Road Princeton, NJ 08544 From owner-structural-nmr@net.bio.net Sun Apr 14 23:00:00 1996 Path: biosci!Merck.Com!yves_aubin From: yves_aubin@Merck.Com (Yves Aubin) Newsgroups: bionet.structural-nmr Subject: Re: shield Date: 15 Apr 1996 07:02:36 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 31 Sender: daemon@net.bio.net Distribution: world Message-ID: <199604151356.JAA02322@igw2> NNTP-Posting-Host: net.bio.net Istvan wrote: >Dear Netters, >I would like to know what mangnetic shields are available for terminals. >Please, let me know your experience. Thanks, >Istvan > In Lewis Kay's laboratory in Toronto, we had two monitors that were severly perturbed by the magnetic field of a 500 and a 600 machines. The perturbation was such that the colors were changing from blue (lower right corner) to red (upper right corner) and the lack of focus made difficult the reading of the screen. I built two shields for less than 200 CDN$ each. The results are excellent in both cases: no color distortion and very good focus. I described the construction of the shield in the February issue of "The NMR newsletter" No. 449. If anyone have any questions, I'll be happy to answer them. Yves 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 From owner-structural-nmr@net.bio.net Sun Apr 14 23:00:00 1996 Path: biosci!INDIANA.EDU!mpagel From: mpagel@INDIANA.EDU (Marty Pagel) Newsgroups: bionet.structural-nmr Subject: Re: shield Date: 15 Apr 1996 06:50:35 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 40 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net Hi Istvan, Amuneal Manufacturing Corp 4737 Darrah Street Philadelphia, PA 19124 (215)-535-3000 (215)-743-1715 (fax) sent us an info sheet an a design questionaire "for all your magnetic shielding needs" from "Shielded enclosures for Video Display Terminals" to "Shielded Rooms for Medical and Research Applications". Approximate cost for a VDT shield = $750. Varian Associates also sells pre-made shields for Sun 17" and 20" monitors. However, we decided that it was far cheaper to reorganize our NMR lab and rewire our ethernet lines than to buy these shields. Marty Pagel mpagel@indiana.edu --- __o Department of Chemistry Phone: (812)-855-6492 --- \<, Indiana University Fax: (812)-855-8300 --- ()/ () Bloomington, IN 47405-4001 http://nmrsg1.chem.indiana.edu/~mpagel On 14 Apr 1996, Istvan Pelczer wrote: > > Dear Netters, > I would like to know what mangnetic shields are available for terminals. > Please, let me know your experience. Thanks, > Istvan > > wwww,wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww > Istvan Pelczer, Ph.D. Email: ipelczer@princeton.edu > Senior NMR Spectroscopist > Princeton University > Department of Chemistry ph# (609) 258 2342 > Frick Laboratory fax# (609) 258 6746 > Washington Road > Princeton, NJ 08544 > > From owner-structural-nmr@net.bio.net Sun Apr 14 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: "Graham E Jackson" Newsgroups: bionet.structural-nmr Subject: XPLOR Date: 15 Apr 1996 09:50:51 +0100 Lines: 27 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4kt2lb$917@mserv1.dl.ac.uk> X-mailer: Pegasus Mail v3.22 Original-To: str-nmr@dl.ac.uk Help! I am trying to use XPLOR to do nmr constrained molecular dynamics on a peptide. I have already done this using BIOSYM but want to check using another program. My first problem is to generate a structure file (.psf file). I used the BIOSYM pdb file and a suitably modified generate.inp script. I had to add pyroglutamic acid to the topology file. I have tried defining the sequence explicitly and using the pdb file. Xplor runs without any error messages but when you look at the structure file the first atoms are all bonded to themselves. This obviously causes error when doing any energy runs. I have also tried using pdb and inp files given as tutorials but get the same problem. What is my mistake? Thanks for any help. Graham Graham E Jackson Associate Professor Department of Chemistry University of Cape Town Cape Town South Africa Fax: (027 21) 6503788 Tel: (027 21) 6502531 E-mail: jackson@psipsy.uct.ac.za From owner-structural-nmr@net.bio.net Sun Apr 14 23:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!infobiogen.fr!jussieu.fr!oleane!plug.news.pipex.net!pipex!tank.news.pipex.net!pipex!swrinde!cs.utexas.edu!howland.reston.ans.net!surfnet.nl!swsbe6.switch.ch!scsing.switch.ch!news.belwue.de!fu-berlin.de!cs.tu-berlin.de!uni-erlangen.de!lrz-muenchen.de!news From: Rainer Gratias Newsgroups: bionet.structural-nmr Subject: Announcement of educational material for nmr spectroscopy Date: 15 Apr 1996 07:48:27 GMT Organization: TU Muenchen Lines: 22 Distribution: world Message-ID: <4ksv0b$fgs@sparcserver.lrz-muenchen.de> NNTP-Posting-Host: pebbles.org.chemie.tu-muenchen.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1S (X11; I; IRIX 5.3 IP22) X-URL: news:bionet.structural-nmr A number of tasks (together with elaborate solutions) are available in german via ftp.lrz-muenchen.de in the directory /pub/science/chemistry/analytic/nmr For more details see the README file within this directory. Rainer Haessner rh@linda.org.chemie.tu-muenchen.de -- ******************************************************************************** Technische Universitaet Muenchen Institut fuer Organische Chemie und Biochemie Lehrstuhl fuer Organische Chemie II Rainer Gratias Lichtenbergstr. 4 D-85747 Garching Tel : ++49 ++89 3209-3324 FAX : ++49 ++89 3209-3210 e-mail: rg@joshua.org.chemie.tu-muenchen.de ******************************************************************************** From owner-structural-nmr@net.bio.net Sun Apr 14 23:00:00 1996 Path: biosci!bloom-beacon.mit.edu!newsxfer2.itd.umich.edu!newsfeed.internetmci.com!csn!news-1.csn.net!magnus.acs.ohio-state.edu!infoserver.bgsu.edu!dad.bgsu.edu!aguliae From: aguliae@dad.bgsu.edu (Anton B. Guliaev) Newsgroups: bionet.structural-nmr Subject: Water supression on nmr Date: 15 Apr 1996 19:49:50 GMT Organization: Bowling Green State Univ. Lines: 12 Distribution: world Message-ID: <4ku98u$6gl@infoserver.bgsu.edu> NNTP-Posting-Host: ernie.bgsu.edu Keywords: WaterGAte, imino protons, DNA Does anybody know what's the best method to supress water ? We have DNA sample 95%H2O/5%d2o. We used WaterGate wich gave us pretty good water supression, but it looks like we also lost some NOE signal from imino region . We have very poor resolution in the imino-amino-aromatic( cytosin) part of the spectrum. Are there any new methods to supress the water except WaterGAte and jump-return? Our imino signals are very weak compaire with other parts of the spectrum. Thanks for your help and time, Anton B. Guliaev aguliae@rosalind.bgsu.edu aguliae@bgnet.bgsu.edu From owner-structural-nmr@net.bio.net Mon Apr 15 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!info.ucla.edu!nnrp.info.ucla.edu!usenet From: Flint Smith Newsgroups: bionet.structural-nmr Subject: Re: Water supression on nmr Date: 16 Apr 1996 22:44:06 GMT Organization: UCLA Lines: 9 Message-ID: <4l17rm$lf6@saba.info.ucla.edu> References: <4ku98u$6gl@infoserver.bgsu.edu> NNTP-Posting-Host: holmes.mbi.ucla.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; IRIX 5.3 IP22) To: aguliae@dad.bgsu.edu X-URL: news:4ku98u$6gl@infoserver.bgsu.edu aguliae@dad.bgsu.edu (Anton B. Guliaev) wrote: >any new methods to supress the water except WaterGAte and jump-return? How about 11echo? Works well for us. Flint Smith flint@ucla.edu From owner-structural-nmr@net.bio.net Mon Apr 15 23:00:00 1996 Path: biosci!PHOENIX.PRINCETON.EDU!ipelczer From: ipelczer@PHOENIX.PRINCETON.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: Water supression on nmr Date: 15 Apr 1996 17:27:07 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 46 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <4ku98u$6gl@infoserver.bgsu.edu> NNTP-Posting-Host: net.bio.net Hi Anton, Before you abandon WATERGATE, make it sure that you use the lowest power gradient possible. You may have lost some signals because of the too strong gradients applied. This may be true in case of any other gradient based methods, such as Shaka's novel excitation sculpting, too. A good review on water suppression is: Gueron, Plateau and Decorps, Progress in NMR Spectroscopy 23(1991)135-209. Also, for applications to nucleic acids (DNA in particular) Sklenar and Bax presented a paper using JR-echo in FEBS Letters to my best recollection. It needs no gradients, and can give you satisfactory results, especially with time domain filtering of the residual signal in data processing. Good luck, Istvan wwww,wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww Istvan Pelczer, Ph.D. Email: ipelczer@princeton.edu Senior NMR Spectroscopist Princeton University Department of Chemistry ph# (609) 258 2342 Frick Laboratory fax# (609) 258 6746 Washington Road Princeton, NJ 08544 On 15 Apr 1996, Anton B. Guliaev wrote: > Does anybody know what's the best method to supress water ? We have DNA sample > 95%H2O/5%d2o. We used WaterGate wich gave us pretty good water supression, but > it looks like we also lost some NOE signal from imino region . We have very poor > resolution in the imino-amino-aromatic( cytosin) part of the spectrum. Are there > any new methods to supress the water except WaterGAte and jump-return? Our > imino signals are very weak compaire with other parts of the spectrum. > Thanks for your help and time, > Anton B. Guliaev > aguliae@rosalind.bgsu.edu > aguliae@bgnet.bgsu.edu > > > > From owner-structural-nmr@net.bio.net Mon Apr 15 23:00:00 1996 Path: biosci!chem.umu.se!buevich From: buevich@chem.umu.se (Alexei Buevich) Newsgroups: bionet.structural-nmr Subject: LIS analysis software Date: 16 Apr 1996 00:15:43 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <199604160712.JAA19582@chem.umu.se> NNTP-Posting-Host: net.bio.net Dear Netters, Does anyone know where I can find the program (preferably freeware) for elucidating the molecular structure from lanthanide-induced shift data? Any information will be very appreciable. Alexei =========================================================== Dr. Alexei V. Buevich Department of Organic Chemistry University of Umea S-90187 Umea, Sweden Tel: +46-90/166 286 Fax: +46-90/138 885 E-mail: buevich@chem.umu.se =========================================================== From owner-structural-nmr@net.bio.net Tue Apr 16 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!nntp.inet.fi!news.funet.fi!luotsi.uku.fi!usenet From: niemitz@skanssi.uku.fi (Matthias Niemitz) Newsgroups: bionet.structural-nmr Subject: Re: LIS analysis software Date: 17 Apr 1996 15:10:27 GMT Organization: University of Kuopio, Finland Lines: 22 Distribution: world Message-ID: <4l31l3$qjc@luotsi.uku.fi> References: <199604160712.JAA19582@chem.umu.se> NNTP-Posting-Host: skanssi11.uku.fi Mime-Version: 1.0 Content-Type: Text/Plain; charset=ISO-8859-1 X-Newsreader: WinVN 0.99.5 In article <199604160712.JAA19582@chem.umu.se>, buevich@chem.umu.se says... > >Dear Netters, > >Does anyone know where I can find the program (preferably freeware) for >elucidating the molecular structure from lanthanide-induced shift data? > >Any information will be very appreciable. Hi Alexei, Have you tried the LANTA program in the PERCH package? LANTA is freeware, although appropriate citation is appreciated. Regards, Matthias Niemitz Department of Chemistry phone: + 358 71 163241 University of Kuopio fax: + 358 71 163259 P.O.B. 1627 e-mail: Matthias.Niemitz@uku.fi FIN-70211 Kuopio, FINLAND WWW: http://www.uku.fi/perch.html From owner-structural-nmr@net.bio.net Wed Apr 17 23:00:00 1996 Path: biosci!MIDWAY.UCHICAGO.EDU!hchen2 From: hchen2@MIDWAY.UCHICAGO.EDU (Huifen Chen) Newsgroups: bionet.structural-nmr Subject: subscrib Date: 18 Apr 1996 13:44:44 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: <199604182041.PAA10097@kimbark.uchicago.edu> NNTP-Posting-Host: net.bio.net Hi, I would like to subscrib to your net. ------------------------------------------------------------------------------- Huifen Chen Dept. of Biochemistry & hchen2@midway.uchicago.edu Molecular Biology (312)-702-2017 office The University of Chicago (312)-702-5347 fax 920 East 58th Street Chicago, ILL 60637 From owner-structural-nmr@net.bio.net Wed Apr 17 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: "<"<@ICINECA.CINECA.IT:orena@anvax1.cineca.it> Newsgroups: bionet.structural-nmr Subject: H-bonding: need help Date: 18 Apr 1996 10:32:15 +0100 Lines: 60 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4l526v$lar@mserv1.dl.ac.uk> Original-To: str-nmr@dl.ac.uk Dear netters, I'm a young organic chemist and I'm working in the organic synthesis field. I usually use the NMR in order to determine the structures of our synthesized compounds. We have observed an unusual phenomenon, unusual for our knoledge. We have recently synthesized a bicyclo formed by a cyclopropane ring and a pyrrolidinone attached in alpha the carbonyl group of the pyrrolidinonic ring. In alpha to the carbonyl group there is also a CH2OH group. The IUPAC name of this compound is (1S,5R,1'R)-1-Hydroxymethil-2-oxo- 3-aza-3-(1'-phenyl-1'-yl)-bicyclo-[3.1.0]-hexane (C14H17NO2) Here is the structure: HOCH2 CH2 \ / \ C---CH | | O= C CH2 \ / N | R R=Phenylethyl group We observed that signal corresponding to the protons of the CH2OH group changes on varying the concentration of the champion. The spectra has been done in CDCl3. At low concentration it is an AB system con delta ni =0,then on growing concentration it looks like becoming an ABX and then at high concentration it's an AB system with delta ni (Dn) growing on growing concentration. From X-ray data, we observed the formation of an intermolecular H-bond. From molecular mechanics calculations we observed the possibility of both an intermolular (more favorable) and an intramolecular H-bonding formation. We have made a spectrum in DMSO too and we have found a ABX system for the CH2OH protons. Is there anyone who can help us or give us some bibliographic references about this phenomenon? Thanks a lot Giovanna ----------------------------------------------------- Dr. Giovanna Mobbili Universita' di Ancona Dipartimento di Scienze dei Materiali e della Terra via Brecce Bianche Ancona Italy e-mail: orena@anvax1.unian.it fax: 39-71-2204714 From owner-structural-nmr@net.bio.net Wed Apr 17 23:00:00 1996 Path: biosci!PHOENIX.PRINCETON.EDU!ipelczer From: ipelczer@PHOENIX.PRINCETON.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: sum-shields Date: 18 Apr 1996 10:42:05 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 152 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Netters, Just in case, let me post the summary of the responses I received about shields. I left out duplicate suggestions. THanks for all who replied! All the best, Istvan wwww,wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww Istvan Pelczer, Ph.D. Email: ipelczer@princeton.edu Senior NMR Spectroscopist Princeton University Department of Chemistry ph# (609) 258 2342 Frick Laboratory fax# (609) 258 6746 Washington Road Princeton, NJ 08544 ************************************** here it comes: From greig@resunix.ri.sickkids.on.caThu Apr 18 12:33:27 1996 Date: Sun, 14 Apr 1996 20:48:39 -0400 (EDT) From: David Iain Greig To: Istvan Pelczer Subject: Re: shield Oops, hit return there when I didn't mean to. In UC Boulder, Martin Ashley has a lovely metal shield on a 19" monitor that Varian provided him as a fix when they moved a 500 magnet 8 feet away. Works fine. Lewis Kay has a home-brew shield on his Sparc/Inova, I recall from my last trip to the NMR center on campus here at U of T. I'll ask Julie F-K. about it early this week. regards --D. ---- David Iain Greig, UNIX System Administrator Tel: (416) 813-5013 Research Computing Services Fax: (416) 813-7099 Hospital for Sick Children, 555 University Ave, Toronto, Ont. M5G 1X8 greig@sickkids.on.ca "Arbor plena allouatarum" From phbolton@lily.chem.wesleyan.eduThu Apr 18 12:33:49 1996 Date: Sun, 14 Apr 1996 08:52:56 -0400 From: "Philip H. Bolton" To: Istvan Pelczer Subject: Re: shield This is what we did for one of the monitors: Dr. Barry Shapiro Wednesday, July 7, 1993 TAMU Newsletter 966 Elsinore Court Palo Alto, CA 94303 Dear Barry: We have recently installed a SUN computer and monitor near our spectrometer. Even though the 19" color monitor was placed outside of the 5 gauss line there was significant distortion of the images on the monitor. Attempts to remove the distortion by degaussing the monitor, moving the screen around and the like did not meet with success. Thus, we decided to construct a wood box with mu metal lining to shield the screen. Mu metal is a very effective magnetic shield and is quite flexible. The box is 25" tall, 26" deep and 14" wide. A 5" by 14" cutout in the back of the box was made to allow running in the power and connection cables. The box was lined with AD-MU-80 mu metal, thickness of 0.1 inch, obtained from Ad-vance Magnetics of Rochester, IN. A total of 18 feet, at $27.65/foot, of 15" wide strips of mu metal was required to cover the interior of the box at one layer of thickness. For ventilation purposes two louvered vents were added to each side of the box and for aesthetic purposes the box was covered with formica and some other trim. The box works quite well and there is no visible distortion of the images on the monitor. The ventilation provided by the simple vents appears to be adequate for the monitor. The monitor was degaussed after being placed in the box. The scientific support services at Wesleyan could construct similar boxes for other users if there is interest. Please contact Thomas Castelli at 203-344-8544 extension 2752. From ruba@mol.biol.ethz.chThu Apr 18 12:34:11 1996 Date: Mon, 15 Apr 1996 09:14:17 +0200 From: Rudolf Baumann To: ipelczer@phoenix.Princeton.EDU Subject: Re: shield Hi Istvan yes we are using such a shield from a small swiss firm since more than a year on our 20" Sun-monitor in the 750 spectrometer room with great success. The shield is a bit expensive for this size but works great (2600 sFr), we could only see colored stripes before using it. The firm is: Systron Untere Bahnhofstrasse 25 CH-8034 Hinwil Tel: +41 1 937 53 50 Fax: +41 1 937 53 70 Hope I could help you Rudolf ----------------------------------------------------------------------------- Rudolf E. Baumann ruba@mol.biol.ethz.ch Institut fuer Molekularbiologie & Biophysik http://www.mol.biol.ethz.ch/ ETH Hoenggerberg (HPM G6) ,,, Tel. ++41 1 633 33 97 CH-8093 Zuerich/Switzerland (o o) Fax ++41 1 633 10 73 ----------------------------------oOO--(_)--OOo------------------------------ From yves_aubin@Merck.ComThu Apr 18 12:41:33 1996 Date: 15 Apr 1996 07:02:36 -0700 From: Yves Aubin To: str-nmr@net.bio.net Subject: Re: shield Istvan wrote: >Dear Netters, >I would like to know what mangnetic shields are available for terminals. >Please, let me know your experience. Thanks, >Istvan > In Lewis Kay's laboratory in Toronto, we had two monitors that were severly perturbed by the magnetic field of a 500 and a 600 machines. The perturbation was such that the colors were changing from blue (lower right corner) to red (upper right corner) and the lack of focus made difficult the reading of the screen. I built two shields for less than 200 CDN$ each. The results are excellent in both cases: no color distortion and very good focus. I described the construction of the shield in the February issue of "The NMR newsletter" No. 449. If anyone have any questions, I'll be happy to answer them. Yves 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 From owner-structural-nmr@net.bio.net Thu Apr 18 23:00:00 1996 Path: biosci!NMR.UTMB.EDU!david From: david@NMR.UTMB.EDU (David Gorenstein) Newsgroups: bionet.structural-nmr Subject: National Public Radio/PBS Date: 19 Apr 1996 12:07:40 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 92 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Date: Fri, 19 Apr 1996 11:22:00 -0500 For anyone who thinks NPR/PBS is a worthwhile expenditure of $1.12/year of their taxes (as opposed to, say, Newt Gingrich's salary?), petition follows. If you sign, please forward on to others (not back to me). If not, please don't kill it -- send it to the email address listed here: wein2688@blue.univnorthco.edu ---------- PBS, NPR (National Public Radio), and the arts are facing major cutbacks in funding. In spite of the efforts of each station to reduce spending costs and streamline their services, the government officials believe that the funding currently going to these programs is too large a portion of funding for something which is seen as "unworthwhile". Currently, taxes from the general public for PBS equal $1.12 per person per year, and the National Endowment for the Arts equals $.64 a year in total. A January 1995 CNN/USA Today/Gallup poll indicated that 76% of Americans wish to keep funding for PBS, third only to national defense and law enforcement as the most valuable programs for federal funding. Each year, the Senate and House Appropriations committees each have 13 subcommittees with jurisdiction over many programs and agencies. Each subcommittee passes its own appropriation bill. The goal each year is to have each bill signed by the beginning of the fiscal year, which is October 1. In the instance of the Corporation of Public Broadcasting, the bill determines the funding for the next three years. When this issue comes up in 1996, the funding will be determined for fiscal years 1996-1998. The only way that our representatives can be aware of the base of support for PBS and funding for these types of programs is by making our voices heard. Please add your name to this list if you believe in what we stand for. This list will be forwarded to the President of the United States, the Vice President of the United States, and Representative Newt Gingrich, who is the instigator of the action to cut funding to these worthwhile programs. If you happen to be the 50th, 100th, 150th, etc. signer of this petition, please forward a copy to wein2688@blue.univnorthco.edu. If that address is inoperative, please send it to kubi7975@blue.univnorthco.edu. This way we can keep track of the lists and organize them. Forward this to everyone you know, and help us to keep these programs alive. Thank you. 1) Nigel Goldenfeld, Urbana, Il (nigel@uiuc.edu) 2) Tony Leggett,Urbana,Il (tony@amaterasu.physics.uiuc.edu) 3) Anupam Garg, Skokie, IL (garg@gmunch.phys.nwu.edu) 4) Thomas Rosenbaum, Chicago, IL (tfr@rainbow.uchicago.edu) 5) Sidney Nagel, Chicago, IL (sid@rainbow.uchicago.edu) 6) Mel Shochet, Chicago, IL (shochet@uccdf.uchicago.edu) 7) James Shapiro, Chicago, IL (jsha@midway.uchicago.edu) 8) Jim Haber, Waltham, MA (haber@hydra.rose.brandeis.edu) 9) Edward Egelman, Minneapolis, MN (egelman@egel1.med.umn.edu) 10) Len Banaszak, Minneapolis, MN (len_b@dccc.med.umn.edu) 11) Douglas Ohlendorf, Eden Prairie MN (ohlen@dccc.med.umn.edu) 12) Norma Allewell, Minneapolis MN (norma@biosci.cbs.umn.edu) 13) Victor Bloomfield, St. Paul MN (victor@biosci.cbs.umn.edu) 14) David Gorenstein, Galveston, TX (david@nmr.utmb.edu) David Gorenstein Director, Sealy Center for Structural Biology Professor, Dept. of Human Biological Chemistry and Genetics University of Texas Medical Branch Galveston, TX 77555-1157 Office: (409) 747 6801 Main Office/Voice Mail: (409) 747 6800 Fax: (409) 747 6850 E-MAIL ADDRESS: david@nmr.utmb.edu http://www.nmr.utmb.edu/ From owner-structural-nmr@net.bio.net Thu Apr 18 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!tank.news.pipex.net!pipex!lade.news.pipex.net!pipex!ggr.co.uk!ussun2n.glaxo.com!uswsum.glaxo.com!user From: sujoy_ghosh@glaxo.com (sujoy ghosh) Newsgroups: bionet.structural-nmr Subject: lipid structure Date: Fri, 19 Apr 1996 12:00:26 -0500 Organization: glaxo wellcome Lines: 3 Message-ID: NNTP-Posting-Host: uswsum.glaxo.com Does anyone know of any database that stores NMR or X-ray structural coordinates for phospholipids? They are not in the PDB (obviously!) Sujoy (sujoy_ghosh@glaxo.com) From owner-structural-nmr@net.bio.net Thu Apr 18 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!EU.net!Austria.EU.net!newsfeed.ACO.net!mail.boku.ac.at!news From: Andreas Wernitznig Newsgroups: bionet.molec-model,bionet.structural-nmr,bionet.xtallography Subject: GDE under Linux Date: Fri, 19 Apr 1996 14:22:15 +0200 Organization: AWIndustries Lines: 5 Message-ID: <31778577.4FBF@edv1.boku.ac.at> NNTP-Posting-Host: 141.244.88.51 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (WinNT; I) Xref: biosci bionet.molec-model:901 bionet.structural-nmr:1218 bionet.xtallography:2515 Does anybody have experience with Genetic Data Environment under Linux ? I wasn't able to start it (libraries are wrong or/and missing). Is the source code available to compile it by myself ?? Any suggestions are appreciated. Andreas Wernitznig From owner-structural-nmr@net.bio.net Thu Apr 18 23:00:00 1996 Newsgroups: bionet.structural-nmr Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!nih-csl!rvenable From: rvenable@deimos.cber.nih.gov (Rick Venable) Subject: Re: lipid structure Message-ID: <1996Apr19.223808.11630@alw.nih.gov> Sender: postman@alw.nih.gov (AMDS Postmaster) Nntp-Posting-Host: deimos.cber.nih.gov Organization: FDA/CBER Biophysics Lab X-Newsreader: TIN [version 1.2 PL2] References: Date: Fri, 19 Apr 1996 22:38:08 GMT Lines: 21 On Fri, 19 Apr 1996 12:00:26 -0500 sujoy ghosh asked: > Does anyone know of any database that stores NMR or X-ray structural > coordinates for phospholipids? They are not in the PDB (obviously!) > Sujoy (sujoy_ghosh@glaxo.com) Some can be found in the Cambridge database; some with choline headgroups tend to be fairly disorderd, and aren't in any databases. The biologically active fluid phase of lipids is of course too disordered for coordinate determination by any method. A good starting point is: Crystal Structures of Membrane Lipids I Pascher, M Lundmark, PG Nyholm, S Sundell Biochimica et Biophysica Acta 1113:339-373 (1992) -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| / Not an official statement \ rvenable@deimos.cber.nih.gov \/ |=| \ or position of the FDA. / From owner-structural-nmr@net.bio.net Thu Apr 18 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!EU.net!Austria.EU.net!newsfeed.ACO.net!mail.boku.ac.at!news From: Andreas Wernitznig Newsgroups: bionet.molec-model,bionet.structural-nmr,bionet.xtallography Subject: GDE under Linux Date: Fri, 19 Apr 1996 14:18:12 +0200 Organization: AWIndustries Lines: 5 Message-ID: <31778484.2964@edv1.boku.ac.at> References: <4jpo94$8ei@nntp.ucs.ubc.ca> Reply-To: h8760592@edv1.boku.ac.at NNTP-Posting-Host: 141.244.88.51 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (WinNT; I) Xref: biosci bionet.molec-model:900 bionet.structural-nmr:1217 bionet.xtallography:2514 Does anybody have experience with Genetic Data Environment under Linux ? I wasn't able to start it (libraries are wrong or/and missing). Is the source code available to compile it by myself ?? Any suggestions are appreciated. Andreas Wernitznig From owner-structural-nmr@net.bio.net Sun Apr 21 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.structural-nmr Subject: unsubscribe Date: 22 Apr 1996 08:34:51 +0100 Lines: 2 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4lfcqr$i9j@mserv1.dl.ac.uk> Original-To: str-nmr@dl.ac.uk unsubscribe From owner-structural-nmr@net.bio.net Sun Apr 21 23:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.structural-nmr Subject: IMPORTANT - BIOSCI Fundraising Update! Date: 22 Apr 1996 02:01:18 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 154 Sender: daemon@net.bio.net Distribution: world Message-ID: <199604220900.CAA26463@net.bio.net> NNTP-Posting-Host: net.bio.net BIOSCI is about halfway to its funding goal!! I'm interrupting the usual monthly posting of the BIOSCI miniFAQ to bring you up to date on BIOSCI fundraising progress, a topic of concern to your future use of this resource. Thank you in advance for taking the time to read this message carefully. Last year we announced that BIOSCI was going to adopt the U.S. Public Broadcasting System model to fund its operations after our DOE/NSF grant runs out later this year. Unlike PBS, we are not soliciting contributions from users; we are only selling ads on our Web pages solely to cover our operating costs. Our goal is to seek sponsorships until we build up an operating reserve of about $100,000 and then cease further promotions until we need to build the reserve back up. (The accountants among our readership will be familiar with the problem of deferred revenue which we can not safely utilize until ads have been displayed for a period of time.) We are only about halfway to our funding goal and need to raise further funds to avoid having to curtail services at net.bio.net. Fundraising is time-consuming, however, and we need your help as explained further below. Our operating costs consist of our network connection, phone lines, hardware maintenance (we will be getting newer and faster hardware soon!), plus 0.7 FTE of salaries covering UNIX systems admin, technical support, quality assurance, i.e., testing, of our system, and administrative costs (such as the time it takes to actually find/write/call potential sponsors and raise money!). Although the BIOSCI staff does get compensated for a portion of the work that they do, this project has always received a lot of free after-hours and "vacation" time labor, so we hope that no one will begrudge the time that we do charge to the project to serve you. All of the three part-time staff members, Dave Mack, Julie Lawrence, and myself, have full time day jobs and families in addition to working hard to keep this service running for all of you. Julie and Dave Mack are subcontractors for BIOSCI; my time that is charged to the project defrays a portion of my regular salary instead of adding to my income. Besides having to relocate the project, we were very busy this last year building new infrastructure such as our WWW hypermail interface to the system. This was released last December along with scores of WAIS indices for the newsgroups. Virtually everything is complete, although we do continue to find and fix bugs (many through your helpful feedback!). We are still having some problems with our WAIS indexing. The archives continue to grow rapidly. We are running over 100 indexes now versus three previously and any systems crashes cause greater havoc with the indexing than before! We are still working to fix this as fast as our resources permit and appreciate your patience, but we have been able to automate a lot of the infrastructure to reduce labor as compared to past requirements. We have also implemented new software to make moderation of BIOSCI/bionet newsgroups much easier and combat the growing problem of Internet junk mail and USENET "spamming." About 20% of our groups are now moderated, many of them by the BIOSCI staff! This, for example, made a major difference last year in the quality of content in our EMPLOYMENT/bionet.jobs.offered newsgroup which many commercial concerns and recruiting firms are using **without charge** to recruit candidates for positions in the biological sciences. We are also now in a position to have sponsors for individual newsgroups as you will have noticed if you have visited http://www.bio.net/ and clicked on "Access the BIOSCI/bionet newsgroups" recently. So, how can you help?? ---------------------- As noted above it can take a lot of time to contact potential sponsors if I have to do it all myself. Our request is quite simple. You can do two important things which will take very little time for you individually. First, please use our WWW system at http://www.bio.net/ to access the archives. You can now post or reply to messages via your Web browser. 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. Our hope is to quickly raise several large corporate/institutional sponsors on our heavily-used WWW locations (some stats appended below), and then end this sponsorship campaign so that our resources can continue to be used for service provision, not fundraising. Many of our specialty newsgroup WWW archives are still used by small communities of scientists (and they haven't been heavily promoted yet). While these may be valuable niche markets to some advertisers, it will generate more labor and overhead having to find these sponsors, fairly price the locations, and deal with lots of smaller sponsorships than fewer mid-to large sponsors. We are striving to keep our operation as lean and efficient as possible since we are not trying to make careers out of running BIOSCI. We are trying if at all possible to avoid the administrative overhead entailed with processing lots of small payments to reach our fundraising goals. I'd like to thank all of you for your help in advance. In helping us, you are also helping yourselves, not only in keeping this resource available for all of the both large and small research communities that we serve, but also by alleviating the need for us to go back and compete with researchers for tight grant dollars! We promised NSF when we were awarded the BIOSCI grant that we would carry out this mission to make the service self-supporting. With your help, we will succeed in continuing BIOSCI's work into its second decade. Thank you very much! Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net A list of our prime WWW sponsorship locations follow. Please contact us for further details. ---------------------------------------------------------------------- The overall BIOSCI WWW pages are currently visited by users from close to 5500 unique computer hosts per week. Web servers only log the Internet computer/host name and frequently more than one individual can connect to us from a particular host. Main home page, http://www.bio.net, visited recently by about 2100 unique hosts per week Main Newsgroups archives page, http://www.bio.net/archives.html, visited recently by about 1200 Unique hosts per week BIO-JOURNALS archive page, http://www.bio.net/BIO-JOURNALS.html, visited recently by about 1000 unique hosts per week. EMPLOYMENT archive pages: http://www.bio.net:80/hypermail/EMPLOYMENT/ and monthly header pages, visited recently by about 800 unique hosts per week. Address database search page, http://www.bio.net/addrsearch.html, visited recently by about 450 unique hosts per week. Methods newsgroup archive pages, http://www.bio.net:80/hypermail/METHDS- REAGNTS/ and monthly header pages, visited recently by about 350 unique hosts per week. Ads can also be displayed on various combinations of other BIOSCI/bionet newsgroups. Please contact us at biosci-help@net.bio.net for details. ---------------------------------------------------------------------- From owner-structural-nmr@net.bio.net Mon Apr 22 23:00:00 1996 Path: biosci!bioc.unsw.EDU.AU!garry From: garry@bioc.unsw.EDU.AU (Garry King) Newsgroups: bionet.structural-nmr Subject: Postdoctoral Positions Available Date: 22 Apr 1996 18:26:46 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 50 Sender: daemon@net.bio.net Distribution: world Message-ID: <199604232221.WAA10855@toucan.babs.unsw.EDU.AU> NNTP-Posting-Host: net.bio.net POSTDOCTORAL POSITIONS - BIOMOLECULAR NMR The research group of Garry C. King in Sydney, Australia seeks one or two postdoctoral associates to undertake studies of biomolecular recognition, especially the structure, dynamics and interactions of nucleic acids. The positions are available immediately for an initial period of two or three years, renewed annually, with a suggested salary in the range of $A 37,345-40,087 p.a. Candidates should have a solid background in hands-on NMR, preferably with experience in multidimensional biomolecular experiments, although appropriately-qualified chemists with an interest in moving into biomolecular work will be considered. Strong computational skills are a bonus. Research Associates will work with other members of a small group pursuing projects on C-13 relaxation analysis of nucleic acid motions, discovery of new RNA structures/activities using SELEX methods and analysis of protein/nucleic acid-ligand interactions. NMR and computational facilities are competitive. The laboratory has major use of a Bruker DMX-600 equipped with x,y,z gradients, secondary use of a Bruker DMX-500 equipped with a z gradient, and houses a small workstation cluster which includes SGI R8000 Indigo2, Indigo2 Extreme and Indy hardware. These systems currently run a range of MSI and academic software. Please address enquiries to: Dr. Garry C. King School of Biochemistry and Molecular Genetics The University of New South Wales Sydney 2052 Australia Ph: +61-2-385-2021 Fax: +61-2-313-6271 Email: garry@bioc.unsw.edu.au -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Garry C. King School of Biochemistry and Molecular Genetics The University of New South Wales Sydney 2052 Australia Ph: 61-2-385-2021 Fax: 61-2-313-6271 Email: garry@bioc.unsw.edu.au -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From owner-structural-nmr@net.bio.net Tue Apr 23 23:00:00 1996 Path: biosci!LILY.CHEM.WESLEYAN.EDU!phbolton From: phbolton@LILY.CHEM.WESLEYAN.EDU (Philip H. Bolton) Newsgroups: bionet.structural-nmr Subject: position available Date: 23 Apr 1996 17:44:25 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Position Available Ke Yu Wang has just accepted a position at Gilead Sciences and will be joining them in the very near future. Thus, there is a post-doctoral position available to study the structures, metal ion binding and dynamics of aptamer, telomere and other quadruplex DNAs in an NIH funded study. We have a Varian Unityplus 400 which is being upgraded to include 5/8 mm pfg probes and a Varian Inova 500, three channel spectrometer with pfg 5/8 mm probes whose installation begins next week. The group has extensive computational support including IBM and SUN workstations. Please send cv and three letters of recommendation to me at: Philip H. Bolton Chemistry Department Wesleyan University Middletown, CT 06459 From owner-structural-nmr@net.bio.net Wed Apr 24 23:00:00 1996 Path: biosci!agate!newsxfer2.itd.umich.edu!newsfeed.internetmci.com!nntp-hub2.barrnet.net!news.Stanford.EDU!usenet From: Zhan-yang Zhu Newsgroups: bionet.structural-nmr Subject: Re: Hydrogen bond definition Date: 25 Apr 1996 20:52:47 GMT Organization: Stanford University Lines: 24 Message-ID: <4loomv$53b@nntp.Stanford.EDU> References: <9604252146.AA05271@IRIS.lsc.pku.edu.cn> NNTP-Posting-Host: gallery.stanford.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1IS (X11; I; IRIX 5.3 IP22) X-URL: news:9604252146.AA05271@IRIS.lsc.pku.edu.cn Yes, there is no standard defination of H-bond, especially the cutoffs for distances and angles. But the Kabsch & Sander's program (defination) for backbone hydrogen bonds is becoming "standard". It should be OK to use that program to determine the hydrogen bonds in your peptide. Other ref for hydrogen bonds is Baker, E.N. and Hubbard, R.E. (1984): Hydrogen bonding in globular proteins. Prog. Biophys. Molec. Biol. Vol. 44 page 99-179. From this paper, you are able to find the discussions of criteria used for h-bond defination. Good luck! Zhan-yang -- The following is my automatic signature: Zhan-Yang Zhu, Ph.D Department of Mathematics Stanford University Stanford, CA 94305-2125 Tel: (415) 723 2221 Fax: (415) 725 2040 From owner-structural-nmr@net.bio.net Wed Apr 24 23:00:00 1996 Path: biosci!IRIS.LSC.PKU.EDU.CN!qyx From: qyx@IRIS.LSC.PKU.EDU.CN (Qu Youxin) Newsgroups: bionet.structural-nmr Subject: Hydrogen bond definition Date: 24 Apr 1996 23:49:41 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 32 Sender: daemon@net.bio.net Distribution: world Message-ID: <9604252146.AA05271@IRIS.lsc.pku.edu.cn> NNTP-Posting-Host: net.bio.net Dear all, I wish to determine the backbone hydrogen bonds and then the secondary structures in my small peptide NMR structures. However, I cannot find standard values and the allowed deviation from them for the distance between atoms NH and CO and for the angle (N-H...O). Drs. Kabsch and Sander said there was no generally correct H-bond definition (Biopolymers,1983, 22:2577-2637), and I noticed there were several methods to determine hydrogen bonds and secondary structures. Could anyone kindly tell me the parameters for the above distance and angle? Any hint or help is highly appreciated. Youxing. __________________________________________ Youxing Qu National Laboratory of Protein Engineering and Plant Genetic Engineering Life Sciences Center College of Life Sciences Peking University Beijing 100871 P. R. China E-mail: qyx@IRIS.lsc.pku.edu.cn __________________________________________ From owner-structural-nmr@net.bio.net Wed Apr 24 23:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news.ox.ac.uk!news From: "Simon M. Brocklehurst" Newsgroups: bionet.structural-nmr Subject: Re: Hydrogen bond definition Date: Thu, 25 Apr 1996 11:46:10 +0100 Organization: University of Oxford Lines: 43 Message-ID: <317F57F2.41C67EA6@bioch.ox.ac.uk> References: <9604252146.AA05271@IRIS.lsc.pku.edu.cn> 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 2.01 (X11; I; SunOS 4.1.3_U1 sun4m) Qu Youxin wrote: > > Dear all, > > I wish to determine the backbone hydrogen bonds and then the > secondary structures in my small peptide NMR structures. However, > I cannot find standard values and the allowed deviation from > them for the distance between atoms NH and CO and for the angle > (N-H...O). Drs. Kabsch and Sander said there was no generally > correct H-bond definition (Biopolymers,1983, 22:2577-2637), > and I noticed there were several methods to determine hydrogen > bonds and secondary structures. Could anyone kindly tell me > the parameters for the above distance and angle? > > Any hint or help is highly appreciated. > Well for main-chain hydrogen bonds, you can do quite well with a definition: r(HN...O) < 2.5 A, and ang(HN...O=C) > 90 degrees providing that your coordinates are reasonably precise. For secondary structure, remember that although secondary structure and hydrogen bonds are intimitely related, secondary structure is actually a description of the local conformation of a polypeptide chain - you might want to think about this when assigning secondary structural elements. I think the computer program NAOMI is installed on an SGI at LSC, Peking Universty. You might consider using it to assign H-bonds (this will do a slightly better job of things than using the cut-off values mentioned above), analyse local conformation (phi/psi, chain curvature etc), and assign secondary structure, either automatically, or by looking at the H-bond lists and local conformation descriptors by eye in combination with inspecting the structures using interactive graphics. Hope this helps, _____________________________________________________________________________ | | ,_ o Simon M. Brocklehurst, | / //\, Oxford Centre for Molecular Sciences, Department of Biochemistry, | \>> | University of Oxford, Oxford, UK. | \\, E-mail: smb@bioch.ox.ac.uk | WWW: http://www.ocms.ox.ac.uk/~smb/ |____________________________________________________________________________ From owner-structural-nmr@net.bio.net Thu Apr 25 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: bryan@freja.fkem2.lth.se (Bryan Finn) Newsgroups: bionet.structural-nmr Subject: Re: Hydrogen bond definition Date: 26 Apr 1996 14:41:31 +0100 Lines: 33 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4lqjqb$doo@mserv1.dl.ac.uk> Original-To: str-nmr@dl.ac.uk Simon M. Brocklehurst wrote: > Sorry to be pedantic, but I'm not sure I would agree that DSSP is the > "standard" program for determining hydrogen bonds. The model of a > hydrogen bond it uses isn't all that great. It is suitable for doing what > it was designed to do - that is, find enough of the hydrogen bonds in a > protein so that secondary structural motifs can be identified reasonably well. > It is not sensible to use it for other purposes because other software is > available that does a better job. Such as...? ___________________________________________________________________ | | | Dr. Bryan Finn | | Department of Physical Chemistry 2 Tel: +46-46-222-8254 | | Chemical Center Fax: +46-46-222-4543 | | University of Lund | | POB 124 | | S-221 00 Lund Sweden e-mail: bryan@freja.fkem2.lth.se | | WWW: http://www.fkem2.lth.se/personnel/bryan/finn.html | |_________________________________________________________________| From owner-structural-nmr@net.bio.net Thu Apr 25 23:00:00 1996 Path: biosci!daresbury!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!news.ox.ac.uk!news From: "Simon M. Brocklehurst" Newsgroups: bionet.structural-nmr Subject: Re: Hydrogen bond definition Date: Fri, 26 Apr 1996 13:47:14 +0100 Organization: University of Oxford Lines: 22 Message-ID: <3180C5D2.167EB0E7@bioch.ox.ac.uk> References: <9604252146.AA05271@IRIS.lsc.pku.edu.cn> <4loomv$53b@nntp.Stanford.EDU> NNTP-Posting-Host: nmrv.ocms.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (X11; I; SunOS 4.1.3_U1 sun4m) Zhan-yang Zhu wrote: > > Yes, there is no standard defination of H-bond, especially the cutoffs for > distances and angles. But the Kabsch & Sander's program (defination) for > backbone hydrogen bonds is becoming "standard". It should be OK to use that > program to determine the hydrogen bonds in your peptide. > Sorry to be pedantic, but I'm not sure I would agree that DSSP is the "standard" program for determining hydrogen bonds. The model of a hydrogen bond it uses isn't all that great. It is suitable for doing what it was designed to do - that is, find enough of the hydrogen bonds in a protein so that secondary structural motifs can be identified reasonably well. It is not sensible to use it for other purposes because other software is available that does a better job. _____________________________________________________________________________ | | ,_ o Simon M. Brocklehurst, | / //\, Oxford Centre for Molecular Sciences, Department of Biochemistry, | \>> | University of Oxford, Oxford, UK. | \\, E-mail: smb@bioch.ox.ac.uk | WWW: http://www.ocms.ox.ac.uk/~smb/ |____________________________________________________________________________ From owner-structural-nmr@net.bio.net Fri Apr 26 23:00:00 1996 Path: biosci!OTTER.BIOCHEM.UBC.CA!mcintosh From: mcintosh@OTTER.BIOCHEM.UBC.CA (Lawrence McIntosh) Newsgroups: bionet.structural-nmr Subject: Re: Hydrogen bond definition Date: 27 Apr 1996 10:10:56 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 59 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <4lqjqb$doo@mserv1.dl.ac.uk> NNTP-Posting-Host: net.bio.net Hi: I would agree that DSSP is not the "final word" on hydrogen bonds in proteins. Remember that everything is atoms and space - the rest is just opinion. Other relevant programs include VADAR from Wishart and Sykes at the University of Alberta (e-mail: vadar@procyon.biochem.ualberta.ca), and HBPLUS from MacDonald and Thornton at University College London. One might also consider PROMOTIF from Hutchinson and Thornton. The latter two can be found at: http://www.biochem.ucl.ac.uk/bsm/biocomp/index.html Cheers, Lawrence McIntosh Univ. British Columbia On 26 Apr 1996, Bryan Finn wrote: > Simon M. Brocklehurst wrote: > > > Sorry to be pedantic, but I'm not sure I would agree that DSSP is the > > "standard" program for determining hydrogen bonds. The model of a > > hydrogen bond it uses isn't all that great. It is suitable for doing what > > it was designed to do - that is, find enough of the hydrogen bonds in a > > protein so that secondary structural motifs can be identified reasonably well. > > It is not sensible to use it for other purposes because other software is > > available that does a better job. > > Such as...? > > > > > > > > > ___________________________________________________________________ > | | > | Dr. Bryan Finn | > | Department of Physical Chemistry 2 Tel: +46-46-222-8254 | > | Chemical Center Fax: +46-46-222-4543 | > | University of Lund | > | POB 124 | > | S-221 00 Lund Sweden e-mail: bryan@freja.fkem2.lth.se | > | WWW: http://www.fkem2.lth.se/personnel/bryan/finn.html | > |_________________________________________________________________| > > > > > From owner-structural-nmr@net.bio.net Sun Apr 28 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!surfnet.nl!swsbe6.switch.ch!scsing.switch.ch!elna.ethz.ch!usenet From: Reto Koradi Newsgroups: bionet.structural-nmr Subject: Re: Hydrogen bond definition Date: 29 Apr 1996 11:21:49 GMT Organization: Swiss Federal Institute of Technology (ETHZ) Lines: 27 Message-ID: <4m28od$f4j@elna.ethz.ch> References: <9604252146.AA05271@IRIS.lsc.pku.edu.cn> NNTP-Posting-Host: odin.ethz.ch Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12 (X11; I; SunOS 5.4 sun4d) X-URL: news:9604252146.AA05271@IRIS.lsc.pku.edu.cn qyx@IRIS.LSC.PKU.EDU.CN (Qu Youxin) wrote: >I wish to determine the backbone hydrogen bonds and then the >secondary structures in my small peptide NMR structures. However, >I cannot find standard values and the allowed deviation from >them for the distance between atoms NH and CO and for the angle >(N-H...O). Drs. Kabsch and Sander said there was no generally >correct H-bond definition (Biopolymers,1983, 22:2577-2637), >and I noticed there were several methods to determine hydrogen >bonds and secondary structures. Could anyone kindly tell me >the parameters for the above distance and angle? The formula suggested by Kabsch/Sander doesn't use separate limits for distances and angles, they use the following: 0.42 * 0.2 * (1/d(O,N) + 1/d(C,H) - 1/d(O,H) - 1/d(C,N)) * 332.0 < - 0.5 I only use this for determining the secondary structure. For making tables with hydrogen bonds, we use limits on the distance between H and O and on the angle between N-H and N-O. These limits can be given by the user, the default is 2.4 for the distance and 35 degrees for the angle. Check out http://www.mol.biol.ethz.ch/wuthrich/software/molmol/ for a program that can calculate all this (and much more...). Reto Koradi (kor@mol.biol.ethz.ch) From owner-structural-nmr@net.bio.net Sun Apr 28 23:00:00 1996 Path: biosci!rutgers!csn!news-1.csn.net!magnus.acs.ohio-state.edu!lerc.nasa.gov!purdue!ames!lll-winken.llnl.gov!fnnews.fnal.gov!unixhub!news.Stanford.EDU!usenet From: Zhan-yang Zhu Newsgroups: bionet.structural-nmr Subject: Re: Hydrogen bond definition Date: 29 Apr 1996 16:29:48 GMT Organization: Stanford University Lines: 40 Message-ID: <4m2qps$dfb@nntp.Stanford.EDU> References: <9604252146.AA05271@IRIS.lsc.pku.edu.cn> <4loomv$53b@nntp.Stanford.EDU> <3180C5D2.167EB0E7@bioch.ox.ac.uk> NNTP-Posting-Host: gallery.stanford.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1IS (X11; I; IRIX 5.3 IP22) X-URL: news:3180C5D2.167EB0E7@bioch.ox.ac.uk "Simon M. Brocklehurst" wrote: >Zhan-yang Zhu wrote: >> >> Yes, there is no standard defination of H-bond, especially the cutoffs for >> distances and angles. But the Kabsch & Sander's program (defination) for >> backbone hydrogen bonds is becoming "standard". It should be OK to use that >> program to determine the hydrogen bonds in your peptide. >> > Sorry to be pedantic, but I'm not sure I would agree that DSSP is the >"standard" program for determining hydrogen bonds. The model of a >hydrogen bond it uses isn't all that great. It is suitable for doing what >it was designed to do - that is, find enough of the hydrogen bonds in a >protein so that secondary structural motifs can be identified reasonably well. >It is not sensible to use it for other purposes because other software is >available that does a better job. > >_____________________________________________________________________________ >| >| ,_ o Simon M. Brocklehurst, >| / //\, Oxford Centre for Molecular Sciences, Department of Biochemistry, >| \>> | University of Oxford, Oxford, UK. >| \\, E-mail: smb@bioch.ox.ac.uk | WWW: http://www.ocms.ox.ac.uk/~smb/ >|____________________________________________________________________________ I am glad that you said "other software is available that does a better job" for defining H-bonds. I'd be interested in knowing how the comparison is made. Is there any refs? -- The following is my automatic signature: Zhan-Yang Zhu, Ph.D Department of Mathematics Stanford University Stanford, CA 94305-2125 Tel: (415) 723 2221 Fax: (415) 725 2040 From owner-structural-nmr@net.bio.net Mon Apr 29 23:00:00 1996 Path: biosci!MAILBOX.SYR.EDU!lpappala From: lpappala@MAILBOX.SYR.EDU (Lucia Pappalardo) Newsgroups: bionet.structural-nmr Subject: DNA/RNA chemical shifts Date: 30 Apr 1996 13:50:24 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear netters, I am looking for a recent table of chemical shifts for DNA and RNA molecules (1H, 13C and 15N). I will really appreciate any help or suggestion. Thank you very much Lucia Pappalardo From owner-structural-nmr@net.bio.net Tue Apr 30 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!news.kth.se!tybalt.admin.kth.se!celsiustech.se!seunet!news2.swip.net!inet-1.pharmacia.se!usenet From: Per Kraulis Newsgroups: bionet.structural-nmr,bionet.biophysics,bionet.software,bionet.xtallography Subject: Announce: ANSIG software Date: Tue, 30 Apr 1996 12:44:26 +0200 Organization: Pharmacia & Upjohn Lines: 42 Message-ID: <3185EF0A.167E@desmond.sto.pharmacia.se> NNTP-Posting-Host: sgikrpe.sto.se.pnu.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) Xref: biosci bionet.structural-nmr:1236 bionet.biophysics:1925 bionet.software:15353 bionet.xtallography:2538 Protein NMR software announcement: The ANSIG (Assignment of NMR Spectra by Interactive Graphics) program, release 3.3 is now available on the web. The entire documentation can be browsed, and the complete distribution can be fetched. There are two alternative sites (with identical content): http://nirvana.bioc.cam.ac.uk/ Follow the link "ANSIG v3.3". http://nmrsgi1.ncifcrf.gov/ansig/doc/ansig.html ANSIG is a program for inspection and assignment of NMR 2D/3D/4D homo- and heteronuclear spectra, mainly but not exclusively geared towards proteins. Literature references: P.J. Kraulis et al, Biochemistry (1994) v 33, pp 3515-3531, and P.J. Kraulis, J. Magn. Reson. (1989), v 24, pp 627-633. The ANSIG program is *not* in the public domain. A signed license is required. However, the program is free for academic institutions. The distribution contains source code, library files, documentation (in HTML format), and several matrix conversion programs. Two different example data sets are available from the FTP sites. The ANSIG program is written for the Silicon Graphics machines using GL and Fortran 77 (the first version of the program was released in 1989). It will compile on IRIX 5.2 and 5.3 systems, and hopefully also on 4.0.5 and 6.2 systems. I thank Dr. Ernest Laue and Dr. Andrew Raine (Cambridge, UK) and Dr. Andrew Byrd and Dr. Paul Dowling (ABL, NCI-FCRDC, USA) for making space available to set up the web sites. -- Per Kraulis, Ph.D. phone: +46 (8) 695 78 34 Pharmacia & Upjohn Inc fax: +46 (8) 695 40 82 Biopharmaceuticals R&D, N62:5 e-mail: krpx@sgikrpe.sto.pharmacia.se S-112 87 Stockholm or p.j.kraulis@bioc.cam.ac.uk SWEDEN --------------------------------------------------------------------- "Nothing is more difficult than simplicity." Unattributed. From owner-structural-nmr@net.bio.net Tue Apr 30 23:00:00 1996 Path: biosci!PONYEXPRESS.PRINCETON.EDU!ipelczer From: ipelczer@PONYEXPRESS.PRINCETON.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: sum-shields (fwd) Date: 1 May 1996 06:50:48 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 168 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Netters, I am sending this out again just in case; I have not received my copy of it from the net, so I assume it may have been lost somewhere. Should it be a duplicate for you, just discard it. Cheers, Istvan ---------- Forwarded message ---------- Date: 18 Apr 1996 10:42:05 -0700 From: Istvan Pelczer To: str-nmr@net.bio.net Subject: sum-shields Dear Netters, Just in case, let me post the summary of the responses I received about shields. I left out duplicate suggestions. THanks for all who replied! All the best, Istvan wwww,wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww Istvan Pelczer, Ph.D. Email: ipelczer@princeton.edu Senior NMR Spectroscopist Princeton University Department of Chemistry ph# (609) 258 2342 Frick Laboratory fax# (609) 258 6746 Washington Road Princeton, NJ 08544 ************************************** here it comes: From greig@resunix.ri.sickkids.on.caThu Apr 18 12:33:27 1996 Date: Sun, 14 Apr 1996 20:48:39 -0400 (EDT) From: David Iain Greig To: Istvan Pelczer Subject: Re: shield Oops, hit return there when I didn't mean to. In UC Boulder, Martin Ashley has a lovely metal shield on a 19" monitor that Varian provided him as a fix when they moved a 500 magnet 8 feet away. Works fine. Lewis Kay has a home-brew shield on his Sparc/Inova, I recall from my last trip to the NMR center on campus here at U of T. I'll ask Julie F-K. about it early this week. regards --D. ---- David Iain Greig, UNIX System Administrator Tel: (416) 813-5013 Research Computing Services Fax: (416) 813-7099 Hospital for Sick Children, 555 University Ave, Toronto, Ont. M5G 1X8 greig@sickkids.on.ca "Arbor plena allouatarum" >From phbolton@lily.chem.wesleyan.eduThu Apr 18 12:33:49 1996 Date: Sun, 14 Apr 1996 08:52:56 -0400 From: "Philip H. Bolton" To: Istvan Pelczer Subject: Re: shield This is what we did for one of the monitors: Dr. Barry Shapiro Wednesday, July 7, 1993 TAMU Newsletter 966 Elsinore Court Palo Alto, CA 94303 Dear Barry: We have recently installed a SUN computer and monitor near our spectrometer. Even though the 19" color monitor was placed outside of the 5 gauss line there was significant distortion of the images on the monitor. Attempts to remove the distortion by degaussing the monitor, moving the screen around and the like did not meet with success. Thus, we decided to construct a wood box with mu metal lining to shield the screen. Mu metal is a very effective magnetic shield and is quite flexible. The box is 25" tall, 26" deep and 14" wide. A 5" by 14" cutout in the back of the box was made to allow running in the power and connection cables. The box was lined with AD-MU-80 mu metal, thickness of 0.1 inch, obtained from Ad-vance Magnetics of Rochester, IN. A total of 18 feet, at $27.65/foot, of 15" wide strips of mu metal was required to cover the interior of the box at one layer of thickness. For ventilation purposes two louvered vents were added to each side of the box and for aesthetic purposes the box was covered with formica and some other trim. The box works quite well and there is no visible distortion of the images on the monitor. The ventilation provided by the simple vents appears to be adequate for the monitor. The monitor was degaussed after being placed in the box. The scientific support services at Wesleyan could construct similar boxes for other users if there is interest. Please contact Thomas Castelli at 203-344-8544 extension 2752. >From ruba@mol.biol.ethz.chThu Apr 18 12:34:11 1996 Date: Mon, 15 Apr 1996 09:14:17 +0200 From: Rudolf Baumann To: ipelczer@phoenix.Princeton.EDU Subject: Re: shield Hi Istvan yes we are using such a shield from a small swiss firm since more than a year on our 20" Sun-monitor in the 750 spectrometer room with great success. The shield is a bit expensive for this size but works great (2600 sFr), we could only see colored stripes before using it. The firm is: Systron Untere Bahnhofstrasse 25 CH-8034 Hinwil Tel: +41 1 937 53 50 Fax: +41 1 937 53 70 Hope I could help you Rudolf ----------------------------------------------------------------------------- Rudolf E. Baumann ruba@mol.biol.ethz.ch Institut fuer Molekularbiologie & Biophysik http://www.mol.biol.ethz.ch/ ETH Hoenggerberg (HPM G6) ,,, Tel. ++41 1 633 33 97 CH-8093 Zuerich/Switzerland (o o) Fax ++41 1 633 10 73 ----------------------------------oOO--(_)--OOo------------------------------ >From yves_aubin@Merck.ComThu Apr 18 12:41:33 1996 Date: 15 Apr 1996 07:02:36 -0700 From: Yves Aubin To: str-nmr@net.bio.net Subject: Re: shield Istvan wrote: >Dear Netters, >I would like to know what mangnetic shields are available for terminals. >Please, let me know your experience. Thanks, >Istvan > In Lewis Kay's laboratory in Toronto, we had two monitors that were severly perturbed by the magnetic field of a 500 and a 600 machines. The perturbation was such that the colors were changing from blue (lower right corner) to red (upper right corner) and the lack of focus made difficult the reading of the screen. I built two shields for less than 200 CDN$ each. The results are excellent in both cases: no color distortion and very good focus. I described the construction of the shield in the February issue of "The NMR newsletter" No. 449. If anyone have any questions, I'll be happy to answer them. Yves 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