From owner-structural-nmr@net.bio.net Sun Jun 01 23:00:00 1997 Path: biosci!CASPUR.IT!r.ragno From: r.ragno@CASPUR.IT (Gianluca Sbardella) Newsgroups: bionet.structural-nmr Subject: Substituted imidazole isomers Date: 2 Jun 1997 00:28:31 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 34 Sender: daemon@net.bio.net Distribution: world Message-ID: Reply-To: Gianluca Sbardella NNTP-Posting-Host: net.bio.net Dear colleagues, first of all my apologies if my question is trivial, but I'm an organic chemist, not a NMR expert. I arylated the nitrogen of 2-methyl-5-nitroimidazole with a 4-F-nitrobenzene. I obtained principally a compound, but I don't know exactly if it's N-phenyl-2-methyl-5-nitroimidazole or its 4-nitro- isomer (the two isomers deriving from the arylation of N1 or N3 of imidazole ring). Do you have any suggestion or advice? Thank you in advance, Gianluca "Merlino" Sbardella *************************************************************** * * * Dr. Gianluca Sbardella E-mail: r.ragno@caspur.it * * Dip. Studi Farmaceutici * * Universita' "La Sapienza" Phone: 39-6-49913814 * * P.le A. Moro, 5 Fax: 39-6-491491 * * 00185 Roma * * ITALY * * * * * * "Il destino e' quel che e', non c'e' scampo piu' per me.." * * (Gene Wilder, "Frankenstein Junior") * * * * "Destiny, destiny, no escaping that for me..." * * (Gene Wilder, "Young Frankenstein") * * * *************************************************************** From owner-structural-nmr@net.bio.net Sun Jun 01 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: "Alex Breeze" Newsgroups: bionet.structural-nmr Subject: Post-doc position available Date: 2 Jun 1997 14:01:36 +0100 Lines: 40 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5mug7g$mfv@mserv1.dl.ac.uk> Reply-To: breeze@apsg10.zeneca.com Original-To: str-nmr@dl.ac.uk Post-doctoral position in protein NMR ------------------------------------- Applications are invited for a two-year post-doctoral position within the protein NMR laboratory at Zeneca Pharmaceuticals (Alderley Park, Cheshire, UK). The successful applicant, who will have a recent PhD in biomacromolecular NMR, will contribute to a range of NMR protein structural projects in support of Zeneca's drug discovery research. Good computational skills and experience in protein expression, labelling and purification are desirable attributes for this position. The protein NMR laboratory is part of the Protein Structure-Function Group, which includes protein X-ray crystallography, protein and small-molecule modelling and protein function/enzymology. The NMR laboratory is well equipped, with a three-channel, pulsed-field gradient Varian Unity 600 MHz spectrometer and excellent computing facilities. Informal enquiries may be made to Dr Alex Breeze (E-mail: breeze@apsg10.zeneca.com). ---------------------------------------------------------------- This position will shortly be advertised in Nature. Formal applications must be submitted according to the procedure described in the Nature advertisement. ---------------------------------------------------------------- -- ------------------------------------------------------------------------ Alex Breeze breeze@apsg10.zeneca.com Protein Structure Lab (+44) 1625 514651 Zeneca Pharmaceuticals Cheshire SK10 4TG UK ------------------------------------------------------------------------ From owner-structural-nmr@net.bio.net Mon Jun 02 23:00:00 1997 Path: biosci!harl.hitachi.co.jp!tamura From: tamura@harl.hitachi.co.jp ("Mitsuru Tamura") Newsgroups: bionet.structural-nmr Subject: unsubscribe Date: 3 Jun 1997 15:58:18 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <199706032258.HAA00621@harlgw92.harl.hitachi.co.jp> NNTP-Posting-Host: net.bio.net unsubscribe From owner-structural-nmr@net.bio.net Mon Jun 02 23:00:00 1997 Path: biosci!beri.co.jp!hiroakih From: hiroakih@beri.co.jp (Hidekazu HIROAKI) Newsgroups: bionet.structural-nmr Subject: Best recommended M9 recipe (part2) Date: 2 Jun 1997 19:58:35 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 67 Sender: daemon@net.bio.net Distribution: world Message-ID: <199706030258.LAA12570@ns.beri.co.jp> NNTP-Posting-Host: net.bio.net Hi dear all, thank you very much for all replying to my previous question about "best recommended M9 recipes for NMR". After I got three replies from net, I have some requests from others to share the results. Herein, I like to re-post it for your convenience, just like as a "FAQ". I hope these will help. So, I myself imideately examined the recipe from JMB(1996) 264, 1101-1116. In essense, this recipe contains several vitamins. It was very strange, that OD600 after 4hr of IPTG induction is almost same with and without these additives in my case, and the rough estimation of protein production is no difference. Hoever, my colleague had a large improvement of OD600 with Fe, Mn and vitamines. Therefore, I assume the effect of vitamines depends on each host strain and each vector system. On the other hand, I found a good vitamine mixture on the GIBCO/BRL catalog, Basal Medium Eagle (BME) vitamine solution (100x liq.) #21040-050. This contains exactly same vitamines as JMB(1996)264, except additionally containing NaCl and d-inositol. I expect this is useful for M9, but I have not yet tested. Best regards, Hide >======================== >Hidekazu HIROAKI, Ph D, >Research Scientist, Dept of Str Biol, >Bimol. Eng. Res. Institute >======================== >1) From: "Lee, Ji Hyun" > >Hi, Hiroakih > >How does vitamin complex sound to you? Its ingredient is listed in >JMB(1996) 264, 1101-1116. My colleague has successfully prepared a 15N, >13C, 2H-labled sample using it. >Hope this helps. > > >**************************************** >2) From: mastone@indiana.edu (Martin J. Stone) > >We use a cocktail containing thiamine, biotin, and salts of a large number >of trace metals. The formula is published in Stone et. al Biochem J. (1995) >310, 605-614. This formula was used by several people in Peter Wright's >lab (for different proteins) when I was a postdoc there. I hope this helps. >Martin Stone > >**************************** >3) Roger Kautz > >Hiroaki, > >Yoroshiku. Rojaa Kautsude gozaimasu. > >We found a very simple and cheap way to get fantastic yeilds >from M9 media. Rather than trying nutrients one at a time, >we went to a local drugstore and got a bottle of multiple >vitamins, ground one up in 20 ml of water, and added about >200 ul of that to each 100 ml of media. Worked so well >we never looked back to optimize it. > >----------------------------------------- From owner-structural-nmr@net.bio.net Mon Jun 02 23:00:00 1997 Path: biosci!SHIELDING.USI.UTAH.EDU!facelli From: facelli@SHIELDING.USI.UTAH.EDU (Julio Facelli) Newsgroups: bionet.structural-nmr Subject: unsubscribe Date: 3 Jun 1997 09:32:44 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <199706031633.KAA02292@shielding.usi.utah.edu> NNTP-Posting-Host: net.bio.net unsubscribe ________________________________________________________________________________ Julio C. Facelli, PhD. Director Center for High Performance Computing (CHPC) 66 SSB, The University of Utah Salt Lake City, Utah 84112, USA. Phone (801)-581-7529 Fax (801)-585-5366 e-mail facelli@shielding.usi.utah.edu ________________________________________________________________________________ From owner-structural-nmr@net.bio.net Mon Jun 02 23:00:00 1997 Path: biosci!servaly.hobby.nl!wybo From: wybo@servaly.hobby.nl (Wybo Dekker) Newsgroups: bionet.structural-nmr Subject: Re: i'm back.................. Date: 3 Jun 1997 09:13:04 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: <199706031228.OAA03167@servaly.hobby.nl> References: <5n0h76$cmc@news2.cais.com> NNTP-Posting-Host: net.bio.net > From: scott > Date: 3 Jun 1997 07:30:46 GMT > > hello , i'm back... e-mail me let us know how your doing What a stupid mail! Not interesting at all! We're not your girl-friend. -- ===================Servalys Analytical Chemistry Services================= Wybo H. Dekker | Deilsedijk 60 | tel (31)345-652164 wybo@servaly.hobby.nl | 4158 CH Deil, The Netherlands | fax (31)345-652383 From owner-structural-nmr@net.bio.net Mon Jun 02 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.apfel.de!news-fra1.dfn.de!news-ber1.dfn.de!news-lei1.dfn.de!news.uni-leipzig.de!mlucom4.urz.uni-halle.de!mlubio6.biochemtech.uni-halle.de!mddal From: mddal@mlubio6.biochemtech.uni-halle.de (Susanne Drosihn) Newsgroups: bionet.structural-nmr Subject: Triad Date: 3 Jun 1997 08:14:07 GMT Organization: Martin-Luther-University, Dept. Biochem./Biotech. Lines: 11 Message-ID: <5n0jof$hlf@mlucom4.urz.uni-halle.de> NNTP-Posting-Host: mlubio6.biochemtech.uni-halle.de Hallo, is there anyone, who use the sybyl tool TRIAD? It's a modelling program to analyse NOESY data and get distance ranges for further conformational analyses. Susanne Drosihn PhD student institute of plant biochemistry Martin-Luther university Halle From owner-structural-nmr@net.bio.net Tue Jun 03 23:00:00 1997 Path: biosci!SHIELDING.USI.UTAH.EDU!facelli From: facelli@SHIELDING.USI.UTAH.EDU (Julio Facelli) Newsgroups: bionet.structural-nmr Subject: unsubscribe Date: 4 Jun 1997 07:10:16 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <199706041411.IAA03212@shielding.usi.utah.edu> NNTP-Posting-Host: net.bio.net unsubscribe ________________________________________________________________________________ Julio C. Facelli, PhD. Director Center for High Performance Computing (CHPC) 66 SSB, The University of Utah Salt Lake City, Utah 84112, USA. Phone (801)-581-7529 Fax (801)-585-5366 e-mail facelli@shielding.usi.utah.edu ________________________________________________________________________________ From owner-structural-nmr@net.bio.net Tue Jun 03 23:00:00 1997 Path: biosci!daresbury!uninett.no!nntp.uio.no!news.maxwell.syr.edu!news-was.dfn.de!news-fra1.dfn.de!news-ge.switch.ch!news-zh.switch.ch!rzunews.unizh.ch!newsadm From: Oliver Zerbe Newsgroups: bionet.structural-nmr Subject: subscribe Date: Wed, 04 Jun 1997 14:33:07 +0200 Organization: Department of Pharmacy, ETH Zuerich Lines: 9 Message-ID: <33956083.41C6@pharma.ethz.ch> NNTP-Posting-Host: 130.60.204.21 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 5.3 IP22) subscribe -- Dr. Oliver Zerbe Dept. Pharmazie ETH-Zuerich Tel.: 0041-1-257 60 81 Fax: 0041-1-262 15 80 e-mail:oliver.zerbe@pharma.ethz.ch WWW: http://www.pharma.ethz.ch/~oz From owner-structural-nmr@net.bio.net Tue Jun 03 23:00:00 1997 Path: biosci!LCPM.ENSIC.U-NANCY.FR!mariec From: mariec@LCPM.ENSIC.U-NANCY.FR ("Marie Christine Petit") Newsgroups: bionet.structural-nmr Subject: (none) Date: 4 Jun 1997 00:15:12 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <9706040850.ZM7506@lcpm.ensic.u-nancy.fr> NNTP-Posting-Host: net.bio.net subscribe -- ******************************************************************************** Marie Christine Petit LCPM - ENSIC - BP 451 1, rue Grandville 54001 Nancy - France tel: (33) 3 83 17 50 54 fax: (33) 3 83 17 99 77 ******************************************************************************** From owner-structural-nmr@net.bio.net Tue Jun 03 23:00:00 1997 Path: biosci!sfu.ca!rstorjoh From: rstorjoh@sfu.ca (Rasmus Storjohann) Newsgroups: bionet.structural-nmr Subject: BioNMR software for the PC Date: 3 Jun 1997 18:19:58 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 27 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <199706032258.HAA00621@harlgw92.harl.hitachi.co.jp> NNTP-Posting-Host: net.bio.net Dear netters, We want to do protein structure calculations based on multidimensional NMR data on a PC, and we would like some advice as to what software is available. We will most likely use the Linux versions of NMRPipe and X-plor for NMR data processing and structure calculations respectively. The question is: What would we use for assignment/constraint file generation? Currently we're using PIPP (made by Dan Garret) wich is working quite well, but there is no Linux version available. Any suggestions? Thanks, Rasmus __ Rasmus Storjohann / /\ Institute of Molecular Biology / / \ and Biochemistry / / /\ \ Simon Fraser University / / /\ \ \ Burnaby, British Columbia V5A 1S6 / /_/__\ \ \ e-mail: rstorjoh@sfu.ca /________\ \ \ Phone: (604) 436-5025 \___________\/ FAX: (604) 291-3765 From owner-structural-nmr@net.bio.net Wed Jun 04 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!newsfeed.internetmci.com!news.wolsi.com!news.aros.net!not-for-mail From: "DAVID G. JENSON" Newsgroups: bionet.structural-nmr Subject: MUST READ Date: 5 Jun 1997 05:25:04 GMT Organization: ArosNet Inc. Lines: 14 Message-ID: <01bc7179$5e576aa0$6e19adcf@default> NNTP-Posting-Host: dm3-13.slc.aros.net X-Newsreader: Microsoft Internet News 4.70.1155 I just found a web site that offers 7.9˘/min long distance and 14.9˘/min PhoneCards (with no hidden fees!) This is a great deal for those of us who make a lot of long distance calls at home and on the road. (They make Customized cards too!) They gave me a FREE phonecard just for visiting them. Click on: http://www.unikey.net D. Jenson From owner-structural-nmr@net.bio.net Wed Jun 04 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!newsfeed.internetmci.com!news.wolsi.com!news.aros.net!not-for-mail From: "DAVID G. JENSON" Newsgroups: bionet.structural-nmr Subject: MUST READ Date: 5 Jun 1997 05:24:35 GMT Organization: ArosNet Inc. Lines: 14 Message-ID: <01bc7179$4d0cd780$6e19adcf@default> NNTP-Posting-Host: dm3-13.slc.aros.net X-Newsreader: Microsoft Internet News 4.70.1155 I just found a web site that offers 7.9˘/min long distance and 14.9˘/min PhoneCards (with no hidden fees!) This is a great deal for those of us who make a lot of long distance calls at home and on the road. (They make Customized cards too!) They gave me a FREE phonecard just for visiting them. Click on: http://www.unikey.net D. Jenson From owner-structural-nmr@net.bio.net Thu Jun 05 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!feed1.news.erols.com!newsfeed.internetmci.com!in1.uu.net!204.253.184.11!news.shout.net!not-for-mail From: Gary Turner Newsgroups: bionet.structural-nmr Subject: Used NMR Equipment Newsletter Date: Thu, 05 Jun 1997 21:53:19 -0700 Organization: Spectral Data Services Lines: 38 Message-ID: <339797BF.6559@sdsnmr.com> NNTP-Posting-Host: poolb-141.shout.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (Win16; U) The Larmor Letter is a free on-line newsletter for announcements of used NMR, MRI, and EPR equipment for sale, wanted, or for trade. This newsletter is distributed freely to all concerned, and there is no charge to list your announcement. There are no restrictions as to whom may submit announcements. Types of equipment can be spectrometers, probes, consoles, amplifiers, "spare parts", or any other equipment used in MR. To submit an announcement for MR equipment available or wanted, send a brief description of the equipment to sdsnmr@sdsnmr.com. Include the name of a contact person, and his e-mail address and phone/fax number. Please note that The Larmor Letter will neither buy, sell, or trade equipment, or make recommendations. The Larmor Letter will not assume any liability for non-performance of any equipment listed herein. The Larmor Letter will not act as an agent in any transaction. Anyone wishing to receive this free newsletter should send a request to sdsnmr@sdsnmr.com. This newsletter can also be viewed at http://www.sdsnmr.com The website also has links to other pre-owned equipment sites. -- Gary ************************************************************************ Gary Turner Spectral Data Services, Inc. Contract NMR Data Acquisition 818 Pioneer Street Champaign, IL 61820 phone : (217)352-7084 fax : (217)352-9748 e-mail :sdsnmr@sdsnmr.com http://www.sdsnmr.com From owner-structural-nmr@net.bio.net Thu Jun 05 23:00:00 1997 Path: biosci!STUDENTS.WISC.EDU!esomsook From: esomsook@STUDENTS.WISC.EDU (Ekasith Somsook) Newsgroups: bionet.structural-nmr Subject: NOE build up curves of a small molecule Date: 5 Jun 1997 18:50:04 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: <3.0.32.19970605204956.00694620@students.wisc.edu> NNTP-Posting-Host: net.bio.net Hi there, I wonder if there is anyone has seen a paper about NOE build up curves of a small molecule like organic compounds. Thanks a lot. Best regards, Ekasith From owner-structural-nmr@net.bio.net Thu Jun 05 23:00:00 1997 Path: biosci!POUND.MED.UTORONTO.CA!vincent From: vincent@POUND.MED.UTORONTO.CA (Sebastien Vincent) Newsgroups: bionet.structural-nmr Subject: Re: NOE build up curves of a small molecule Date: 6 Jun 1997 05:05:02 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 24 Sender: daemon@net.bio.net Distribution: world Message-ID: <199706061205.IAA26609@pines.med.utoronto.ca> NNTP-Posting-Host: net.bio.net > From esomsook@students.wisc.edu Thu Jun 5 21:58:50 1997 > I wonder if there is anyone has seen a paper about NOE build up curves of > a small molecule like organic compounds. Thanks a lot. Ekasith, check the following papers by the Keeler and Shaka's groups on the GOESY: J. Stonehouse et al., J. Am. Chem. Soc., 116 (1994) 6037-6038 K. Stott et al., J. Am. Chem. Soc., 117 (1995) 4199-4200 K. Stott et al., J. Magn. Reson., 125 (1997) 302-324 Sebastien (::) (::) (::) (::) (::) (::) (::) (::) (::) (::) (::) (::) (::) (::) Sebastien Vincent University of Toronto vincent@redfield.med.utoronto.ca Department of Medical Genetics, Voice: ++(416) 978-0642 1, King's College Circle, Fax: ++(416) 978-6885 Toronto, Ontario, CANADA M5S 1A8 www: http://abragam.med.utoronto.ca/~vincent/ "Half the world population has never made a phone call." (M. Murphy, 12.96) From owner-structural-nmr@net.bio.net Sun Jun 08 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!vixen.cso.uiuc.edu!news.uoregon.edu!news.rediris.es!news.upc.es!lilith.uab.es!newsmgr From: Carles Borrego i Moré Newsgroups: bionet.structural-nmr Subject: Deconvolution spectra Date: Mon, 09 Jun 1997 15:00:15 +0000 Organization: Universitat de Girona Lines: 15 Distribution: inet Message-ID: <339C1A7F.1D59@xamba.udg.es> Reply-To: ieacbm@xamba.udg.es NNTP-Posting-Host: chlorobium.udg.es Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Macintosh; I; 68K) I'm currently working on photosynthetic pigments of green sulfur bacteria and I'm interested on resolving (deconvoluting) absorption spectra of several bacteriochlorophylls. Does anyone know how to do it? Does anyone know any software to perform deconvolution spectra? Please send e-mail to: ieacbm@xamba.udg.es Or post to bionet.biophysics Thanks Dr. Carlos Borrego Lab. Microbiology University of Girona, Spain From owner-structural-nmr@net.bio.net Mon Jun 09 23:00:00 1997 Path: biosci!rutgers!gatech!csulb.edu!hammer.uoregon.edu!vixen.cso.uiuc.edu!howland.erols.net!news.maxwell.syr.edu!news-was.dfn.de!news-fra1.dfn.de!news-ge.switch.ch!news-zh.switch.ch!elna.ethz.ch!not-for-mail From: Reto Koradi Newsgroups: bionet.structural-nmr Subject: Re: Visualising NMR structures - inertial displacements Date: Tue, 10 Jun 1997 13:54:07 +0200 Organization: Swiss Federal Institute of Technology (ETHZ) Lines: 23 Message-ID: <339D405F.11A4@mol.biol.ethz.ch> References: <339D21FF.41C6@icrf.icnet.uk> NNTP-Posting-Host: odin.ethz.ch Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; SunOS 5.4 sun4d) islam wrote: > We are using inertial displacement tensors to semi-quantatively > visualise NMR structures within the PDB. An example of this > display can be found at > > http://www.icnet.uk/bmm/people/suhail/2crd-0.html I'm not sure what inertial displacement tensors exactly are, must be the usual displacements, just that they have a direction? Are they calculated as the inertia tensor of the coordinates of one atom in all conformers of the bundle? Anyway, the right part of the image (displacement used as radius of spline) looks like the images that we frequently produce with MOLMOL (http://www.mol.biol.ethz.ch/wuthrich/software/molmol/). I've also seen similar representations from other programs, I think it was Insight. Drawing circles with the displacements as radius (left part) is also supported by MOLMOL, and could be done with older programs from our group (Billeter et al. 1985, J. Mol. Graphics, 3, 79-83, 97-98). -- Reto Koradi (kor@mol.biol.ethz.ch, http://www.mol.biol.ethz.ch/~kor) From owner-structural-nmr@net.bio.net Mon Jun 09 23:00:00 1997 Path: biosci!rutgers!gatech!www.nntp.primenet.com!nntp.primenet.com!newsfeed.nacamar.de!disgorge.news.demon.net!demon!dispatch.news.demon.net!demon!delos.dra.hmg.gb!server1.netnews.ja.net!server5.netnews.ja.net!server3.netnews.ja.net!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!charlie.lif.icnet.uk!not-for-mail From: islam Newsgroups: bionet.structural-nmr Subject: Visualising NMR structures - inertial displacements Date: Tue, 10 Jun 1997 02:44:31 -0700 Organization: Imperial Cancer Research Fund Message-ID: <339D21FF.41C6@icrf.icnet.uk> NNTP-Posting-Host: palm.lif.icnet.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) Lines: 25 We are using inertial displacement tensors to semi-quantatively visualise NMR structures within the PDB. An example of this display can be found at http://www.icnet.uk/bmm/people/suhail/2crd-0.html (the molecular graphics package is called PREPI and details located at http://www.icnet.uk/bmm/software) I have not seen this representation used else where (although it is very similar to thermal ellipsoidal representations) and was wondering if anyone knows if it (or something similar) has been used for visualising NMR structures - if so could you please let me have a reference. Thanks. ____________________________________________ Suhail A Islam Biomolecular Modelling Laboratory Imperial Cancer Research Fund, P.O. Box 123 44 Lincoln's Inn Fields, London WC2A 3PX Tel: (0171) 269 3380, Fax: (0171) 269 3479 email: islam@icrf.icnet.uk http://www.icnet.uk/bmm/ ____________________________________________ From owner-structural-nmr@net.bio.net Tue Jun 10 23:00:00 1997 Path: biosci!ukc.ac.uk!M.J.Howard From: M.J.Howard@ukc.ac.uk ("M.J.Howard") Newsgroups: bionet.structural-nmr Subject: Subscribe Date: 11 Jun 1997 08:07:17 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 5 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Subscribe From owner-structural-nmr@net.bio.net Tue Jun 10 23:00:00 1997 Path: biosci!sfu.ca!rstorjoh From: rstorjoh@sfu.ca (Rasmus Storjohann) Newsgroups: bionet.structural-nmr Subject: Req.: Help with phase cycling Date: 11 Jun 1997 06:38:24 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <339D21FF.41C6@icrf.icnet.uk> NNTP-Posting-Host: net.bio.net Reading papers on new pulse sequences, the phase cycle is not normally included. What is the most usefull strategy for working out the phase cycle? I'm currently struggeling with a 2D gradient-selected DQF-COSY (basic, but I have to start somewhere!) so phase cycling is not needed for coherence level selection. Thanks, Rasmus Storjohann From owner-structural-nmr@net.bio.net Tue Jun 10 23:00:00 1997 Path: biosci!sfu.ca!rstorjoh From: rstorjoh@sfu.ca (Rasmus Storjohann) Newsgroups: bionet.structural-nmr Subject: Phase cycling Date: 11 Jun 1997 06:31:10 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <339D405F.11A4@mol.biol.ethz.ch> NNTP-Posting-Host: net.bio.net Reading papers on new pulse sequences, the phase cycle is not normally included. What is the most usefull strategy for working out the phase cycle? I'm currently struggeling with a 2D gradient-selected DQF-COSY (basic, but I have to start somewhere!) so phase cycling is not needed for coherence level selection. Thanks, Rasmus __ Rasmus Storjohann / /\ Institute of Molecular Biology / / \ and Biochemistry / / /\ \ Simon Fraser University / / /\ \ \ Burnaby, British Columbia V5A 1S6 / /_/__\ \ \ e-mail: rstorjoh@sfu.ca /________\ \ \ Phone: (604) 291-5657 / 415-0575 \___________\/ FAX: (604) 291-3765 From owner-structural-nmr@net.bio.net Tue Jun 10 23:00:00 1997 Path: biosci!MOLE.BIO.CAM.AC.UK!mjh46 From: mjh46@MOLE.BIO.CAM.AC.UK (Mark J Howard) Newsgroups: bionet.structural-nmr Subject: unsubscribe Date: 11 Jun 1997 03:46:23 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 3 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net unsubscribe From owner-structural-nmr@net.bio.net Tue Jun 10 23:00:00 1997 Path: biosci!PHOENIX.PRINCETON.EDU!ipelczer From: ipelczer@PHOENIX.PRINCETON.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: Req.: Help with phase cycling Date: 11 Jun 1997 14:38:31 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 30 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <9706120605.ZM7259@pharma.ethz.ch> NNTP-Posting-Host: net.bio.net Dear Netters, James Keeler's excellent paper what Oliver mentioned was published as follows: J. Keeler; "Phase cycling procedures in multiple pulse NMR spectroscopy of liquids" in: "Multinuclear Magnetic Resonance in Liquids and Solids -- Chemical Applications" (Eds.: P. Granger and R. K. Harris) Kluwer, Dordrecht, The Netherlands, 1990 (sorry, no pp) You will find lots of useful recipes and hints in "Two-Dimensional NMR Spectroscopy" 2nd edition (Eds.: Croasmun & Carlson), VCH, 1994. among many others, including some of the first papers on this issue from Ernst's lab (Bodenhausen, Kogler, Ernst; JMR 58(1984)370, or Griesinger, Sorensen, Ernst; JMR 84(1989)14, for example). Cheers, Istvan wwww,wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww Istvan Pelczer, Ph.D. Email: ipelczer@princeton.edu Senior NMR Spectroscopist Princeton University Department of Chemistry, Frick Lab., ph# (609) 258 2342 Washington Road fax# (609) 258 6746 Princeton, NJ 08544, USA From owner-structural-nmr@net.bio.net Tue Jun 10 23:00:00 1997 Path: biosci!pharma.ethz.ch!oz From: oz@pharma.ethz.ch ("Oliver Zerbe") Newsgroups: bionet.structural-nmr Subject: Req.: Help with phase cycling Date: 11 Jun 1997 12:06:02 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 34 Sender: daemon@net.bio.net Distribution: world Message-ID: <9706120605.ZM7259@pharma.ethz.ch> NNTP-Posting-Host: net.bio.net hi Rasmus, I think everyone who has started writing phase cycles has gone through frustrating period in the beginning, at least that happened to me. But when you have a more detailed look at phase cycles they are usually rather simple and mostly contain 180 degree shifts for a certain pulse in the sequence together with a 180 degree shift of the receiver phase (assuming that the coherence level changes by +/- 1). There is an excellent description about it in the marvelous book of Cavanagh/Fairbrother/Palmer/Skelton (Protein NMR Spectroscopy, AP, pg. 203ff), which also contains a nice introduction to gradients. There is also a excellent review from James Keeler in Methods of Enzymology, Vol. 239, pg 145ff. I have a very instructive description of how to write phasecycles from Keeler, whch originally was an handout at an seminar course, maybe someone knows, whether it has appeared in literature. It includes examples of phasecycles for different sequences and explains them. If you can't get it, I'll post it for you. The order of the phasecycle depends on how severe the artifactws are, and may be different from instrument to instrument. Anyhow, make sure that the relative phases are right, sometimes you just have them 90 degree out of phase and nothing comes through. Usually the best way is to build up your phasecycle stepwise and watch the resulting spectrum. Best regards, Oliver -- Dr. Oliver Zerbe Dept. Pharmazie ETH-Zuerich Tel.: 0041-1-257 60 81 Fax: 0041-1-262 15 80 e-mail:oliver.zerbe@pharma.ethz.ch WWW: http://www.pharma.ethz.ch/~oz From owner-structural-nmr@net.bio.net Tue Jun 10 23:00:00 1997 Path: biosci!sfu.ca!rstorjoh From: rstorjoh@sfu.ca (Rasmus Storjohann) Newsgroups: bionet.structural-nmr Subject: PDB viewer for NMR structures (Linux or Windows) Date: 11 Jun 1997 10:38:23 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net This is for people who run X-plor under Linux and use it for NMR structure calculations. What software do you use for looking at an ensemble of NMR structures? Thanks, Rasmus __ Rasmus Storjohann / /\ Institute of Molecular Biology / / \ and Biochemistry / / /\ \ Simon Fraser University / / /\ \ \ Burnaby, British Columbia V5A 1S6 / /_/__\ \ \ e-mail: rstorjoh@sfu.ca /________\ \ \ Phone: (604) 291-5657 / 415-0575 \___________\/ FAX: (604) 291-3765 From owner-structural-nmr@net.bio.net Tue Jun 10 23:00:00 1997 Path: biosci!rutgers!gatech!news-out.communique.net!communique!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!News1.Ottawa.iSTAR.net!news.istar.net!cam-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!surfnet.nl!news.belnet.be!news.vub.ac.be!chaos.kulnet.kuleuven.ac.be!usenet From: Eveline Lescrinier Newsgroups: bionet.structural-nmr Subject: long range coupling Date: Wed, 11 Jun 1997 17:45:38 +0200 Organization: REGA-Institute, KULeuven Lines: 18 Message-ID: <339EC822.167E@s151h17.rega.kuleuven.ac.be> NNTP-Posting-Host: s151h17.rega.kuleuven.ac.be Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0S (X11; I; IRIX64 6.2 IP28) Hi there, does anyone can give a literature reference on 1'-3' lang range couplings in dna? Thanks a lot! Best regards Eveline ---- Eveline Lescrinier Laboratory of Medicinal Chemistry Rega Institute of Medical Research Katholieke Universiteit Leuven Ph: +32 16 33 73 79 Minderbroedersstraat 10, Fax: +32 16 33 73 40 B-3000 Leuven, Belgium E-mail: eveline@s151h17.rega.kuleuven.ac.be -- From owner-structural-nmr@net.bio.net Wed Jun 11 23:00:00 1997 Path: biosci!daresbury!is.bbsrc.ac.uk!news.ox.ac.uk!news From: Brian Marsden Newsgroups: bionet.structural-nmr Subject: Re: PDB viewer for NMR structures (Linux or Windows) Date: Thu, 12 Jun 1997 08:18:06 +0100 Organization: Biochemistry Dept. University of Oxford Lines: 13 Message-ID: <339FA2AD.167E@bioch.ox.ac.uk> References: NNTP-Posting-Host: nmrw.ocms.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (X11; I; IRIX 5.3 IP22) Rasmus Storjohann wrote: > > This is for people who run X-plor under Linux and use it for NMR > structure calculations. What software do you use for looking at an > ensemble of NMR structures? Molmol: http://www.mol.biol.ethz.ch/wuthrich/software/molmol/ -- --------------------------------------------------------------------- Brian Marsden marsden@bioch.ox.ac.uk Home:01865 552696 OCMS, Oxford http://users.ox.ac.uk/~hert0479 Work:01865 275720 --------------------------------------------------------------------- From owner-structural-nmr@net.bio.net Thu Jun 12 23:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news.ox.ac.uk!news From: "Mike Glazer" Newsgroups: alt.office.management,alt.online-service.america-online,alt.online-service.compuserve,bionet.structural-nmr,bionet.xtallography,biz.marketplace.international,easynet.announce,eunet.news,misc.jobs.fields.chemistry,misc.jobs.misc,sci.materials,sc Subject: PROMOTIONS REPRESENTATIVE Date: 13 Jun 1997 11:39:05 GMT Organization: Oxford University Lines: 29 Message-ID: <01bc77ee$a2730520$29f001a3@mike.physics.ox.ac.uk> NNTP-Posting-Host: mac5.physics.ox.ac.uk X-Newsreader: Microsoft Internet News 4.70.1155 Xref: biosci bionet.structural-nmr:2032 bionet.xtallography:3534 INTERNATIONAL UNION OF CRYSTALLOGRAPHY PROMOTIONS REPRESENTATIVE The International Union of Crystallography (IUCr) is seeking a dynamic person to promote its journals, books and new electronic publications. Candidates should have a proven track record in promotion and marketing. The post will involve improving advertising revenues, preparing promotional material, extending market penetration of current publications and marketing new electronic products. This would entail keeping abreast of developments in pricing, access routes and publications in electronic form. The promotions representative would also be expected to publicize IUCr events and raise the profile of crystallography and the IUCr in the scientific community. The successful applicant would be an employee of the Chester Office of the IUCr (although not necessarily resident in Chester) and would be appointed for a three-year period in the first instance with a view to subsequent permanent employment. Salary subject to negotiation. Applications, with full CV and names and addresses of two referees, should be sent to The Executive Secretary, International Union of Crystallography, 2 Abbey Square, Chester CH1 2HU. Closing date for applications: 31 July 1997. IUCr web address: http://www.iucr.ac.uk/welcome.html From owner-structural-nmr@net.bio.net Sat Jun 14 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!worldnet.att.net!newsadm From: "Michael Curtis" Newsgroups: bionet.molbio.proteins,bionet.software,bionet.structural-nmr,sci.techniques.mag-resonance Subject: Aurelia for Analyzing Protein Spectra Date: 15 Jun 1997 15:49:54 GMT Organization: AT&T WorldNet Services Lines: 7 Message-ID: <01bc79be$1ac81a80$c7cc74cf@908145029worldnet.att.net> NNTP-Posting-Host: 207.116.204.199 X-Newsreader: Microsoft Internet News 4.70.1155 Xref: biosci bionet.molbio.proteins:10970 bionet.software:18833 bionet.structural-nmr:2037 I'm looking for someone who is using the Aurelia package from Bruker to analyze protein NMR spectra. I am specifically interested in the amino acid J-coupling database. If anyone has created this database please let me know. Thanks for any information. Mike Curtis SUNY-HSC From owner-structural-nmr@net.bio.net Sat Jun 14 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!newsfeed.internetmci.com!news-was.dfn.de!news-fra1.dfn.de!news-ge.switch.ch!serra.unipi.it!sirio.cineca.it!carbon.foodsci.unibo.it!mauro From: "Mauro A. Cremonini" Newsgroups: bionet.structural-nmr Subject: Re: http://www.planetfun.com/videosex.htm Date: Mon, 16 Jun 1997 08:58:03 +0200 Organization: Cineca Lines: 14 Message-ID: References: <5ntbgm$eb3@nimitz.fibr.net> NNTP-Posting-Host: carbon.foodsci.unibo.it Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In-Reply-To: <5ntbgm$eb3@nimitz.fibr.net> YES! This newsgroup really needs to be moderated! ################# PLEASE NOTE CHANGE OF ADDRESS ############# ============================================ Mauro Andrea Cremonini, PhD Food Science and Technology Laboratory University of Bologna Via Ravennate 1020 - Cesena - Italy FAX:+39.547.382348 e-mail: mauro@carbon.foodsci.unibo.it 73 de IK4QIX ============================================ From owner-structural-nmr@net.bio.net Sun Jun 15 23:00:00 1997 Path: biosci!sbphrd.com!Lesley_K_Maclachlan From: Lesley_K_Maclachlan@sbphrd.com (Lesley K Maclachlan) Newsgroups: bionet.structural-nmr Subject: Post-doctoral position available Date: 16 Jun 1997 05:32:54 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 32 Sender: daemon@net.bio.net Distribution: world Message-ID: <9706161533.AB1365@pho903.sbphrd.com> NNTP-Posting-Host: net.bio.net Drug Research with a World leader SmithKline Beecham remains at the forefront of drug discovery with an impressive 2 million a day investment in research and development, and as part of our continued commitment to discovery technologies, we have concentrated our UK R&D at a new state-of-the-art facility in Harlow. We are currently looking for enthusiastic, experienced individuals with excellent teamworking and organisational skills to join our Department of Computational and Structural Sciences, a part of Medicinal Chemistry. Biomolecular NMR You will work in our NMR team configuring new Varian UnityPlus 600 and Bruker DRX 400 spectrometers, focusing on biostructural topics to support the discovery process. With a PhD in Biochemistry, Chemistry or Physics, you will be experienced in modern NMR spectroscopy and the technical aspects of biostructural NMR (including pulse programming and experiment implementation for both protein and oligonucleotide studies). Data processing, analysis and structure generation skills would be an advantage. This is a one year postdoctoral appointment with the possibility for renewal. Ref: CAS04. ________ These positions attract an excellent benefits package which includes bonus, pension, and medical plans, share-matching scheme, profit-related pay, flexible working hours, subsidised restaurant and superb sports and social facilities. Please send your full career details, quoting the appropriate reference on both the letter and envelope, to the UK Recruitment Manager, SmithKline Beecham Pharmaceuticals, PO Box 2489, London W1A 2YL. Closing date for applications: 7th July 1997. For more information on SmithKline Beecham, visit our web site at http://www.sb.com From owner-structural-nmr@net.bio.net Mon Jun 16 23:00:00 1997 Path: biosci!VIOL.ROCKEFELLER.EDU!roberto From: roberto@VIOL.ROCKEFELLER.EDU (Roberto Sanchez) Newsgroups: bionet.structural-nmr Subject: ** ANNOUNCING NEW VERSION OF MODELLER-4 Date: 17 Jun 1997 06:58:17 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 118 Sender: daemon@net.bio.net Distribution: world Message-ID: <199706171354.JAA09964@viol.rockefeller.edu> NNTP-Posting-Host: net.bio.net ANNOUNCEMENT A NEW VERSION OF MODELLER-4, A PROGRAM FOR COMPARATIVE PROTEIN STRUCTURE MODELING, IS RELEASED. Please see the README file below for how to get the program. New features include faster execution, a better manual, more robust modeling of protein structure. A Linux version is also available. Current users can use the same keyword as for version 3 (you can find it in your .cshrc file). There is no need to resend the licensing agreement. Best Wishes, Andrej Sali ------------------------------------------------------------------------------- A review of CASP2 that qualifies MODELLER: R.L. Dunbrack~Jr., D.L. Gerloff, M. Bower, X. Chen, O. Lichtarge & F.E. Cohen. Meeting review: the second meeting on the critical assessment of techniques for protein structure prediction (CASP2), Asilomar California, December 13-16, 1996. Folding & Design 2, R27-R42, 1997. ------------------------------------------------------------------------------- MODELLER PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS MODELLER 4, June 15, 1997 Copyright(c) 1989-1997 Andrej Sali All Rights Reserved Written by Andrej Sali, Roberto Sanchez, and Azat Badretdinov Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Andrej Sali, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA. Tel: +1-212-327-7550. Fax: +1-212-327-7540 (or 7974). E-mail: sali@rockvax.rockefeller.edu. URL: http://guitar.rockefeller.edu/. ** DESCRIPTION: MODELLER is most frequently used for homology or comparative modeling of protein three-dimensional structure: the user provides an alignment of a sequence to be modeled with known related structures and MODELLER will automatically calculate a full-atom model. More generally, MODELLER models protein 3D structure by satisfaction of spatial restraints (A. Sali & T.L. Blundell. J.Mol.Biol. 234, 779-815, 1993). In principle, the restraints can be derived from a number of different sources. These include homologous structures (comparative modeling), NMR experiments (NMR refinement), rules of secondary structure packing (combinatorial modeling), cross-linking experiments, fluorescence spectroscopy, image reconstruction in electron microscopy, site-directed mutagenesis, intuition, residue-residue and atom-atom potentials of mean force, etc. The output of MODELLER is a 3D structure of a protein that satisfies these restraints as well as possible. The optimization is carried out by the variable target function procedure employing methods of conjugate gradients and molecular dynamics with simulated annealing. MODELLER can also do several other tasks, including multiple comparison of protein sequences and/or structures, clustering, and searching of sequence databases. The program is described in a 150-page manual. MODELLER is written in Fortran and is meant to run on a UNIX system. ** DISTRIBUTION: MODELLER is available free of charge to academic non-profit institutions. First, please use the anonymous ftp account on guitar.rockefeller.edu (IP 129.85.13.198) to copy at least the following files from the pub/modeller directory to your computer: the license form (PostScript file academic-license.ps), the distribution file that contains the data files necessary to run MODELLER (modeller4-data.tar.Z), and an executable for each machine type that you want to use (described in file INSTALLATION). Next, please sign, and mail or fax the license form to Andrej Sali. You will then receive the key (MODELLER_KEY) that has to be assigned to the environment variable KEY_MODELLER4 in your login script (.cshrc). See file INSTALLATION for installation instructions. There is also a MODELLER home page on World Wide Web at URL http://guitar.rockefeller.edu that can be used to ftp the program and view the manual. A graphical interface to MODELLER is available as part of QUANTA, InsightII, and WEBLab, interactive molecular modeling programs with many tools for protein modeling and structural analysis. QUANTA, InsightII, and WEBLab facilitate preparation of input files for MODELLER (eg, alignment file) as well as an analysis of results (eg, an evaluation of the models). If you are interested in these programs, please contact Ms. Brenda Pfeiffer, Molecular Simulations Inc., 9685 Scranton Road, San Diego, CA 92121-3752, tel: +1-619-546-5319, fax: +1-619-458-0136, email: blp@msi.com. ** CONTENTS: src\ sources or executables for MODELLER; modlib\ libraries and data files for the programs; scripts\ script files used to compile and use MODELLER; doc\ MODELLER documentation; Makefile Makefile for compiling/installing MODELLER modules; modeller4.README this file; INSTALLATION how to install MODELLER; Install compilation and installation script relying on Makefile; examples\ examples; ------------------------------------------------------------------------------- Posted to: bionet.molec-model bionet.software bionet.structural-nmr bionet.xtallography bionet.software.source bionet.molbio.proteins bionet.biophysics bionet.announce ------------------------------------------------------------------------------- From owner-structural-nmr@net.bio.net Mon Jun 16 23:00:00 1997 Path: biosci!HEMEBASE.BIO.UCI.EDU!raman From: raman@HEMEBASE.BIO.UCI.EDU (CS Raman) Newsgroups: bionet.structural-nmr Subject: Re: Deconvolution spectra Date: 17 Jun 1997 10:38:24 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: <199706171739.RAA08514@hemebase.bio.uci.edu> References: <33a6990f.0@news.tpnet.pl> NNTP-Posting-Host: net.bio.net Carlos: {*} > bacteria and I'm interested on resolving (deconvoluting) absorption {*} > spectra of several bacteriochlorophylls. Does anyone know how to do it? {*} > Does anyone know any software to perform deconvolution spectra? {*} You may want to try LABCALC marketed by Galactic Inc., in New Hampshire. Cheers -raman ___________________________________________________________________ C.S.Raman Tel: (714) 824-4322 University of California Fax: (714) 824-8540 Dept. MB & B email: raman@indigo1.bio.uci.edu 3205 Bio Sci II Irvine, CA 92697-3900 ------------------------------------------------------------------- In a time of drastic change it is the learners who inherit the future. The learned usually find themselves equipped to live in a world that no longer exists. --Eric Hoffer ___________________________________________________________________ From owner-structural-nmr@net.bio.net Mon Jun 16 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!newsfeed.internetmci.com!howland.erols.net!news.apfel.de!news.rediris.es!news.upc.es!lilith.uab.es!newsmgr From: Carles Borrego i Moré Newsgroups: bionet.structural-nmr Subject: Deconvolution spectraHi, I received some information concerning powerful software to perform deconvolution and other spectral data manipulations. The programs are GRAMS32/GRAMS386 or PeakSolve from Galactic Industries (http://www. galactic.com) and PeakFit from Jandel Scientific (http://www.spss.com). Hope you like it! Deconvolution software Date: Tue, 17 Jun 1997 18:37:21 +0000 Organization: Universitat de Girona Lines: 10 Distribution: inet Message-ID: <33A6D961.4052@xamba.udg.es> Reply-To: ieacbm@xamba.udg.es NNTP-Posting-Host: chlorobium.udg.es Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Macintosh; I; 68K) Hi, I received some information concerning powerful software to perform deconvolution and other spectral data manipulations. The programs are GRAMS32/GRAMS386 or PeakSolve from Galactic Industries (http://www. galactic.com) and PeakFit from Jandel Scientific (http://www.spss.com). Hope you like it! Carlos From owner-structural-nmr@net.bio.net Mon Jun 16 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!newsfeed.internetmci.com!howland.erols.net!surfnet.nl!news-zh.switch.ch!elna.ethz.ch!torda From: Andrew.Torda@anu.edu.au (Andrew Torda) Newsgroups: bionet.molec-model,bionet.info-theory,bionet.molbio.proteins,bionet.structural-nmr,bionet.molec-model Subject: Post doc in Australia with Andrew Torda (biological calculation/simulation) Date: 17 Jun 1997 00:11:41 GMT Organization: Research School of Chemistry, Australian National University Lines: 60 Sender: Andrew.Torda@anu.edu.au Message-ID: <5o4knt$kvh$1@elna.ethz.ch> Reply-To: Andrew.Torda@anu.edu.au NNTP-Posting-Host: igc-chem.chem.ethz.ch Originator: torda@igc.chem Xref: biosci bionet.molec-model:1606 bionet.info-theory:5271 bionet.molbio.proteins:10981 bionet.structural-nmr:2040 POST DOCTORAL POSITION in Canberra, Australia with Andrew Torda. Each year, the Research School of Chemistry at the Australian National University has a series of post-doctoral fellowships awarded on a competitive basis. Applications for the current round will be taken until about July 31, 1997. Expected starting date January 1998. There are positions in several groups. This ad mainly describes my group. The research group of Andrew Torda is oriented towards biomolecular calculation and simulation. We are working in areas such as low-resolution (protein fold recognition) force fields, refinement of experimental structures using MD simulation, mixing knowledge-based force fields and experimental data. All the projects in the group involve coding - not just applications. It would be an advantage to have a reasonable knowledge of data structures and algorithms and programming experience in civilized languages (not fortran). Currently, possible projects would be centred around some new algorithms for aligning amino acid sequences to structures, based on the force fields we have developed. We are also looking at protein fold classification using topological and graph theory methods. Projects are negotiable. Salary: $40,963 - $43,834 per annum. Grants are provided towards travel and removal. Positions are initially for two years with a possible extension to a third year. There is a housing office to help find accommodation. The Research School of Chemistry is part of the Institute of Advanced Studies which runs special research schools, in parallel to the normal teaching schools, and without any undergraduate teaching duties. The university is in the centre of Canberra (the nation's capital). Given the research orientation of the school, there is a lively academic environment. We have close contacts with the school's other theoretical groups in statistical mechanics, quantum chemistry and chemical physics. From the point of view of experimental groups, we maintain close ties to the school's NMR, X-ray crystallography and molecular biology groups. Anyone interested in the Torda group should look at http://www.rsc.anu.edu.au/~torda That also contains a pointer to a page of recent publications. The official advertisement is at http://www.rsc.anu.edu.au/RSC/AcademicPositions/RSC_Academic_Positions.html and read under "Postdoctoral Fellowships". This contains instructions for how to apply. Andrew Torda From owner-structural-nmr@net.bio.net Mon Jun 16 23:00:00 1997 Path: biosci!biosci!not-for-mail From: Roberto Sanchez Newsgroups: bionet.molec-model,bionet.software,bionet.structural-nmr,bionet.xtallography,bionet.software.source,bionet.molbio.proteins,bionet.biophysics Subject: ** ANNOUNCING NEW VERSION OF MODELLER-4 Date: 16 Jun 1997 18:20:22 -0700 Organization: The Rockefeller University Lines: 121 Sender: daemon@net.bio.net Distribution: world Message-ID: <33A5E464.4487@rockvax.rockefeller.edu> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.molec-model:1607 bionet.software:18844 bionet.structural-nmr:2041 bionet.xtallography:3544 bionet.molbio.proteins:10983 bionet.biophysics:3145 ANNOUNCEMENT A NEW VERSION OF MODELLER-4, A PROGRAM FOR COMPARATIVE PROTEIN STRUCTURE MODELING, IS RELEASED. Please see the README file below for how to get the program. New features include faster execution, a better manual, more robust modeling of protein structure. A Linux version is also available. Current users can use the same keyword as for version 3 (you can find it in your .cshrc file). There is no need to resend the licensing agreement. Best Wishes, Andrej Sali ------------------------------------------------------------------------------- A review of CASP2 that qualifies MODELLER: R.L. Dunbrack~Jr., D.L. Gerloff, M. Bower, X. Chen, O. Lichtarge & F.E. Cohen. Meeting review: the second meeting on the critical assessment of techniques for protein structure prediction (CASP2), Asilomar California, December 13-16, 1996. Folding & Design 2, R27-R42, 1997. ------------------------------------------------------------------------------- MODELLER PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS MODELLER 4, June 15, 1997 Copyright(c) 1989-1997 Andrej Sali All Rights Reserved Written by Andrej Sali, Roberto Sanchez, and Azat Badretdinov Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Andrej Sali, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA. Tel: +1-212-327-7550. Fax: +1-212-327-7540 (or 7974). E-mail: sali@rockvax.rockefeller.edu. URL: http://guitar.rockefeller.edu/. ** DESCRIPTION: MODELLER is most frequently used for homology or comparative modeling of protein three-dimensional structure: the user provides an alignment of a sequence to be modeled with known related structures and MODELLER will automatically calculate a full-atom model. More generally, MODELLER models protein 3D structure by satisfaction of spatial restraints (A. Sali & T.L. Blundell. J.Mol.Biol. 234, 779-815, 1993). In principle, the restraints can be derived from a number of different sources. These include homologous structures (comparative modeling), NMR experiments (NMR refinement), rules of secondary structure packing (combinatorial modeling), cross-linking experiments, fluorescence spectroscopy, image reconstruction in electron microscopy, site-directed mutagenesis, intuition, residue-residue and atom-atom potentials of mean force, etc. The output of MODELLER is a 3D structure of a protein that satisfies these restraints as well as possible. The optimization is carried out by the variable target function procedure employing methods of conjugate gradients and molecular dynamics with simulated annealing. MODELLER can also do several other tasks, including multiple comparison of protein sequences and/or structures, clustering, and searching of sequence databases. The program is described in a 150-page manual. MODELLER is written in Fortran and is meant to run on a UNIX system. ** DISTRIBUTION: MODELLER is available free of charge to academic non-profit institutions. First, please use the anonymous ftp account on guitar.rockefeller.edu (IP 129.85.13.198) to copy at least the following files from the pub/modeller directory to your computer: the license form (PostScript file academic-license.ps), the distribution file that contains the data files necessary to run MODELLER (modeller4-data.tar.Z), and an executable for each machine type that you want to use (described in file INSTALLATION). Next, please sign, and mail or fax the license form to Andrej Sali. You will then receive the key (MODELLER_KEY) that has to be assigned to the environment variable KEY_MODELLER4 in your login script (.cshrc). See file INSTALLATION for installation instructions. There is also a MODELLER home page on World Wide Web at URL http://guitar.rockefeller.edu that can be used to ftp the program and view the manual. A graphical interface to MODELLER is available as part of QUANTA, InsightII, and WEBLab, interactive molecular modeling programs with many tools for protein modeling and structural analysis. QUANTA, InsightII, and WEBLab facilitate preparation of input files for MODELLER (eg, alignment file) as well as an analysis of results (eg, an evaluation of the models). If you are interested in these programs, please contact Ms. Brenda Pfeiffer, Molecular Simulations Inc., 9685 Scranton Road, San Diego, CA 92121-3752, tel: +1-619-546-5319, fax: +1-619-458-0136, email: blp@msi.com. ** CONTENTS: src\ sources or executables for MODELLER; modlib\ libraries and data files for the programs; scripts\ script files used to compile and use MODELLER; doc\ MODELLER documentation; Makefile Makefile for compiling/installing MODELLER modules; modeller4.README this file; INSTALLATION how to install MODELLER; Install compilation and installation script relying on Makefile; examples\ examples; ------------------------------------------------------------------------------- Posted to: bionet.molec-model bionet.software bionet.structural-nmr bionet.xtallography bionet.software.source bionet.molbio.proteins bionet.biophysics bionet.announce ------------------------------------------------------------------------------- From owner-structural-nmr@net.bio.net Mon Jun 16 23:00:00 1997 From: ewert Newsgroups: bionet.structural-nmr Subject: Re: Deconvolution spectra NNTP-Posting-Host: ppp12.plock.tpnet.pl Message-ID: <33a6990f.0@news.tpnet.pl> Date: 17 Jun 97 14:02:55 GMT Lines: 16 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.radio.cz!news.icm.edu.pl!news.tpnet.pl!ppp12.plock.tpnet.pl Carles Borrego i Moré zapisuje: > I'm currently working on photosynthetic pigments of green sulfur > bacteria and I'm interested on resolving (deconvoluting) absorption > spectra of several bacteriochlorophylls. Does anyone know how to do it? > Does anyone know any software to perform deconvolution spectra? > > Please send e-mail to: > ieacbm@xamba.udg.es > Or post to bionet.biophysics > > Thanks > > > Dr. Carlos Borrego > Lab. Microbiology > University of Girona, Spain From owner-structural-nmr@net.bio.net Tue Jun 17 23:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!vixen.cso.uiuc.edu!howland.erols.net!ix.netcom.com!tor-nn1.netcom.ca!news From: Jesse M Alexander Newsgroups: bionet.structural-nmr Subject: Low cost software for sale Date: Wed, 18 Jun 1997 16:35:37 GMT Organization: Netcom Canada Lines: 4 Message-ID: <5o92k4$9qj@tor-nn1-hb0.netcom.ca> NNTP-Posting-Host: trt-on10-31.netcom.ca X-NETCOM-Date: Wed Jun 18 12:33:08 PM EDT 1997 X-Newsreader: NETCOMplete/3.2 hey are you sick of paying tons of money for software? Then email me, ill give you the software before you pay becuase really ive got nothing to lose cuz i got the software free! Anarchy_@netcom.ca From owner-structural-nmr@net.bio.net Tue Jun 17 23:00:00 1997 Path: biosci!NETCOM.CA!Anarchy_ From: Anarchy_@NETCOM.CA (J Alexander) Newsgroups: bionet.structural-nmr Subject: Software Date: 18 Jun 1997 11:56:52 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <1.5.4.32.19970618185937.00668d70@netcom.ca> NNTP-Posting-Host: net.bio.net yeah the pricel list was in the ad i left anything else you want priced just email me like if you have a specific program you want. The reason the software is at a low cost is because its not registered with the company and i get the software for free. My prices are very fair, in fact most of my prices are less then half the cost you would pay in a store.To place an order just email me and i can do it over the phone,IRC or email.Phone and IRC are recommended. From owner-structural-nmr@net.bio.net Thu Jun 19 23:00:00 1997 Path: biosci!biosci!not-for-mail From: Tim Hubbard Newsgroups: bionet.biophysics,bionet.info-theory,bionet.molbio.proteins,bionet.molec-model,bionet.structural-nmr,bionet.xtallography Subject: FINAL CALL FOR APPLICANTS: FEBS advanced course: frontiers of protein Date: 20 Jun 1997 10:38:27 -0700 Organization: Sanger Centre Lines: 63 Sender: daemon@net.bio.net Distribution: world Message-ID: <33AA51D3.2781@sanger.ac.uk> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.biophysics:3171 bionet.info-theory:5280 bionet.molbio.proteins:11022 bionet.molec-model:1615 bionet.structural-nmr:2053 bionet.xtallography:3559 Final call for applications =========================== ** NOTE ** No applications received after 30th June 1997 will be considered. FEBS advanced course: frontiers of protein structure prediction 1997 http://predict.sanger.ac.uk/irbm-course97/ The course, which is being run for the second time (see http://predict.sanger.ac.uk/irbm-course95), is directed at young scientists with some experience and a strong interest in protein structure and structure prediction who wish to learn about the latest developments in the field. The aim of the workshop is to predict as much as possible about the structure of a number of proteins of biological interest, taking advantage of the most recent methodologies for fold recognition and ab initio prediction. The participants will be divided into working groups assisted by an instructor. Each group will be equipped with state of the art software and hardware (kindly provided by Silicon Graphics) and assigned the sequences of proteins whose structure has to be predicted. The predictions will be made public as a technical document and also available via World Wide Web. Suggestions for target proteins can also be submitted by non-participants via WWW (see accompanying email) Organizers: Tim Hubbard (Sanger Centre), Anna Tramontano (IRBM) Instructors: G. Barton (Oxford), T. Hubbard (Cambridge), D. Jones (London), M. Sippl (Salzburg), A. Valencia (Madrid), B. Rost (Heidelberg). Lecturers: A. Lesk (Cambridge), J. Moult (Rockville), A. Murzin (Cambridge) Dates: 7-20 October 1997 Deadline for applications: 30th June 1997. Registration fee 1200 DM (includes accomodation and meals) Location: IRBM (Istituto di Ricerche di Biologia Molecolare) Pomezia, Rome, Italy Further information and on-line application forms: http://predict.sanger.ac.uk/irbm-course97/ Prof. Anna Tramontano IRBM, Via Pontina Km 30.600 I-00040 Pomezia (Rome) Tel: +39 6 91093207 Fax: +39 6 91093654 email: tramontano@irbm.it Tim Hubbard, Anna Tramontano From owner-structural-nmr@net.bio.net Thu Jun 19 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: Tim Hubbard Newsgroups: bionet.structural-nmr Subject: FINAL CALL FOR APPLICANTS: FEBS advanced course: frontiers of protein structure prediction 1997 Date: 20 Jun 1997 10:31:54 +0100 Lines: 76 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5odima$9hh@mserv1.dl.ac.uk> X-Sender: th@netra.sanger.ac.uk Original-To: pdb-l@pdb.pdb.bnl.gov, bioforum@dl.ac.uk, bionews@dl.ac.uk, biophys@dl.ac.uk, bio-soft@dl.ac.uk, comp-bio@dl.ac.uk, methods@dl.ac.uk, molmodel@dl.ac.uk, proteins@dl.ac.uk, xtal-log@dl.ac.uk, str-nmr@dl.ac.uk Final call for applications =========================== ** NOTE ** No applications received after 30th June 1997 will be considered. FEBS advanced course: frontiers of protein structure prediction 1997 http://predict.sanger.ac.uk/irbm-course97/ The course, which is being run for the second time (see http://predict.sanger.ac.uk/irbm-course95), is directed at young scientists with some experience and a strong interest in protein structure and structure prediction who wish to learn about the latest developments in the field. The aim of the workshop is to predict as much as possible about the structure of a number of proteins of biological interest, taking advantage of the most recent methodologies for fold recognition and ab initio prediction. The participants will be divided into working groups assisted by an instructor. Each group will be equipped with state of the art software and hardware (kindly provided by Silicon Graphics) and assigned the sequences of proteins whose structure has to be predicted. The predictions will be made public as a technical document and also available via World Wide Web. Suggestions for target proteins can also be submitted by non-participants via WWW (see accompanying email) Organizers: Tim Hubbard (Sanger Centre), Anna Tramontano (IRBM) Instructors: G. Barton (Oxford), T. Hubbard (Cambridge), D. Jones (London), M. Sippl (Salzburg), A. Valencia (Madrid), B. Rost (Heidelberg). Lecturers: A. Lesk (Cambridge), J. Moult (Rockville), A. Murzin (Cambridge) Dates: 7-20 October 1997 Deadline for applications: 30th June 1997. Registration fee 1200 DM (includes accomodation and meals) Location: IRBM (Istituto di Ricerche di Biologia Molecolare) Pomezia, Rome, Italy Further information and on-line application forms: http://predict.sanger.ac.uk/irbm-course97/ Prof. Anna Tramontano IRBM, Via Pontina Km 30.600 I-00040 Pomezia (Rome) Tel: +39 6 91093207 Fax: +39 6 91093654 email: tramontano@irbm.it Tim Hubbard, Anna Tramontano ------------------------------------------------------------------------- Dr Tim Hubbard email: th@sanger.ac.uk Sanger Centre Tel (direct): +44 1223 494983 Wellcome Trust Genome Campus Tel (switch): +44 1223 834244 Hinxton Fax: +44 1223 494919 Cambridgeshire. CB10 1SA. URL: http://www.sanger.ac.uk/ ------------------------------------------------------------------------- ------------------------------------------------------------------------- Dr Tim Hubbard email: th@sanger.ac.uk Sanger Centre Tel (direct): +44 1223 494983 Wellcome Trust Genome Campus Tel (switch): +44 1223 834244 Hinxton Fax: +44 1223 494919 Cambridgeshire. CB10 1SA. URL: http://www.sanger.ac.uk/ ------------------------------------------------------------------------- From owner-structural-nmr@net.bio.net Thu Jun 19 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: Tim Hubbard Newsgroups: bionet.structural-nmr Subject: FINAL CALL FOR TARGETS: have you a protein to predict? Date: 20 Jun 1997 10:31:58 +0100 Lines: 41 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5odime$9h8@mserv1.dl.ac.uk> X-Sender: th@netra.sanger.ac.uk Original-To: pdb-l@pdb.pdb.bnl.gov, bioforum@dl.ac.uk, bionews@dl.ac.uk, biophys@dl.ac.uk, bio-soft@dl.ac.uk, comp-bio@dl.ac.uk, methods@dl.ac.uk, molmodel@dl.ac.uk, proteins@dl.ac.uk, xtal-log@dl.ac.uk, str-nmr@dl.ac.uk Final call for prediction targets ================================= ** NOTE ** No targets received after 30th June 1997 will be considered for prediction during this course. The previous mail to this list announced the FEBS advanced course: frontiers of protein structure prediction 1997. The aim of the workshop is to predict as much as possible about the structure of a number of proteins of biological interest, taking advantage of the most recent methodologies for fold recognition and ab initio prediction. If you are interested in a structure prediction being made on a protein for which there is no sign of an experimental structure and does not appear to be homologous to any known structure, please consider submitting it as a target for this course. For further information and on-line target submission forms see: http://predict.sanger.ac.uk/irbm-course97/ For the automatic analysis carried out on the 113 targets received for the 1995 course and the predictions made for 17 of them see: http://predict.sanger.ac.uk/irbm-course95/ Tim Hubbard, (Sanger Centre) Anna Tramontano, (IRBM) ------------------------------------------------------------------------- Dr Tim Hubbard email: th@sanger.ac.uk Sanger Centre Tel (direct): +44 1223 494983 Wellcome Trust Genome Campus Tel (switch): +44 1223 834244 Hinxton Fax: +44 1223 494919 Cambridgeshire. CB10 1SA. URL: http://www.sanger.ac.uk/ ------------------------------------------------------------------------- From owner-structural-nmr@net.bio.net Thu Jun 19 23:00:00 1997 Path: biosci!biosci!not-for-mail From: Tim Hubbard Newsgroups: bionet.biophysics,bionet.info-theory,bionet.molbio.proteins,bionet.molec-model,bionet.structural-nmr,bionet.xtallography Subject: FINAL CALL FOR TARGETS: have you a protein to predict? Date: 20 Jun 1997 10:38:43 -0700 Organization: Sanger Centre Lines: 36 Sender: daemon@net.bio.net Distribution: world Message-ID: <33AA5305.446B@sanger.ac.uk> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.biophysics:3172 bionet.info-theory:5281 bionet.molbio.proteins:11023 bionet.molec-model:1616 bionet.structural-nmr:2054 bionet.xtallography:3560 Final call for prediction targets ================================= ** NOTE ** No targets received after 30th June 1997 will be considered for prediction during this course. The previous mail to this list announced the FEBS advanced course: frontiers of protein structure prediction 1997. The aim of the workshop is to predict as much as possible about the structure of a number of proteins of biological interest, taking advantage of the most recent methodologies for fold recognition and ab initio prediction. If you are interested in a structure prediction being made on a protein for which there is no sign of an experimental structure and does not appear to be homologous to any known structure, please consider submitting it as a target for this course. For further information and on-line target submission forms see: http://predict.sanger.ac.uk/irbm-course97/ For the automatic analysis carried out on the 113 targets received for the 1995 course and the predictions made for 17 of them see: http://predict.sanger.ac.uk/irbm-course95/ Tim Hubbard, (Sanger Centre) Anna Tramontano, (IRBM) From owner-structural-nmr@net.bio.net Fri Jun 20 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!news.maxwell.syr.edu!news.cis.ohio-state.edu!nntp.sei.cmu.edu!bb3.andrew.cmu.edu!andrew.cmu.edu!lgb+ From: Laura G Barrientos Newsgroups: bionet.structural-nmr Subject: ANSIG Date: Sat, 21 Jun 1997 12:11:55 -0400 Organization: Chemistry, Carnegie Mellon, Pittsburgh, PA Lines: 9 Message-ID: NNTP-Posting-Host: po9.andrew.cmu.edu Hi there, Does anyone know where can I find the program ANSIG? Can I download it from the internet? Also, how useful is this program for 2D NMR data of a 10K protein? How is the program when compared to the automatic assignment mode in Felix95? Have a nice weekend, Laura. From owner-structural-nmr@net.bio.net Fri Jun 20 23:00:00 1997 Path: biosci!HEMEBASE.BIO.UCI.EDU!raman From: raman@HEMEBASE.BIO.UCI.EDU (CS Raman) Newsgroups: bionet.structural-nmr Subject: Re: ANSIG Date: 21 Jun 1997 10:17:31 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 28 Sender: daemon@net.bio.net Distribution: world Message-ID: <199706211714.RAA24622@indigo4.bio.uci.edu> References: NNTP-Posting-Host: net.bio.net Laura: {*} Does anyone know where can I find the program ANSIG? Can I download it {*} from the internet? Please take a look at the follwing web site: nmrsgi1.ncifcrf.gov/ansig/doc/ansig.html#address It lists all the details for obtaining, installing and successfully configuring ANSIG to run on your platform. Per Kraulis, the author of ANSIG can be reached at: krpx@sgikrpe.sto.pharmacia.se Cheers -raman ___________________________________________________________________ C.S.Raman Tel: (714) 824-4322 University of California Fax: (714) 824-8540 Dept. MB & B email: raman@indigo1.bio.uci.edu 3205 Bio Sci II Irvine, CA 92697-3900 ------------------------------------------------------------------- In a time of drastic change it is the learners who inherit the future. The learned usually find themselves equipped to live in a world that no longer exists. --Eric Hoffer ___________________________________________________________________ From owner-structural-nmr@net.bio.net Sat Jun 21 23:00:00 1997 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.structural-nmr Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 22 Jun 1997 02:00:06 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199706220900.CAA26406@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. From owner-structural-nmr@net.bio.net Sat Jun 21 23:00:00 1997 Path: biosci!INTREPID.CHM.JHU.EDU!rlk From: rlk@INTREPID.CHM.JHU.EDU ("rlk") Newsgroups: bionet.structural-nmr Subject: Chemical shift to electron density calculations Date: 22 Jun 1997 12:05:56 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 25 Sender: daemon@net.bio.net Distribution: world Message-ID: <9706221509.ZM29209@intrepid.chm.jhu.edu> NNTP-Posting-Host: net.bio.net I've been toying with the idea of taking the nitrogen and carbon chemical shifts of an FMN cofactor in a protein I'm studying and calculating the electron densities across the whole molecule. Could someone with experience in this type of thing suggest a good program for it? I seem to find lots of programs that claim to predict chemical shifts but none that mention moving in the other direction. Does anyone have a feel for how good such predictions are? How would one judge such a thing (besides back-calculating what the predicted chemical shifts are, which seems like a circular argument to me.) thanks, -- -ron 'if I can't dance, I don't want to be a part of your revolution' Emma Goldman From owner-structural-nmr@net.bio.net Sat Jun 21 23:00:00 1997 Path: biosci!INTREPID.CHM.JHU.EDU!rlk From: rlk@INTREPID.CHM.JHU.EDU ("rlk") Newsgroups: bionet.structural-nmr Subject: Re: !!!PSYCHIC PREDICTIONS/TRY IT FREE - An idea to stop this. Date: 22 Jun 1997 12:00:18 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: <9706221503.ZM29203@intrepid.chm.jhu.edu> NNTP-Posting-Host: net.bio.net I have an idea, but I don't know if it will work. Evidently this list is getting on to more and more group mailing lists, and no-one seems to be willing to take the time to moderate it. Does anyone think it will work if we just slightly change the name of the list? Like maybe to nmr-str or something. It will at least give us some time until the new address starts to show up on bulk mailer address lists. Then maybe we could change it again. I don't think it would be THAT much trouble for the people that are really interested in this list. -- -ron 'if I can't dance, I don't want to be a part of your revolution' Emma Goldman From owner-structural-nmr@net.bio.net Sun Jun 22 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.tamu.edu!news.utdallas.edu!nrchh45.rich.nt.com!bcarh189.bnr.ca!nott!nrccsb2.di.nrc.ca!not-for-mail From: Yi Zhu Newsgroups: bionet.structural-nmr Subject: Postdoctoral positions at BRI Date: Mon, 23 Jun 1997 09:45:17 -0400 Organization: biotechnology Research Institute Lines: 48 Message-ID: <33AE7DED.446B@bri.nrc.ca> NNTP-Posting-Host: kringle.bri.nrc.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii; name="fengni_ad.061997" Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.3 IP22) CC: fengni@bri.nrc.ca Content-Disposition: inline; filename="fengni_ad.061997" Subject: Postdoctoral positions at BRI (fwd) Please help me display this ad in the net sites. Thanks. Feng ------------------------------------------------------------------------------- STRUCTURAL STUDIES OF PROTEIN-PEPTIDE COMPLEXES BY ULTRA-HIGH-FIELD (800 MHZ) NMR Our NMR group has postdoctoral positions to determine the structures of protein- peptide complexes by use of ultra-high-field (800 MHz) NMR spectroscopy. You may work on either one of the following projects: (1) complexes of the small GTPase Cdc42 (19 kD) with natural and designed peptides; (2) complexes of the complement protein C5a or the parathyroid hormone with receptor fragments; (3) human angiogenin in complex with inhibitors. All the proteins are expressed and labelled with the 15N and/or 13C isotopes. The projects will have significant access to our new 800 MHz NMR spectrometer which has become operational and produces NMR spectra with significantly increased sensitivity. Candidates must have a recent Ph.D. (within the last 5 years) in chemistry, biochemistry or a related field and have demonstrated abilities to carry out and publish original research of high quality. Ideal candidates should have experience in the determination of the three-dimensional structures of proteins by NMR or in the conformational analysis of bioactive peptides. Experience in protein expression and purification is an important asset. Salaries are in the range of $24,000-$27,000, but can go up to $35,000 commensurate with experience and with your project responsibilities. Interested candidates should address their inquiries to: Feng Ni, Ph.D. Head of Biomolecular NMR Biotechnology Research Institute 6100 Royalmount Avenue Montreal, Quebec, H4P 2R2, Canada phone: (514)-496-6729; fax: (514)-496-5143 e_mail: fengni@bri.nrc.ca Applications will be accepted until the end of August, 1997. The positions are available immediately, but can be taken up as late as the begining of January, 1998. I thank all the applicants for their interests, but we may contact only those being considered if there are many applications. ------------------------------------------------------------------------------- From owner-structural-nmr@net.bio.net Sun Jun 22 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!news.bbnplanet.com!xfer.kren.nm.kr!news.snu.ac.kr!plaza.snu.ac.kr!newera From: newera@plaza.snu.ac.kr () Newsgroups: bionet.structural-nmr Subject: Possible to Backbone Assign a Dimer with Wutrich's Method? Date: 23 Jun 1997 05:19:09 GMT Organization: Seoul National University, Republic of Korea Lines: 29 Message-ID: <5ol10d$afl$1@news.kren.nm.kr> NNTP-Posting-Host: plaza.snu.ac.kr X-Newsreader: TIN [version 1.2 PL2] I am trying to sequential-assign a 1H sample and a 15N-full labeled sample of 55-amino acid dimeric protein (mw 6500 X 2 = 13000) which has no X-ray structure. 1. Are 1H-1H 2D's and 15N-edited 3D's enough to sequential-assign 55 amino-acid dimeric protein (mw 6500 X 2 = 13000)? 2. Could you tell me any paper where they successfully back-bone assign around 55 amono acid dimeric protein using 15N-full labeled protein? I expect that inter, intra and comonomer NOE of dimer will make peak assigning very difficult and that 15N- signle or double half fielter will not be helpful so much; so that triple resonance experiments might be a must using a 13C-15N labeled sample where backbone assigning does not require NOE spectrum. Any comment will be appreciated regarding this experiement. E-mail me, please. I will collect all the replies and post them back to you and this news group. Thank you very much. -- Lee, Ji Hyun newera@plaza.snu.ac.kr Laboratory of Physical Pharmacy(Prof. Lee, Bong Jin) College of Pharmacy Seoul National University Shinlim-Dong, Kwanak-Gu Seoul 151-742, Korea. Tel : 82-2-880-7869 Fax : 82-2-872-3632 From owner-structural-nmr@net.bio.net Mon Jun 23 23:00:00 1997 Path: biosci!CHEM.UNR.EDU!lcary From: lcary@CHEM.UNR.EDU (lew cary) Newsgroups: bionet.structural-nmr Subject: Re: Newsgroup moderation Date: 24 Jun 1997 13:19:18 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 5 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <199706241653.QAA10267@hemebase.bio.uci.edu> NNTP-Posting-Host: net.bio.net A quick suggestion: if this group had a list of 'approved' posters, then all spam would be automatically rejected. Cheers, Lew PS: I use the 'd' key alot and I am not yet to the point where I feel the need for a moderator. From owner-structural-nmr@net.bio.net Mon Jun 23 23:00:00 1997 Path: biosci!HEMEBASE.BIO.UCI.EDU!raman From: raman@HEMEBASE.BIO.UCI.EDU (CS Raman) Newsgroups: bionet.structural-nmr Subject: Newsgroup moderation Date: 24 Jun 1997 09:52:38 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: <199706241653.QAA10267@hemebase.bio.uci.edu> NNTP-Posting-Host: net.bio.net It appears that the delay in changing the status of STR-NMR to "moderated" is at BIOSCI. I have been bombarding them with emails to convert us over to the new status, but, am not getting through. There is also change in personnel at BIOSCI at the administrative level. So, if everyone could bear with me, we will soon be rid of all the junk that comes through. thanks very much for your patience. Cheers -raman ___________________________________________________________________ C.S.Raman Tel: (714) 824-4322 University of California Fax: (714) 824-8540 Dept. MB & B email: raman@indigo1.bio.uci.edu 3205 Bio Sci II Irvine, CA 92697-3900 ------------------------------------------------------------------- In a time of drastic change it is the learners who inherit the future. The learned usually find themselves equipped to live in a world that no longer exists. --Eric Hoffer ___________________________________________________________________ From owner-structural-nmr@net.bio.net Mon Jun 23 23:00:00 1997 Path: biosci!rutgers!gatech!news-out.communique.net!communique!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!europa.clark.net!dispatch.news.demon.net!demon!delos.dra.hmg.gb!server2.netnews.ja.net!news.qub.ac.uk!not-for-mail From: Andrew Wallace Newsgroups: bionet.structural-nmr Subject: Re: !!!PSYCHIC PREDICTIONS/TRY IT FREE - An idea to stop this. Date: Tue, 24 Jun 1997 10:54:42 +0100 Organization: Queens University Belfast Message-ID: <33AF995F.1C07@qub.ac.uk.see.signature> References: <9706221503.ZM29203@intrepid.chm.jhu.edu> <1997Jun23.232122.47546@yogi.urz.unibas.ch> Reply-To: a.wallace@qub.ac.uk.see.signature NNTP-Posting-Host: awall.bc.qub.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; PPC) Lines: 28 > >I have an idea, but I don't know if it will work. > > >Evidently this list is getting on to more and more group > >mailing lists, and no-one seems to be willing > >to take the time to moderate it. > > >Does anyone think it will work if we just slightly change the > >name of the list? Like maybe to nmr-str or something. > This might work, but the name would probably have to be changed every week or so. The resulting confusion and extra workload for the BioSci support staff (as if they hadn't enough to do already!) would not be justified. The only answer is for someone to moderate the group. I do this for the bionet.molecules.repertoires newsgroup and it is only a few minutes of very easy work each morning. Any volunteers? Andrew -- - note antispam feature in return address. My real address is: ================================================================== Andrew Wallace,Ph.D., Queens University Belfast, N. Ireland (UK) a.wallace@qub.ac.uk http://web.qub.ac.uk/bb/awpage/wallace.html ================================================================== From owner-structural-nmr@net.bio.net Mon Jun 23 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!newsfeed.nacamar.de!blackbush.xlink.net!news-ge.switch.ch!news-zh.switch.ch!ubaclu.unibas.ch!ubaclu.unibas.ch!nntp Newsgroups: bionet.structural-nmr Subject: Re: !!!PSYCHIC PREDICTIONS/TRY IT FREE - An idea to stop this. Message-ID: <1997Jun23.232122.47546@yogi.urz.unibas.ch> From: Andrei Alexandrescu Date: 23 Jun 97 23:21:22 MET References: <9706221503.ZM29203@intrepid.chm.jhu.edu> Organization: Biozentrum, U-Basel Nntp-Posting-Host: secsy.bioz.unibas.ch X-Mailer: Mozilla 1.1N (Macintosh; I; PPC) MIME-Version: 1.0 X-URL: news:9706221503.ZM29203@intrepid.chm.jhu.edu Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Lines: 22 >I have an idea, but I don't know if it will work. >Evidently this list is getting on to more and more group >mailing lists, and no-one seems to be willing >to take the time to moderate it. >Does anyone think it will work if we just slightly change the >name of the list? Like maybe to nmr-str or something. Why would people send less junk mail to "nmr-str" than "bionet.structural-nmr" Even better names: 1) "poor scientists with no money" 2) "free evaluation of your magnetic spin aura - send money now" 3) "humorless non-crystallographers" From owner-structural-nmr@net.bio.net Tue Jun 24 23:00:00 1997 Path: biosci!agate!spool.mu.edu!sol.net!spool.mu.edu!newsspool.sol.net!howland.erols.net!EU.net!news.eunet.fi!NewsWatcher!user From: piero.pollesello@rd.orion.orion.mailnet.fi (Piero Pollesello) Newsgroups: bionet.structural-nmr Subject: 15N-14N coupling Date: Wed, 25 Jun 1997 06:53:47 +0200 Organization: NMR-lab, Drug Discovery, R&D, Orion-Pharma, FIN Lines: 26 Message-ID: NNTP-Posting-Host: protein.orion.fi I wish to acquire a 15N-NMR spectrum of a non-labelled organic molecule (500 Dalton) which can be dissolved up to 50-100 mM in DMSO. In the molecule there are several nitrogen atoms (e.g. -N=, -CN, -N-N=, =NH, etc.). When I acquire 64 scans in inverse gated mode, with a repetition delay of 60 sec and pulse corresponding to a flip angle of 45°, I see very well the 2 peaks of the protonated nitrogens which do not have a vicinal second nitrogen. In the F1 projection of the spectrum of a PFG1H-15N HMBC, 4 signals out of 8 are visible (2 of which come from the protonated nitrogens). I start to believe that the proximity of 14N to 15N may cause trouble to the 15N signals: could someone tell me if it make sense? Are there any suggestions? Thanks a lot Piero Pollesello Orion, FIN-02101 Espoo, Finland -- Piero Pollesello, Ph.D., dos NMR-lab, Drug-Discovery, R&D, Orion-Pharma, Orion-Corp. FIN-02101 Espoo, Finland From owner-structural-nmr@net.bio.net Sat Jun 28 23:00:00 1997 Path: biosci!UGA.CC.UGA.EDU!JLEE From: JLEE@UGA.CC.UGA.EDU Newsgroups: bionet.structural-nmr Subject: unsubscribe Date: 28 Jun 1997 19:10:01 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: <970628.220950.EDT.JLEE@UGA.CC.UGA.EDU> NNTP-Posting-Host: net.bio.net John Lee Department of Biochemistry University of Georgia Athens GA 30602-7229 USA Phone 706-542-1764 FAX 706-542-1738 From owner-structural-nmr@net.bio.net Sat Jun 28 23:00:00 1997 Path: biosci!CMGM.STANFORD.EDU!cramos From: cramos@CMGM.STANFORD.EDU (Carlos Ramos) Newsgroups: bionet.structural-nmr Subject: (none) Date: 29 Jun 1997 12:58:58 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <33b41baa.0@news.genesisnetwork.net> NNTP-Posting-Host: net.bio.net unsubscribe From owner-structural-nmr@net.bio.net Sun Jun 29 23:00:00 1997 Path: biosci!NMR1.BCH.MSU.EDU!gao From: gao@NMR1.BCH.MSU.EDU (Jinhai Gao) Newsgroups: bionet.structural-nmr Subject: ft3d of Kay's noesy3dn Date: 30 Jun 1997 12:13:07 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <33B805A3.41C6@nmr1.bch.msu.edu> NNTP-Posting-Host: net.bio.net HI, everyone, I have collect a set of 3D noesy-hsqc data using L. Kay's sequence in our Inova600. But I failed to process this data using ft3d command ( I have the updated ft3d and ft1da within new ProteinPack. I have try use ft3d with f1corf='' and f2coef='1 0 -1 0 0 -1 0 -1', but the results looks unnormal. ( phase=1,2, phase2=1,2 and array=phase2,phase) I also have the 2D noesy-hsqc data( ni=128, ni2=0, phase=1,2,phase2=1), I tried to process using wft2da, but the result still looks not right. Would some one pls help me? Thanks a million. Jinhia Gao From owner-structural-nmr@net.bio.net Sun Jun 29 23:00:00 1997 Path: biosci!CMGM.STANFORD.EDU!cramos From: cramos@CMGM.STANFORD.EDU (Carlos Ramos) Newsgroups: bionet.structural-nmr Subject: Re: a great book Date: 30 Jun 1997 13:16:46 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 42 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net Hi, I'd like to know if someone has more books about NMR to suggest. In special, related to biological research. Thanks a lot. Carlos Ramos On 30 Jun 1997, Istvan Pelczer wrote: > Dear Netters, > > Some of you might know this already, but let me turn your attention to a > new book, which I think is one of the best of its kind in this field, > published recently by Elsevier: > > "NMR Spectroscopy and its Application to Biomedical Research" > (Ed.: Susanta K. Sarkar) > Elsevier, Amsterdam (etc.), 1996 > ISBN 0-444-89410-1 > > The word: biomedical may be a bit misleading -- no imaging or in vivo NMR > are discussed at all. However, all who are dealing with biomolecular > NMR, from preparation of labeled samples and design of experiments > through modeling, will benefit of this book a lot. > > Ejoy! All the best, > > Istvan > > wwww,wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww > Istvan Pelczer, Ph.D. Email: ipelczer@princeton.edu > Senior NMR Spectroscopist > Princeton University > Department of Chemistry, Frick Lab., ph# (609) 258 2342 > Washington Road fax# (609) 258 6746 > Princeton, NJ 08544, USA > > From owner-structural-nmr@net.bio.net Sun Jun 29 23:00:00 1997 Path: biosci!PHOENIX.PRINCETON.EDU!ipelczer From: ipelczer@PHOENIX.PRINCETON.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: a great book Date: 30 Jun 1997 10:32:56 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 28 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Netters, Some of you might know this already, but let me turn your attention to a new book, which I think is one of the best of its kind in this field, published recently by Elsevier: "NMR Spectroscopy and its Application to Biomedical Research" (Ed.: Susanta K. Sarkar) Elsevier, Amsterdam (etc.), 1996 ISBN 0-444-89410-1 The word: biomedical may be a bit misleading -- no imaging or in vivo NMR are discussed at all. However, all who are dealing with biomolecular NMR, from preparation of labeled samples and design of experiments through modeling, will benefit of this book a lot. Ejoy! All the best, Istvan wwww,wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww Istvan Pelczer, Ph.D. Email: ipelczer@princeton.edu Senior NMR Spectroscopist Princeton University Department of Chemistry, Frick Lab., ph# (609) 258 2342 Washington Road fax# (609) 258 6746 Princeton, NJ 08544, USA From owner-structural-nmr@net.bio.net Mon Jun 30 23:00:00 1997 Path: biosci!PHOENIX.PRINCETON.EDU!ipelczer From: ipelczer@PHOENIX.PRINCETON.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: a great book Date: 1 Jul 1997 10:50:29 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 38 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net Dear Netters, Carlos' reply reminds me to another message from the past; I recommended another great book with just a very lousy reference. Here it comes now in full: J. Cavanagh, W.J. Fairbrother, A.G. Palmer III, and N.J. Skelton; "Protein NMR Spectroscopy. Principles and Practice" Academic Press, San Diego (etc.), 1996 ISBN 0-12-164490-1 There are several good books out there on modern (biomolecular) NMR now (I mentioned a couple in that former message). I look forward to hearing others' suggestions, too. Cheers, Istvan wwww,wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww Istvan Pelczer, Ph.D. Email: ipelczer@princeton.edu Senior NMR Spectroscopist Princeton University Department of Chemistry, Frick Lab., ph# (609) 258 2342 Washington Road fax# (609) 258 6746 Princeton, NJ 08544, USA On Mon, 30 Jun 1997, Carlos Ramos wrote: > > Hi, > > I'd like to know if someone has more books about NMR to suggest. > In special, related to biological research. > > Thanks a lot. > > Carlos Ramos From owner-structural-nmr@net.bio.net Mon Jun 30 23:00:00 1997 Path: biosci!HEMEBASE.BIO.UCI.EDU!raman From: raman@HEMEBASE.BIO.UCI.EDU (CS Raman) Newsgroups: bionet.structural-nmr Subject: Moderation of STR-NMR Date: 30 Jun 1997 17:05:31 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: <199707010006.AAA16804@hemebase.bio.uci.edu> NNTP-Posting-Host: net.bio.net I have been informed by BIOSCI personnel that we should be switched over to the moderated state within a week. Until then, let us be patient. Cheers -raman ___________________________________________________________________ C.S.Raman Tel: (714) 824-4322 University of California Fax: (714) 824-8540 Dept. MB & B email: raman@indigo1.bio.uci.edu 3205 Bio Sci II Irvine, CA 92697-3900 ------------------------------------------------------------------- In a time of drastic change it is the learners who inherit the future. The learned usually find themselves equipped to live in a world that no longer exists. --Eric Hoffer ___________________________________________________________________ From owner-structural-nmr@net.bio.net Mon Jun 30 23:00:00 1997 Path: biosci!agate!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!dispatch.news.demon.net!demon!delos.dra.hmg.gb!server1.netnews.ja.net!server5.netnews.ja.net!server6.netnews.ja.net!server4.netnews.ja.net!server2.netnews.ja.net!news.qub.ac.uk!not-for-mail From: Andrew Wallace Newsgroups: bionet.structural-nmr Subject: Re: Newsgroup moderation Date: Tue, 01 Jul 1997 11:49:43 +0100 Organization: Queens University Belfast Message-ID: <33B8E0C5.7681@qub.ac.uk.see.signature> References: <199706241653.QAA10267@hemebase.bio.uci.edu> Reply-To: a.wallace@qub.ac.uk.see.signature NNTP-Posting-Host: awall.bc.qub.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; PPC) Lines: 33 CS Raman wrote: > > It appears that the delay in changing the status of STR-NMR > to "moderated" is at BIOSCI. I have been bombarding them with > emails to convert us over to the new status, but, am not getting > through. There is also change in personnel at BIOSCI at the > administrative level. So, if everyone could bear with me, > we will soon be rid of all the junk that comes through. > I would like to add my voice to that of Raman in calling for patience on the part of STR-NMR subscribers. See the message from the BioSci staff on the bionet.general newsgroup about moderation. BioSci have just moved their computers about 50 miles across the Bay area of San Francisco to Stanford without hardly missing a beat. I bet that most of you didn't even notice, the mail and newsgroups just kept working as usual. There are a lot of newsgroups going into moderation right now as a result of the spam flood, so I imagine the support staff are run off their feet. Please bear with the situation for a while longer and give them a chance. Andrew P.S. Congratulations to the BioSci staff and the folks at HighWire Press, Stanford for such a smooth transition so far, in spite of the spam situation. -- - note antispam feature in return address. My real address is: ================================================================== Andrew Wallace,Ph.D., Queens University Belfast, N. Ireland (UK) a.wallace@qub.ac.uk http://web.qub.ac.uk/bb/awpage/wallace.html ================================================================== From owner-structural-nmr@net.bio.net Mon Jun 30 23:00:00 1997 Path: biosci!ukc.ac.uk!M.J.Howard From: M.J.Howard@ukc.ac.uk ("M.J.Howard") Newsgroups: bionet.structural-nmr Subject: Re: a great book Date: 1 Jul 1997 01:56:48 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 52 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net On 30 Jun 1997, Carlos Ramos wrote: > > Hi, > > I'd like to know if someone has more books about NMR to suggest. > In special, related to biological research. > > Thanks a lot. > > Carlos Ramos > > I would definately recommend: PROTEIN NMR SPECTROSCOPY, Principles and Practice by J.Cavanagh, W.J.Fairbrother, A.G.Palmer III and N.J.Skelton ISBN: 0-12-164490-1 Hope that is useful. Mark *********************************************************** Dr. Mark J. Howard Research School of Biosciences University of Kent Canterbury Kent U.K. CT2 1JY e-mail: mjh7@kiwi.ukc.ac.uk Tel No: (01227) 764000 x7117/8 x7012 *********************************************************** From owner-structural-nmr@net.bio.net Mon Jun 30 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!cpk-news-hub1.bbnplanet.com!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!news.bbnplanet.com!nih.gov!not-for-mail From: John Kuszewski Newsgroups: bionet.molbio.proteins,bionet.software.x-plor,bionet.xtallography,bionet.structural-nmr Subject: Ca virtual torsion angles Date: Mon, 30 Jun 1997 20:44:21 -0400 Organization: Nat'l Insts of Health Lines: 26 Message-ID: <33B852E5.31CD@spork.niddk.nih.gov> NNTP-Posting-Host: spork.niddk.nih.gov Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; SunOS 5.5 sun4u) Xref: biosci bionet.molbio.proteins:11111 bionet.software.x-plor:1360 bionet.xtallography:3594 bionet.structural-nmr:2093 Hi, I've been playing with using the "virtual torsion angle" defined by the positions of four consecutive residues' alpha carbons to define pieces of structure. I've heard of other people doing this before. Does anyone know if there's a standard name for this angle (ala calling the N..Ca..C..N angle "psi")? -- _____________ | ___/_ | |/ / -- /\ // /-- || || / /|| || || / / || || ||/ / || John Kuszewski || |/ /| || johnk@spasm.niddk.nih.gov || / /|| || \/ / / || \/ that's MISTER protein G to you! |/__/| | /_________| My parents went to Zaire and all I got was this lousy retrovirus. From owner-structural-nmr@net.bio.net Mon Jun 30 23:00:00 1997 Path: biosci!PHOENIX.PRINCETON.EDU!ipelczer From: ipelczer@PHOENIX.PRINCETON.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: ps/eps Date: 1 Jul 1997 12:07:54 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Netters, Would you advise me on (possibly free) good conversion software to transfer conventional PS files to EPS? Thanks in advance, Istvan wwww,wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww Istvan Pelczer, Ph.D. Email: ipelczer@princeton.edu Senior NMR Spectroscopist Princeton University Department of Chemistry, Frick Lab., ph# (609) 258 2342 Washington Road fax# (609) 258 6746 Princeton, NJ 08544, USA From owner-structural-nmr@net.bio.net Mon Jun 30 23:00:00 1997 Path: biosci!pravda.ucr.edu!newsfeed2.aimnet.com!news.maxwell.syr.edu!newsfeed.nacamar.de!supernews.com!Supernews69!not-for-mail From: adfkj@woeiruffsr.com Newsgroups: bionet.structural-nmr Subject: DO YOU NEED A 800 SERVICE?? Date: 1 Jul 1997 21:04:52 GMT Organization: All USENET -- http://www.Supernews.com Lines: 2 Message-ID: <5pbrdk$4od$3@usenet85.supernews.com> NNTP-Posting-Host: 207.211.62.221 From owner-structural-nmr@net.bio.net Mon Jun 30 23:00:00 1997 Path: biosci!PHOENIX.PRINCETON.EDU!ipelczer From: ipelczer@PHOENIX.PRINCETON.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: wide Date: 1 Jul 1997 11:50:31 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Netters, I am looking for experience and advise of those who run WATERGATE type (or similar water suppression) experiments for a sample with hyperfine shifts. My problem is, that the 180 pulse will cover (way) less than the desired frequency range. I look forward to receiving some suggestions, Thanks, Istvan wwww,wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww Istvan Pelczer, Ph.D. Email: ipelczer@princeton.edu Senior NMR Spectroscopist Princeton University Department of Chemistry, Frick Lab., ph# (609) 258 2342 Washington Road fax# (609) 258 6746 Princeton, NJ 08544, USA