From owner-structural-nmr@net.bio.net Mon Jan 01 22:00:00 1996 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: methyl exchange Date: 2 Jan 1996 08:29:15 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 72 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <4cbetq$p7e@whitbeck.ncl.ac.uk> NNTP-Posting-Host: net.bio.net Happy New Year to all in the Net! Now, to James' question: It may be a little off-line suggestion, but have you considered to look at 13C instead of 1H? All the best, Istvan =========================================================================== Istvan Pelczer, Ph.D. (ipelczer@mailbox.syr.edu) Res. Assist. Professor Visiting Assist. Professor Chemistry Department, CST Bldg. SUNY ESF, Chemistry Department Syracuse University One Forestry Drive Syracuse, NY 13244-4100 Syracuse, NY 13210-2778 ph: (315) 443 1023 or x-5932 ph# (315) 470 6596 or x-6855(Dept.) fax: x-1022 or x-4070(Dept.) On 2 Jan 1996, james swar wrote: > METHYL EXCHANGE RATE FROM SELECTIVE INVERSION EXPERIMENTS > > HELLO! > > I do realise that this is not exactly a bionet str.-nmr question but is > of a nature which may have been treated in biological systems. > > I have a system in which 2 methyls (2) and (3) (slow on chem. shift timescale) > are exchanging (from ROESY exps). The system is of the following form: > > (1)Me Metal > | | > -CH-N-Me(2) > | > Me(3) > > The methyls are sufficiently far apart to permit selective inversion > experiments.This confirms the exchange phenomena.The problem is to > calculate an exchange rate for this process. The non inverted signal > passes through a minimum during the recovery and hence K > cross.rel.rate > const (SIGMA). From non selective T1 experiments both give the same > slope which suggests that the relaxation is dominated by intramolecular > methyl relaxation or/and that the exchange is fast compared to T1 > relaxation. The overall motion of the molecule is such that WT~1 and > as a result the NOEs are very small (hence the use of ROESY spectra). > > Is there a way without having to consider the general solution involving > the methyls to find the exchange rate? i.e. can I do a similar treatment > as Dalquist et al in which the RHOs were assumed to be equal, and SIGMA=0. > Of course SIGMA is not =0 in my case but this may be found from a related > compound in which no exchange takes place (i.e. as in Campbell et al). > > If I do this approach, and use the method of 'sums and differences' do I > have to consider intramethyl relaxation implicitly i.e. from this method > and treating the two methyls like two protons in exchange (neglecting > intramethyl relaxation) will I in effect get a minimum value for the rate > constant? How do I do this? The two methyls are sufficiently far apart > that the usual line width/temperature experiments are not appropriate. > > Well thanks for reading. Happy New Year! > > James. > > > Dalquist et al J Mag Res 17 406 1975 > Campbell et al J Mag Res summer 1977 > > From owner-structural-nmr@net.bio.net Mon Jan 01 22:00:00 1996 Path: biosci!MEDNET.SWMED.EDU!DWOESS From: DWOESS@MEDNET.SWMED.EDU (Don Woessner) Newsgroups: bionet.structural-nmr Subject: Info requested Date: 2 Jan 1996 08:35:05 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Please mail me information concerning the purposes, function, activities, etc., of thie e-mail address. Thanks very much, Don Woessner From owner-structural-nmr@net.bio.net Mon Jan 01 22:00:00 1996 Path: biosci!agate!howland.reston.ans.net!newsfeed.internetmci.com!usenet.eel.ufl.edu!warwick!news.ncl.ac.uk!usenet From: james swar Newsgroups: bionet.structural-nmr Subject: methyl exchange Date: 2 Jan 1996 14:19:38 GMT Organization: Newcastle University, UK Lines: 47 Message-ID: <4cbetq$p7e@whitbeck.ncl.ac.uk> NNTP-Posting-Host: fernwood.ncl.ac.uk X-Newsreader: WinVN 0.92.6+ METHYL EXCHANGE RATE FROM SELECTIVE INVERSION EXPERIMENTS HELLO! I do realise that this is not exactly a bionet str.-nmr question but is of a nature which may have been treated in biological systems. I have a system in which 2 methyls (2) and (3) (slow on chem. shift timescale) are exchanging (from ROESY exps). The system is of the following form: (1)Me Metal | | -CH-N-Me(2) | Me(3) The methyls are sufficiently far apart to permit selective inversion experiments.This confirms the exchange phenomena.The problem is to calculate an exchange rate for this process. The non inverted signal passes through a minimum during the recovery and hence K > cross.rel.rate const (SIGMA). From non selective T1 experiments both give the same slope which suggests that the relaxation is dominated by intramolecular methyl relaxation or/and that the exchange is fast compared to T1 relaxation. The overall motion of the molecule is such that WT~1 and as a result the NOEs are very small (hence the use of ROESY spectra). Is there a way without having to consider the general solution involving the methyls to find the exchange rate? i.e. can I do a similar treatment as Dalquist et al in which the RHOs were assumed to be equal, and SIGMA=0. Of course SIGMA is not =0 in my case but this may be found from a related compound in which no exchange takes place (i.e. as in Campbell et al). If I do this approach, and use the method of 'sums and differences' do I have to consider intramethyl relaxation implicitly i.e. from this method and treating the two methyls like two protons in exchange (neglecting intramethyl relaxation) will I in effect get a minimum value for the rate constant? How do I do this? The two methyls are sufficiently far apart that the usual line width/temperature experiments are not appropriate. Well thanks for reading. Happy New Year! James. Dalquist et al J Mag Res 17 406 1975 Campbell et al J Mag Res summer 1977 From owner-structural-nmr@net.bio.net Tue Jan 02 22:00:00 1996 Path: biosci!ggr.co.uk!rhf23484 From: rhf23484@ggr.co.uk (Dr R H Fogh) Newsgroups: bionet.structural-nmr Subject: RE: Info requested Date: 2 Jan 1996 23:54:08 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <14594.199601030746@mailhub.ggr.co.uk> NNTP-Posting-Host: net.bio.net Dear Netters, Re D. Woessners request for info about the 'function purposes etc.' of str-nmr, I suggest NOT answering unless given some kind of explanation for who he is and why he wants to know. One would think that anyone who might be interested in our field would likely recognise what it is about from the title and a couple of looks at the kind of letters it receives. With apologies to D. Woessner the possible reasons for the question include: targeted advertising database, search for 'indecent' newsgroups, statistics of net use (whose?) ... Does it seem unreasonable to ask for a one-sentence introduction before helping the man out? With welcome to all interested participants, Rasmus Fogh Glaxo SpA, Via Fleming 4, Verona, Italy. From owner-structural-nmr@net.bio.net Tue Jan 02 22:00:00 1996 Newsgroups: bionet.structural-nmr Path: biosci!agate!msunews!uwm.edu!newsfeed.internetmci.com!in2.uu.net!sangam!iitb!powai!n1403305 From: n1403305@powai.cc.iitb.ernet.in (ramakrishna) Subject: peptide aggregation Message-ID: Date: Tue, 2 Jan 1996 16:23:03 GMT Organization: Computer Centre, Indian Institute of Technology, Bombay X-Newsreader: TIN [version 1.2 PL2] Lines: 8 dear friends, i am working on a beta hairpin peptide and am using NMR to characterize it in aqueous solution. there appears to be aggregation of the peptide (even at low conc ~ 2mM). can aploar solvents like methanol be used to prevent or decrease the extent of aggregation. any information will be greatly appreciated. Ramkrishna From owner-structural-nmr@net.bio.net Wed Jan 03 22:00:00 1996 Path: biosci!IR2CBM.CNRS-MRS.FR!darbon From: darbon@IR2CBM.CNRS-MRS.FR (herve darbon) Newsgroups: bionet.structural-nmr Subject: Re peptide aggregation Date: 4 Jan 1996 01:56:26 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <9601040954.AA18016@ir2cbm.cnrs-mrs.fr> NNTP-Posting-Host: net.bio.net >dear friends, >i am working on a beta hairpin peptide and am using NMR to characterize >it in aqueous solution. there appears to be aggregation of the peptide >(even at low conc ~ 2mM). can aploar solvents like methanol be used to >prevent or decrease the extent of aggregation. any information will be >greatly appreciated. > >Ramkrishna Tri Fluoro Ethanol (TFE) is usually a good solvent for such purpose. Try variuos concentrations, but some 20% in water sould be OK. Good luck Herve From owner-structural-nmr@net.bio.net Wed Jan 03 22:00:00 1996 Path: biosci!BIOC01.UTHSCSA.EDU!raman From: raman@BIOC01.UTHSCSA.EDU (C.S.RAMAN) Newsgroups: bionet.structural-nmr Subject: Re: XEASY software Date: 4 Jan 1996 07:39:21 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 30 Sender: daemon@net.bio.net Distribution: world Message-ID: <9601041536.AA01916@bioc01.uthscsa.edu> References: <9601041558.AA15037@iason.cc.uoi.gr> NNTP-Posting-Host: net.bio.net Athan: > does anybody know how can l get the program XEASY ? You may want to contact Christian Bartels at: bartels@molbio.ethz.ch regarding XEASY. Cheers -raman -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ C.S.RAMAN _/ _/ Department of Biochemistry _/ _/ University of Texas Health Science Center _/ _/ 7703 Floyd Curl Drive _/ _/ San Antonio, TX 78284-7760 _/ _/ USA _/ _/ _/ _/ Tel: (210) 567-6623 _/ _/ Fax: (210) 567-6595 _/ _/ E-mail: raman@bioc01.uthscsa.edu _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ How can it be that mathematics, a product of human thought _/ _/ independent of experience, is so admirably adapted to the _/ _/ objects of reality? -Albert Einstein _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From owner-structural-nmr@net.bio.net Wed Jan 03 22:00:00 1996 Path: biosci!agate!newsxfer2.itd.umich.edu!newsfeed.internetmci.com!tank.news.pipex.net!pipex!warwick!bham!bhamcs!news.ox.ac.uk!news From: "Simon M. Brocklehurst" Newsgroups: bionet.structural-nmr Subject: ANNOUNCE: NAOMI version upgrade Date: Thu, 04 Jan 1996 15:07:38 +0000 Organization: University of Oxford Lines: 76 Message-ID: <30EBED3A.ABD322C@bioch.ox.ac.uk> NNTP-Posting-Host: nmrv.ocms.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0b4 (X11; I; SunOS 4.1.3_U1 sun4m) NAOMI - Version Upgrade Announcement (Please note, NAOMI is provided at zero charge for academic use) (e-mail contact smb@bioch.ox.ac.uk) _____________________________________________________________________________ The computer program NAOMI Version 2.3b is available as of now from the NAOMI Web site at: http://www.ocms.ox.ac.uk/~smb/Software/N_details/naomi.html or via anonymous ftp ftp://nmrz.ocms.ox.ac.uk/pub/smb/naomi i.e. at nmrz.ocms.ox.ac.uk in directory pub/smb/naomi/ Users of versions older than 2.10 will need new license keys to allow the upgrade to work (please contact the author in this case). _____________________________________________________________________________ Upgrade features : Side-chain manipulations now include hydrogen atoms where appropriate. This makes for more seamless integration with X-PLOR (e.g. for molecular dynamics simulations, energy minimization, NMR structure calculation etc after manipulation of protein structures using NAOMI). _____________________________________________________________________________ What is NAOMI? NAOMI is an easy-to-use, state-of-the-art computer program which is aimed at both specialist and non-specialist researchers who make use of three-dimensional structures of proteins in their work. It has hundreds of users Worldwide. Some facilities offered by the program for working with structure include: automatic 'key' residue identification automatic hydrophobic core/packing analysis automatic hydrogen bonds main-chain and side-chain identification (including high quality energy calculations) automatic secondary structure (helix, strand and turn) classification using fuzzy logic automatic supersecondary structure classification (beta-hairpin loops) conformational parameters: phi,psi,chi1,chi2,chi3,chi4,chi5 etc solvent accessibility (both absolute and percentage) calculations automatic identification of disulphide bonds, salt bridges, chain-breaks side-chain modelling and manipulation applying symmetry operators automatic structure repair (building in missing atoms) NMR structure refinement module interfaces to graphics programs (MOLSCRIPT (and thus Raster3D), INSIGHT, QUANTA to allow automatic preparation of figures More details are available on the Web site. NB NAOMI currently works only on Silicon Graphics workstations running IRIX 5.* _____________________________________________________________________________ | | ,_ o Simon M. Brocklehurst, | / //\, Oxford Centre for Molecular Sciences, Department of Biochemistry, | \>> | University of Oxford, Oxford, UK. | \\, E-mail: smb@bioch.ox.ac.uk | WWW: http://www.ocms.ox.ac.uk/~smb/ |____________________________________________________________________________ From owner-structural-nmr@net.bio.net Wed Jan 03 22:00:00 1996 Path: biosci!geri4680.geri.re.kr!jhlee From: jhlee@geri4680.geri.re.kr (test) Newsgroups: bionet.structural-nmr Subject: (no subject) Date: 3 Jan 1996 18:37:18 -0800 Organization: KRIBB Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <9601040237.AA07048@geri4680.geri.re.kr> NNTP-Posting-Host: net.bio.net I isolated a polysaccharide with immunostimulating activity from a basidiomycete, mushroom. But the structure is not determined yet. I would like to determine the fine chemical structure of the polysaccharide by using various NmR. From owner-structural-nmr@net.bio.net Wed Jan 03 22:00:00 1996 Path: biosci!ggr.co.uk!rhf23484 From: rhf23484@ggr.co.uk (Dr R H Fogh) Newsgroups: bionet.structural-nmr Subject: Re: Info-request Date: 4 Jan 1996 00:07:53 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 3 Sender: daemon@net.bio.net Distribution: world Message-ID: <883.199601040800@mailhub.ggr.co.uk> NNTP-Posting-Host: net.bio.net Please disregard my last message. With apologies for wasting your time, Rasmus Fogh From owner-structural-nmr@net.bio.net Wed Jan 03 22:00:00 1996 Path: biosci!cc.uoi.gr!astavrak From: astavrak@cc.uoi.gr (Athanasios Stavrakoudis) Newsgroups: bionet.structural-nmr Subject: XEASY software Date: 4 Jan 1996 07:08:39 -0800 Organization: University of Ioannina Computer Center Ioannina, Greece 451 10 tel: +30-651-45298, fax: +30-651-45298 Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <9601041558.AA15037@iason.cc.uoi.gr> NNTP-Posting-Host: net.bio.net Dear netters, does anybody know how can l get the program XEASY ? thanks a lot, Huppy New Year !!!! Athanassios Stavrakoudis e-mail : astavrak@cc.uoi.gr From owner-structural-nmr@net.bio.net Thu Jan 04 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!usenet.eel.ufl.edu!news.ultranet.com!bigboote.WPI.EDU!news3.near.net!news.ner.bbnplanet.net!das-news2.harvard.edu!oitnews.harvard.edu!cmcl2!newsserv.cs.sunysb.edu!news.cc.sunysb.edu!delbruck!culli From: culli@delbruck (David Cullinan) Newsgroups: bionet.structural-nmr Subject: Acetylcholine structure? Date: 4 Jan 1996 19:45:04 GMT Organization: State University of New York at Stony Brook Lines: 14 Message-ID: <4chao0$of@abel.cc.sunysb.edu> NNTP-Posting-Host: delbruck.pharm.sunysb.edu X-Newsreader: TIN [version 1.2 PL2] Greetings! Does anyone know where I could obtain pdb file atomic coordinates for acetylcholine, carbamylcholine, bethanechol, nicotine, curare, and/or atrophine? I'm primarily interested in their structural orientation when binding to the acetylcholine receptor. I know I can find 2-dimensional drawings of these in any decent reference book, but I'd like to get pdb coordinates that I could input to a program like Insight or MIDAS. Many thanks. ______________________________________________________________________ David Cullinan (Graduate student) Dept of Biophysics email: culli@delbruck.pharm.sunysb.edu SUNY Stony Brook http://www.pharm.sunysb.edu/~culli/home.html From owner-structural-nmr@net.bio.net Thu Jan 04 22:00:00 1996 Path: biosci!cc.uoi.gr!astavrak From: astavrak@cc.uoi.gr (Athanasios Stavrakoudis) Newsgroups: bionet.structural-nmr Subject: Re: ANNOUNCE: NAOMI version upgrade Date: 5 Jan 1996 02:28:07 -0800 Organization: University of Ioannina Computer Center Ioannina, Greece 451 10 tel: +30-651-45298, fax: +30-651-45298 Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <9601051224.AA18771@iason.cc.uoi.gr> NNTP-Posting-Host: net.bio.net From owner-structural-nmr@net.bio.net Thu Jan 04 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!swrinde!howland.reston.ans.net!EU.net!Portugal.EU.net!news.rccn.net!scsing.switch.ch!ubaclu.unibas.ch!ubaclu.unibas.ch!nntp Newsgroups: bionet.structural-nmr Subject: Felix macros for Varian files (3D, gradient sensitivity enhanced) Message-ID: <30ED2D26.167E@yogi.ubaclu.unibas.ch> From: Ronald Wiltscheck Date: Fri, 05 Jan 1996 13:52:38 +0000 Organization: Biozentrum der Universitaet Basel Nntp-Posting-Host: nmr.bioz.unibas.ch X-Mailer: Mozilla 2.0b3 (X11; I; IRIX 5.3 IP17) MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 22 Dear netters, does anyone of you use Felix software for processing Varian 3D NMR files? (gradient sensitivity enhanced!) If yes, could you please send me a macro for processing such a 3D? Thanks a lot, Ronald. ====================================================================== Dr. Ronald Wiltscheck e-mail: wiltscheck@ubaclu.unibas.ch University of Basel phone: ++41-61/267-2091 Biozentrum/Structural Biology fax: ++41-61/267-2190 CH-4053 Basel/Switzerland home: ++41-51/361-8605 ====================================================================== From owner-structural-nmr@net.bio.net Sat Jan 06 22:00:00 1996 Path: biosci!IRIS.LSC.PKU.EDU.CN!qyx From: qyx@IRIS.LSC.PKU.EDU.CN (Qu Youxin) Newsgroups: bionet.structural-nmr Subject: Address Inquiry Date: 6 Jan 1996 22:34:44 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: <9601072133.AA07644@IRIS.lsc.pku.edu.cn> NNTP-Posting-Host: net.bio.net Dear netters, Does anyone know the current mail and email address of Professor Per Kraulis, the author of MOLSCRIPT program? Thanks a lot, Youxing. Youxing Qu National Laboratory of Protein Engineering and Plant Genetic Engineering Life Sciences Center College of Life Sciences Peking University Beijing 100871 P. R. China E-mail: qyx@IRIS.lsc.pku.edu.cn From owner-structural-nmr@net.bio.net Sat Jan 06 22:00:00 1996 Path: biosci!agate!cgl!cerpa From: cerpa@cgl.ucsf.edu (Robert Cerpa) Newsgroups: bionet.structural-nmr Subject: Re: Re peptide aggregation Date: 7 Jan 1996 17:56:33 GMT Organization: Computer Graphics Laboratory, UCSF Lines: 40 Distribution: world Message-ID: <4cp1gh$dcq@cgl.ucsf.edu> References: <9601040954.AA18016@ir2cbm.cnrs-mrs.fr> NNTP-Posting-Host: socrates.ucsf.edu In article <9601040954.AA18016@ir2cbm.cnrs-mrs.fr> darbon@IR2CBM.CNRS-MRS.FR (herve darbon) writes: >>dear friends, >>i am working on a beta hairpin peptide and am using NMR to characterize >>it in aqueous solution. there appears to be aggregation of the peptide >>(even at low conc ~ 2mM). can aploar solvents like methanol be used to >>prevent or decrease the extent of aggregation. any information will be >>greatly appreciated. >> >>Ramkrishna > >Tri Fluoro Ethanol (TFE) is usually a good solvent for such purpose. Try >variuos concentrations, but some 20% in water sould be OK. >Good luck >Herve One word of caution about using TFE with a peptide you want to keep in beta conformation: I was working on a 14-mer that had a beta hairpin conformation in DMSO. I put it in TFE to do some CD on it, and I got a CD spectrum that looked weakly alpha helical! This was particularly interesting since the peptide was cyclic (the first and last residues were cysteines and there was a disulfide between them). I didn't follow up on the structure. But be aware that altering solvent conditions to increase solubility can change your structure, perhaps drastically. You might want to do some studies comparing your mixed solvent system versus water using CD or IR spectroscopy, where you can work at lower concentrations. Getting the same spectrum in both solvents would be a strong (but not definite) indication that your conformation hadn't changed by changing solvent systems. If the spectra are different, though, then you're definitely changing the structure. Also, if you have a 10mm probe for your NMR, you can get alot more sample into the coil than in a 5mm probe, and you may be able to get a usable spectrum. I got an excellent NOESY of a helical peptide at about 500 micromolar concentration on a Varian Unity 600 system with a 10mm probe. Good luck-- Robert K. Cerpa, Ph.D. Graduate Group in Biophysics, UC San Francisco From owner-structural-nmr@net.bio.net Sun Jan 07 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!nntp.coast.net!swidir.switch.ch!swsbe6.switch.ch!scsing.switch.ch!elna.ethz.ch!usenet From: Fred Damberger Newsgroups: bionet.structural-nmr Subject: Re: XEASY software Date: 8 Jan 1996 18:20:23 GMT Organization: Swiss Federal Institute of Technology (ETHZ) Lines: 15 Message-ID: <4crn97$ckc@elna.ethz.ch> References: <9601041558.AA15037@iason.cc.uoi.gr> <9601041536.AA01916@bioc01.uthscsa.edu> NNTP-Posting-Host: odin.ethz.ch Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; SunOS 5.4 sun4d) X-URL: news:9601041536.AA01916@bioc01.uthscsa.edu Actually Christian has recently moved and the person to contact now is Ralf Glaser. A good permanent address to make inquiries is: xeasy@mol.biol.ethz.ch Also check out the Wuthrich group home-page for info on XEASY and other software developed here. URL: http://www.mol.biol.ethz.ch/ Cheers -Fred Fred Damberger ETH Hoenggerberg 8093 Zurich SWITZERLAND From owner-structural-nmr@net.bio.net Mon Jan 08 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!news-e1a.megaweb.com!newstf01.news.aol.com!newsbf02.news.aol.com!not-for-mail From: nalorac@aol.com (Nalorac) Newsgroups: bionet.structural-nmr Subject: Nalorac ENC NMR Symposium Date: 8 Jan 1996 19:39:30 -0500 Organization: America Online, Inc. (1-800-827-6364) Lines: 31 Sender: root@newsbf02.news.aol.com Message-ID: <4csdg2$ae6@newsbf02.news.aol.com> Reply-To: nalorac@aol.com (Nalorac) NNTP-Posting-Host: newsbf02.mail.aol.com You are invited to attend a special symposium prior to ENC ADVANCES IN NMR APPLICATIONS S Y M P O S I U M Featuring the Latest Developments in Experimental Techniques The Inn at Spanish Bay Pebble Beach, California Sunday, March 17, 1:30 to 5:00 p.m. This NMR Symposium will be held Sunday afternoon prior to the start of ENC. The Symposium site is located approximately one mile from the Asilomar Conference Center, site of the 1996 ENC. The agenda includes a presentation of recent results by leading NMR experimentalists concerning applications of pulsed field gradient and classical NMR techniques to both large and small molecular systems. The results obtained will be of interest to all liquid state NMR spectroscopists. Request a detailed program or RSVP by contacting our ENC Coordinator via our E-Mail address: sales@nalorac.com. N A L O R A C 841A Arnold Drive, Martinez, CA 94553 Phone: (510) 229-3501 FAX: (510) 229-1651 E-mail: sales@nalorac.com From owner-structural-nmr@net.bio.net Thu Jan 11 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: bryan@freja.fkem2.lth.se (Bryan Finn) Newsgroups: bionet.structural-nmr Subject: D-DTT Date: 12 Jan 1996 15:25:13 -0000 Lines: 27 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4d5ugp$km5@mserv1.dl.ac.uk> Original-To: str-nmr@dl.ac.uk Hi NMRers (NMRites?), Can anyone reccommend a good source (i.e. cheap but reliable) source of deuterated DTT? Bryan ___________________________________________________________________ | | | Dr. Bryan Finn | | Department of Physical Chemistry 2 Tel: +46-46-222-8254 | | Chemical Center Fax: +46-46-222-4543 | | University of Lund | | POB 124 | | S-221 00 Lund Sweden e-mail: bryan@freja.fkem2.lth.se | | WWW: http://www.fkem2.lth.se/personnel/bryan/finn.html | |_________________________________________________________________| From owner-structural-nmr@net.bio.net Sat Jan 13 22:00:00 1996 Path: biosci!TOUCAN.BABS.UNSW.EDU.AU!alfred From: alfred@TOUCAN.BABS.UNSW.EDU.AU ("Alfred Ross") Newsgroups: bionet.structural-nmr Subject: subscribe Date: 14 Jan 1996 14:45:31 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <9601150941.ZM551@toucan.babs.unsw.EDU.AU> NNTP-Posting-Host: net.bio.net subscribe From owner-structural-nmr@net.bio.net Sat Jan 13 22:00:00 1996 Path: biosci!bloom-beacon.mit.edu!newsfeed.internetmci.com!howland.reston.ans.net!plug.news.pipex.net!pipex!tube.news.pipex.net!pipex!dish.news.pipex.net!pipex!soap.news.pipex.net!pipex!usenet From: M J Geisow Newsgroups: bionet.structural-nmr Subject: THE '95 STRUCTURAL BIOLOGY MEETING! Date: 14 Jan 1996 16:12:24 GMT Organization: BIODIGM Ltd. Lines: 38 Message-ID: <4dba18$pj@soap.news.pipex.net> NNTP-Posting-Host: am126.du.pipex.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1 (Windows; I; 16bit) THE EUROPEAN STRUCTURAL BIOLOGY CONFERENCE OF '96! http://www.cryst.bbk.ac.uk/CEC/pope5.html MAIN PROGRAMME: Molecular Bioinformatics, Molecular Evolution and Design Biocatalysis and control of transcription and translation http://www.cryst.bbk.ac.uk/CEC/program.html OPEN SATELLITE MINISYMPOSIA GLUTAMATE RECEPTORS http://www.cryst.bbk.ac.uk/CEC/bockaer.htm PROTEIN TRANSLATION FACTORS http://www.cryst.bbk.ac.uk/CEC/clark.htm SCATTER FACTOR / HUMAN GROWTH FACTOR http://www.cryst.bbk.ac.uk/CEC/egherard.htm PLANTIBODIES - ENDOW PLANTS WITH NEW FUNCTIONS http://www.cryst.bbk.ac.uk/CEC/schots.htm CELLULASE STRUCTURE FUNCTION AND ENGINEERING http://www.cryst.bbk.ac.uk/CEC/rhaser.htm IMABIO (French Structural Biology) meeting of 7 main centres: (Grenoble, Marseille, Montpellier, Paris Sud, Strasbourg and Toulouse) http://www.cryst.bbk.ac.uk/CEC/imabio.htm REGISTER NOW! (on-line form) http://www.cryst.bbk.ac.uk/CEC/5info.html ______________________________________________________________________ -- BIODIGM Tel: +44 (0) 1949 839077 Fax: +44 (0) 1949 831886 Email: biodigm@dial.pipex.com From owner-structural-nmr@net.bio.net Sun Jan 14 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!EU.net!news.eunet.fi!newsmaster From: piero pollesello Newsgroups: bionet.structural-nmr Subject: Re: D-DTT Date: 15 Jan 1996 08:30:22 GMT Organization: POLYbios, Area Science Park, Trieste, Italy Lines: 17 Message-ID: <4dd3au$ptm@idefix.eunet.fi> References: <4d5ugp$km5@mserv1.dl.ac.uk> NNTP-Posting-Host: protein.orion.fi Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12(Macintosh; I; 68K) To: bryan@freja.fkem2.lth.se X-URL: news:4d5ugp$km5@mserv1.dl.ac.uk Hej Brian I bought 0.5 g of perdeuterated DTT from CIL (Cambridge Isotope laboratories) 98% deuterated 7500 FIM (2500 DM, 1500 USD) payed to the finnish dealer (Oriola-Prolab) It is very difficolt to compare its quality with other products (they are in any case so expernsive!). If you hear cheper prices, please let me know! Piero Pollesello NMR-lab, Che.Res.Dept. Orion-Farmos, Orion Corp. P.O.box 65, FIN-02101 Espoo, Finland From owner-structural-nmr@net.bio.net Tue Jan 16 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!uwm.edu!msunews!netnews.upenn.edu!news.tju.edu!usenet From: James Varnum Newsgroups: bionet.structural-nmr Subject: Birder Date: 17 Jan 1996 14:36:59 GMT Organization: Thomas Jefferson University Lines: 4 Message-ID: <4dj1ib$qqr@mail.TJU.EDU> NNTP-Posting-Host: watson.jci.tju.edu I need the address of Brian Reed or L. Zhu to obtain a cpoy of the program Birder From owner-structural-nmr@net.bio.net Thu Jan 18 22:00:00 1996 Path: biosci!rutgers!gatech!newsfeed.internetmci.com!vixen.cso.uiuc.edu!howland.reston.ans.net!torn!nott!nrcnet0.nrc.ca!BRI.NRC.CA!Feng.Ni From: Feng.Ni@BRI.NRC.CA (Feng Ni) Newsgroups: bionet.structural-nmr Subject: RESEARCH ASSOCIATE POSITIONS IN PROTEIN NMR Date: 19 Jan 1996 00:14:07 GMT Organization: Institut de recherche en biotechnologie, Montréal Lines: 46 Distribution: world Message-ID: <4dmnof$fgv@nrcnet0.nrc.ca> NNTP-Posting-Host: indy.bri.nrc.ca RESEARCH ASSOCIATE POSITIONS IN PROTEIN NMR SPECTROSCOPY AND MOLECULAR DESIGN Candidates are being sought to fill a research associate position in the NMR laboratory at the Biotechnology Research Institute (Montreal, Quebec, Canada). This is a two-year limited term appointment from the date of reporting with a salary of CND $38-45K/annum. The successful candidate will determine the bioactive conformations of peptides and protein fragments, study protein-peptide interactions by use of multi- dimensional NMR spectroscopy and participate in the design of novel molecules through the use of the NMR structures of peptides and proteins. This work is part of a multidisciplinary effort for the design of inhibitors of protease regulation and signal transduction. Specific protein targets include blood coagulation factors (e.g., thrombin), cysteine protease cathepsins, growth factor receptors and protein tyrosine phosphotases (PTPases). The proteins or their fragments for NMR analysis include EGF-like domains, kringle proteins, protease activation fragments and SH2 domains. You are expected to lead your own projects and to collaborate with other members of the Institute and with industrial scientists. Applicants must demonstrate within the content of their application that they meet the following screening criteria in order to be given further considera- tion as candidates: 1) a recent Ph.D. in chemistry, biochemistry or a related field, and solid training in protein structure and protein biochemistry, 2) research experience in conformational study of peptides and structure deter- mination of proteins by use of multidimensional NMR spectroscopy. The candidates will be assessed on the basis of the following criteria: 1) knowledge of the principles of protein structure, the solution behavior of peptides and proteins and the advantages and limitations of NMR spectroscopy for conformational analysis and structure determination, 2) familarity with the acquisition and processing of homo- and hetero-nuclear NMR data using state-of-the-art NMR hardware and software, 3) demonstrated abilities to plan and lead research projects and to carry out interdisciplinary collaborations with scientists from different fields, 4) abilities and skills to write peer- reviewed scientific articles (as demonstrated by an excellent publication record) and to communicate clearly and effectively in oral presentations, and 5) demonstrated ability to work independently as well as a member of a multidisciplinary team. Applications, which demonstrate qualifications for the above requirements, may be submitted to the e_mail address: fengni@bri.nrc.ca or by regular mail to: Dr. Feng Ni, Biotechnology Research Institute, 6100 Royalmount Avenue, Montreal, Quebec, H4P 2R2 Canada or by fax to: (514)-496-6232 c/o Dr. Feng Ni. From owner-structural-nmr@net.bio.net Fri Jan 19 22:00:00 1996 Path: biosci!BIOSYM.COM!johrn From: johrn@BIOSYM.COM (Judy Ohrn) Newsgroups: bionet.structural-nmr Subject: NMR Opportunity for Distribution Date: 19 Jan 1996 16:21:50 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 41 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net BIOSYM and Molecular Simulations Inc. have merged! Creating a dynamic new company signifying a new era in computer-aided molecular science. We are the premier supplier of molecular simulation software serving 3,500 sites at leading companies in the pharmaceutical, biotech, food, agrochemical, petrochemical, materials and engineering fields. Join us as we strive to give our customers enhanced ability to improve their R&D processes through state of the art application of molecular science. SCIENTIFIC PROGRAMMER-NMR We currently enhancing our integrated system for elucidating molecular structures from NMR data. Several NMR molecule modules are integrated with FELIX, NMR REFINE, and NMRWORKBENCH (BIOSYM/MSI's NMR spectral processing, visualation and analysis software), INSIGHT11, QUANTA, and CERUIS2 (BIOSYM/MSI's NMR molecular modeling software) and DISCOVER and XPLOR (BIOSYM/MSI's NMR molecular simulation software). The package includes multidimensional NMR data processing and analysis tools, computer-assisted resonance and peak assignment procedures, and structure generation, refinement and analysis tools. We have an opening for an innovative and creative professional to futher develop and enhance this software through software design, scientific validation and product-oriented research. Candidates will possess the following: * MS or Ph.D in either biochemistry or biophysics. * A minimum of two years experience using NMR spectroscopy and solution state analysis of organic compounds. * Experience using and developing structure generation and refinement methods such as distance geomentry, simulated annealing and NOE refinement required. * Knowledge of C and Fortran in UNIX is required, with experience in C++ and Mac/PC environments highly desired. * Familiarity with LIMS and sSpectral databases is a plus. We offer highly competitive compensation and benefits programs and are a EOE/AA employer. Interested candidates should submit their resumes to Judith M. Ohrn, Director, Human Resources at BIOSYM/MSI, Sorrento Valley, 9685 Scranton Road, San Diego, CA 92121, Fax (619) 458-0136 or email johrn@biosym.com. From owner-structural-nmr@net.bio.net Sun Jan 21 22:00:00 1996 Path: biosci!INDIANA.EDU!mpagel From: mpagel@INDIANA.EDU (Marty Pagel) Newsgroups: bionet.structural-nmr Subject: Re: looking for ribbon program for DNA Date: 22 Jan 1996 09:54:43 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 48 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <4djakg$lo0@highway.leidenuniv.nl> NNTP-Posting-Host: net.bio.net Hi Jeroen, We like RIBBONS, by Mike Carson, for N.A. ribbon models. From our RIBBONS license file: Postal Address: UAB/CMC University Station, Box 79 THT Birmingham, AL 35294 E-mail address: carson@luna.cmc.uab.edu carson@uabcmc.bitnet Phone / FAX: 205-934-1983 / 205-934-0480 (author) 205-934-7277 / 205-934-0480 (maxine) $100.00 Academic users. Executable version only. As is, no questions asked. $300.00 Academic users. Above, plus source code and E-mail support. Marty Pagel mpagel@indiana.edu --- __o Department of Chemistry Phone: (812)-855-6492 --- \<, Indiana University Fax: (812)-855-8300 --- ()/ () Bloomington, IN 47405-4001 http://nmrsg1.chem.indiana.edu/~mpagel On 17 Jan 1996, Jeroen Pikkemaat wrote: > Dear structural NMR fans, > > I'm looking for a (cheap) computer program which can > draw ribbon models of DNA structures (coordinates > in PDB format). > > Can anybody help me? > > Jeroen > > > ---------------------------------------------------------------------- > \==) Jeroen Pikkemaat | phone +31 71 5274563 > X Leiden Institute of Chemistry | +31 71 5274505 > /==) Gorlaeus Laboratories | FAX +31 71 5274488 > (==/ P.O. Box 9502 | ---------------------------- > X NL-2300 RA Leiden | E-mail > (==\ The Netherlands | jeroen@chemde4.Leidenuniv.nl > ---------------------------------------------------------------------- > From owner-structural-nmr@net.bio.net Sun Jan 21 22:00:00 1996 Path: biosci!LAPLACE.CSB.YALE.EDU!abonvin From: abonvin@LAPLACE.CSB.YALE.EDU ("Alexandre Bonvin") Newsgroups: bionet.structural-nmr Subject: Re: looking for ribbon program for DNA Date: 22 Jan 1996 09:12:22 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 24 Sender: daemon@net.bio.net Distribution: world Message-ID: <9601221710.AA23516@laplace.csb.yale.edu> NNTP-Posting-Host: net.bio.net > I'm looking for a (cheap) computer program which can > draw ribbon models of DNA structures (coordinates > in PDB format). What about a great free program running on SGIs: SETOR Contact Steve Evans for more info. Dr. Stephen V. Evans Department of Biochemistry University of Ottawa 451 Smyth, Ottawa Ontario K1H 8M5 elmo@nrcbsa.bio.nrc.ca TEL (613) 990-0858 FAX (613) 941-4475 Alexandre ========================================================================== | Alexandre Bonvin PhD | Phone: (203) 432-5066 | | Mol. Biophys. & Biochemistry | Fax: (203) 432-3923 | | Yale University | Email: abonvin@laplace.csb.yale.edu | | New Haven CT 06520-8114, USA | http://xplor.csb.yale.edu | ========================================================================== From owner-structural-nmr@net.bio.net Sun Jan 21 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!howland.reston.ans.net!news.nic.surfnet.nl!highway.leidenuniv.nl!chemde4!jeroen From: jeroen@chemde4.LeidenUniv.nl (Jeroen Pikkemaat) Newsgroups: bionet.structural-nmr Subject: looking for ribbon program for DNA Date: 17 Jan 1996 17:11:44 GMT Organization: CONFAN group, Organic Chemistry, Leiden University, The Netherlands Lines: 19 Message-ID: <4djakg$lo0@highway.leidenuniv.nl> NNTP-Posting-Host: chemde4.leidenuniv.nl X-Newsreader: TIN [version 1.2 PL2] Dear structural NMR fans, I'm looking for a (cheap) computer program which can draw ribbon models of DNA structures (coordinates in PDB format). Can anybody help me? Jeroen ---------------------------------------------------------------------- \==) Jeroen Pikkemaat | phone +31 71 5274563 X Leiden Institute of Chemistry | +31 71 5274505 /==) Gorlaeus Laboratories | FAX +31 71 5274488 (==/ P.O. Box 9502 | ---------------------------- X NL-2300 RA Leiden | E-mail (==\ The Netherlands | jeroen@chemde4.Leidenuniv.nl ---------------------------------------------------------------------- From owner-structural-nmr@net.bio.net Sun Jan 21 22:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.structural-nmr Subject: BIOSCI miniFAQ, ver. 14-DEC-95 Date: 22 Jan 1996 02:00:30 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 199 Sender: daemon@net.bio.net Distribution: world Message-ID: <199601221000.CAA28569@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 14-DEC-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/. Contents: -------- 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. 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 in addition to the master index for the entire set. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-structural-nmr@net.bio.net Sun Jan 21 22:00:00 1996 Path: biosci!SGI3.MAGNET.FSU.EDU!fengxu From: fengxu@SGI3.MAGNET.FSU.EDU (Feng Xu) Newsgroups: bionet.structural-nmr Subject: Dielectric Constant Calculation Date: 22 Jan 1996 10:42:54 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <9601221833.AA29742@sgi3.magnet.fsu.edu> NNTP-Posting-Host: net.bio.net Dear Structural NMR netters, I'm currently working on the solvent effects on protein conformations. Does anyone know a way to estimate the dielectric constant of a solution composed of different solvents with varying dielectric constatns? Thank you all in advance! Feng From owner-structural-nmr@net.bio.net Mon Jan 22 22:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!newsspool.doit.wisc.edu!night.primate.wisc.edu!nntp.msstate.edu!Isis.MsState.Edu!tlw1 From: Tracy Leon Whitehead Newsgroups: bionet.structural-nmr Subject: Re: Dielectric Constant Calculation Date: Tue, 23 Jan 1996 16:14:38 -0600 Organization: Mississippi State University Lines: 22 Message-ID: References: <9601221833.AA29742@sgi3.magnet.fsu.edu> NNTP-Posting-Host: isis.msstate.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: tlw1@Isis.MsState.Edu In-Reply-To: <9601221833.AA29742@sgi3.magnet.fsu.edu> On 22 Jan 1996, Feng Xu wrote: > Dear Structural NMR netters, > I'm currently working on the solvent effects on protein conformations. > Does anyone know a way to estimate the dielectric constant of a > solution composed of different solvents with varying dielectric > constatns? > > Thank you all in advance! > > Feng > Hello, I also am interested in being able to approximate the dielectric constant in mixed solutions...my research falls along the same lines, and this info could be vital! Thanks, Tracy > > From owner-structural-nmr@net.bio.net Mon Jan 22 22:00:00 1996 Path: biosci!NMR.UTMB.EDU!david From: david@NMR.UTMB.EDU (David Gorenstein) Newsgroups: bionet.structural-nmr Subject: STRUCTURAL BIOLOGY SYMPOSIUM, Galveston, TX Date: 23 Jan 1996 15:19:10 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 289 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net STRUCTURAL BIOLOGY SYMPOSIUM UNIVERSITY OF TEXAS MEDICAL BRANCH AT GALVESTON MARCH 1-3, 1996 Dear Colleague: As we announce the establishment of the Structural Biology Program at the University of Texas Medical Branch, we would like to invite you and your colleagues to join us in our inaugural celebration by participating in our Structural Biology Symposium scheduled for March 1-3, 1996. This meeting will bring together scientists who are interested in applying insights from structural biology and solution thermodynamics to solve biological and biomedical problems. The speakers at the symposium are distinguished researchers from a wide spectrum of scientififc disciplines. If you are planning to attend the Symposium, please inform us of your coming as well as who may be accompanying you by no later than February 20th. Furthermore, if you intend to participate in the poster session, or wish to present a talk in the satellite Sunday afternoon NMR Workshop offered in collaboration with Varian Instruments, all abstracts must be received no later than February 20th as well. Regarding accomodations for the event, a block of rooms has been reserved for Symposium attendants at the beachfront Hotel Galvez. However, prior to your arrival in Galveston it is necessary that you fill out the hotel form provided below to guarantee a reserved room. Although there is no registration fee, $50 will be assessed for those who wish to optionally participate in the Friday reception, Saturday lunch and dinner banquet, and Sunday brunch. Please make all payments made out to UTMB. In addition, checks will be the only form of payment accepted. Send all inquiries and responses to: Jacqueline Luxon; Administrative Secretary ADDRESS: Sealy Center for Structural Biology Dept. for Human Biological Chemistry and Genetics University of Texas Medical Branch Galveston, TX. 77555-1157 PHONE: (409)747-6800 FAX: (409)747-6850 EMAIL: jacky@nmr.utmb.edu Thank you, and we look forward to your participation in the Symposium. UTMB Symposium Organizing Committee: D. Wayne Bolen Werner Braun Wlodzimierz M. Bujalowski Edmund W. Czerwinski Robert Fox David G. Gorenstein James C. Lee Bruce A. Luxon Jan F. Post Stanley Watowich ---------------------------------------------------------------------- Symposium Information and Registration Information and the registration and hotel forms may also be found on the Sealy Center for Structural Biology server- URL http://www.scsb.utmb.edu:90/ You may also e-mail or print the registration and hotel forms below and send them to Jacqueline Luxon at the above address. ---------------------------------------------------------------------- CALL FOR ABSTRACTS, HOTEL AND REGISTRATION FORMS DEADLINE FOR THE SUBMISSION OF ABSTRACTS: FEBRUARY 20, 1996 --------------------------------------------------------------------- PRELIMINARY SCHEDULE _______________________________________________________________________________ FRIDAY, MARCH 1, 1996 _______________________________________________________________________________ 3:00 P.M. - 4.00 P.M. Registration Levin Hall 4:00 P.M. Opening Remarks Levin Hall President Thomas James - UTMB 4:15 P.M. Plenary Lecture Levin Hall Frederic Richards - Yale "The Structure of Proteins - Change in Dogma with Time" 6:00 P.M. - 7:30 P.M. Reception Hotel Galvez ________________________________________________________________________________ SATURDAY, MARCH 2, 1996 ________________________________________________________________________________ 9:00 A.M. - 9:50 A.M. Angela Gronenborn - NIH Levin Hall "Structure of Protein-DNA COmplexes: Intercalation, DNA Bending and Transcriptional Control" 9:50 A.M. - 10:40 A.M. Donald Wiley - Harvard Levin Hall "Structural Biology of Cellular Immunity" 10:40 A.M. - 11:10 A.M. Break & Posters Levin Hall 11:10 A.M. - 12:00 noon Robert L. Baldwin - Stanford Levin Hall "The Molten Globule Intermediate of an Apomyoglobin" 12:00 noon - 12:30 P.M. Werner Braun - UTMB Levin Hall "Self-Correcting Distance Geometry: A New Method for Protein Modeling and NMR Determination" 12:30 P.M. - 2:00 P.M. Lunch and visit to the NMR Center Dockside Blg. 2:00 P.M. - 2:50 P.M. Florante Quiocho - Baylor Levin Hall "Molecular Recognition by Proteins: From the Stringent to the very Loose" 2:50 P.M. - 3:40 P.M. Thomas James - University of Levin Hall California - San Francisco "Nucleic Acid Structure and Dynamics" 3:40 P.M. - 4:00 P.M. Break 4:00 P.M. - 4:50 P.M. Gary Ackers - Washington U. Levin Hall "The Intermediates of Hemoglobin Cooperativity Provide Striking New Insights into Allostery" 4:50 P.M. - 5:20 P.M. Robert Fox - UTMB Levin Hall "SH3 Domain Peptide Recognition" 5:20 P.M. - 6:30 P.M. Poster and Reception Levin Hall 7:30 P.M. Banquet Hotel Galvez ________________________________________________________________________________ SUNDAY, MARCH 3, 1996 ________________________________________________________________________________ 10:00 A.M. - 12:00 noon Discussion - Brunch Dockside Blg. "Future Directions of Strctural Biology" ALL SPEAKERS WILL SERVE AS PANEL MEMBERS 12:00 noon - 1:00 P.M. Break NMR Techniques Workshop Dockside Blg. (In Cooperation with Varian Instruments) 1:00 P.M. - 2:00 P.M. George Gray - Varian Instruments Dockside Blg. "Recent Advances in NMR Technology for Biomolecular NMR" 2:00 P.M. - 2:30 P.M. Shanmin Zhang - UTMB Dockside Blg. "Suppression of Radiation Damping During Acquisition" 2:30 P.M. - 4:00 P.M. Additional short contributions Dockside Blg. 4:00 P.M. - 5:00 P.M. Applicaitons on Varian/Oxford 600 Dockside Blg. and 750 Unity Plus and Varian/HARC 400 MHz Unity PLus systems with George Gray and NMR Center staff ---------------------------------------------------------------------- CLIMATE The weather in Galveston, a resort island off the Texas coast near Houston, in March is warm with average temperatures ranging from a low of 55 degrees to a high of 75 degrees. ---------------------------------------------------------------------- TRAVEL AND ACCOMMODATION Hotel space has been reserved at the Hotel Galvez, however, to insure conference rates, arrangements must be made by February 8th: Rate: $65/Single, $85/Double $95/Triple & Quad, $175/Deluxe Suites FOR RESERVATIONS CALL: 1-800-392-4285 ---------------------------------------------------------------------- COSTS: Payment of $50.00 total for optional receptions, lunches and dinners should be made to University of Texas Medical Branch by February 20th. Please, payment by checks only. ---------------------------------------------------------------------- STRUCTURAL BIOLOGY SYMPOSIUM, UNIVERSITY OF TEXAS MEDICAL BRANCH AT GALVESTON MARCH 1-3, 1996 REGISTRATION FORM NAME:________________________________________________________________________ WORK ADDRESS:________________________________________________________________ INSTITUTION NAME:____________________________________________________________ INSTITUTION NAME:____________________________________________________________ CITY:__________________________________STATE:_____________ZIP CODE:__________ OFFICE PHONE:____________________FAX NUMBER:_________________________________ EMAIL ADDRESS:_______________________________________________________________ CHECK THOSE WHICH APPLY: ______Enclosed is my check for $50.00. ______I will be participating in the Symposium on: FRIDAY_________ SATURDAY_______ SUNDAY_________ ______I will be participating in the poster session and have included a copy of my abstract. ---------------------------------------------------------------------- HOTEL REGISTRATION FORM NAME:________________________________________________________________________ WORK ADDRESS:________________________________________________________________ INSTITUTION NAME:____________________________________________________________ CITY:__________________________________STATE:_____________ZIP CODE:__________ OFFICE PHONE:____________________FAX NUMBER:_________________________________ EMAIL ADDRESS:_______________________________________________________________ ARRIVAL DATE:_____________________DEPARTURE DATE:____________________________ FOR ARRIVALS LATER THAN 6:00 P.M., A CREDIT CARD NUMBER IS NEEDED CREDIT CARD (i.e. type)______________________________________________________ CREDIT CARD ACCT. #_______________________________________EXP. DATE__________ ACCOMMODATION DESIRED: ________SINGLE ACCOMMODATIONS $65.00/NIGHT ________DOUBLE ACCOMMODATIONS $85.00/NIGHT ________TRIPLE AND QUAD ACCOMODATIONS $95.00/NIGHT ________DELUXE SUITES $175.00/NIGHT PLEASE NOTE: TO INSURE CONFERENCE RATES, RESERVATIONS MUST BE MADE NO LATER THAN 2/8/96 ----------------------------------------------------------------------------- Please complete and return the conference registration form and/or hotel registration form, together with your payment, to: Jacqueline Luxon; Administrative Secretary ADDRESS: Sealy Center for Structural Biology Dept. for Human Biological Chemistry and Genetics University of Texas Medical Branch Galveston, TX. 77555-1157 PHONE: (409)747-6800 FAX: (409)747-6850 EMAIL: jacky@nmr.utmb.edu ----------------------------------------------- David Gorenstein Director, Sealy Center for Structural Biology Professor, Dept. of Human Biological Chemistry and Genetics University of Texas Medical Branch Galveston, TX 77555-1157 Office: (409) 747 6801 Main Office/Voice Mail: (409) 747 6800 Fax: (409) 747 6850 E-MAIL ADDRESS: david@nmr.utmb.edu http://www.nmr.utmb.edu/ From owner-structural-nmr@net.bio.net Tue Jan 23 22:00:00 1996 Path: biosci!BIOINFO.ERNET.IN!deva From: deva@BIOINFO.ERNET.IN (deva) Newsgroups: bionet.structural-nmr Subject: Re: Dielectric Constant Calculation Date: 24 Jan 1996 07:20:47 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 32 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net On Tue, 23 Jan 1996, Tracy Leon Whitehead wrote: > > > On 22 Jan 1996, Feng Xu wrote: > > > Does anyone know a way to estimate the dielectric constant of a > > solution composed of different solvents with varying dielectric > > constatns? > I also am interested in being able to approximate the dielectric constant > in mixed solutions...my research falls along the same lines, and this > info could be vital! > Hi, Text books on thin layer chromatography usually mention this. Try looking through some good book on tlc. Hope this helps. Devapriya ______________________________________________________________________ Devapriya Choudhury Ph.D. | Research Associate | Bioinformatics Centre | University of Poona | Pune -411 007 | India | | e-mail deva@bioinfo.ernet.in | ______________________________________|_______________________________ When there were no computers. Programming was no problem. ______________________________________________________________________ From owner-structural-nmr@net.bio.net Wed Jan 24 22:00:00 1996 Path: biosci!RA.MSSTATE.EDU!tlw1 From: tlw1@RA.MSSTATE.EDU (Tracy Leon Whitehead) Newsgroups: bionet.structural-nmr Subject: Re: Dielectric Constant Calculation Date: 25 Jan 1996 08:16:28 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net Thanks... I'll give it a try. Tracy From owner-structural-nmr@net.bio.net Wed Jan 24 22:00:00 1996 Path: biosci!rutgers!gatech!newsfeed.internetmci.com!EU.net!peer-news.britain.eu.net!lyra.csx.cam.ac.uk!bioc.cam.ac.uk!arcr1 From: arcr1@bioc.cam.ac.uk (Andrew Raine) Newsgroups: bionet.structural-nmr Subject: Post-doc Position Vacant (Cambridge, UK) Date: 25 Jan 1996 11:24:10 GMT Organization: Somewhere in the University of Cambridge Lines: 45 Distribution: world Message-ID: <4e7p8q$bu2@lyra.csx.cam.ac.uk> NNTP-Posting-Host: giza.bioc.cam.ac.uk Keywords: Protein, DNA, NMR, Structural Biology The following is the text of an advert which appeared in NATURE on the 11th of January: If you are interested in applying, you are encouraged to make contact (by email if neccessary) as soon as possible. -------------------------------------------------------------------------------- University of Cambridge Cambridge Centre for Molecular Recognition Department of Biochemistry Post-doctoral Research Associate Applications are invited for a post-doctoral research associate to assist in the running of the CCMR NMR computing facility in the Department of Biochemistry. The facility provides support for data processing and spectral analysis. The successful candidate will collaborate on structure-determination projects, train researchers, and administer the CCMR cluster of workstations. He/she would also be expected to carry out research into the methodology of structural analysis using NMR. It is essential that candidates have programming skills, and a strong interest in structural biology. Experience of the administration of UNIX workstations would be an advantage. The post is available immediately until 28 February 1998 in the first instance, at a salary of L 14,317 - 19,848 Letters of application, a full CV including names and addresses of two referees should be forwarded as soon as possible to Dr. Ernest Laue, CCMR, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK. Informal enquiries may be made of Dr. Laue (email: E.D.Laue@bioc.cam.ac.uk, tel: +44 1223 333677) or Dr. Andrew Raine (email: A.R.C.Raine@bioc.cam.ac.uk, tel: +44 1223 333744) The Department of Biochemistry has a no-smoking policy. The University follows an equal opportunities policy and aims to achieve the highest quality in teaching and research. From owner-structural-nmr@net.bio.net Thu Jan 25 22:00:00 1996 Path: biosci!SGI3.MAGNET.FSU.EDU!fengxu From: fengxu@SGI3.MAGNET.FSU.EDU (Feng Xu) Newsgroups: bionet.structural-nmr Subject: Dipole Calculation Date: 25 Jan 1996 19:36:52 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <9601260327.AA06903@sgi3.magnet.fsu.edu> NNTP-Posting-Host: net.bio.net Dear netters, I'm trying to calculate the net dipole moment of my small peptide using GRASP, which requires partial charge assignement. Since trytophans are the only possbile dipole moment contributors in my peptide, I can simply ignore the rest residues. NOw my questions are what is the appropriate way to make the partial charge assignement, i.e. which atom(s) should be assigned and what value(s) to use. Could anybody kindly give me some hints on that? Many thanks! feng From owner-structural-nmr@net.bio.net Sun Jan 28 22:00:00 1996 Newsgroups: bionet.structural-nmr Path: biosci!agate!howland.reston.ans.net!gatech!newsfeed.internetmci.com!in1.uu.net!nih-csl!rvenable From: rvenable@deimos.cber.nih.gov (Rick Venable) Subject: Re: Dipole Calculation Message-ID: <1996Jan29.035617.19040@alw.nih.gov> Sender: postman@alw.nih.gov (AMDS Postmaster) Nntp-Posting-Host: deimos.cber.nih.gov Organization: FDA/CBER Biophysics Lab X-Newsreader: TIN [version 1.2 PL2] References: <9601260327.AA06903@sgi3.magnet.fsu.edu> Date: Mon, 29 Jan 1996 03:56:17 GMT Lines: 23 On 25 Jan 1996 19:36:52 -0800 Feng Xu asked: > I'm trying to calculate the net dipole moment of > my small peptide using GRASP, which requires > partial charge assignement. Since trytophans > are the only possbile dipole moment contributors > in my peptide, I can simply ignore the rest > residues. NOw my questions are what is the > appropriate way to make the partial charge > assignement, i.e. which atom(s) should be assigned > and what value(s) to use. What, and ignore all the dipoles from C=O and N-H bonds in the backbone? You could possibly ignore hydrocarbon sidechains for residues like Leu or Val, but not their backbone atoms. Partial charges are published in a variety of places, esp. for protein modeling parameter sets; typically, partial charges are obtained from quantum calculations. -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| / Not an official statement \ rvenable@deimos.cber.nih.gov \/ |=| \ or position of the FDA. / From owner-structural-nmr@net.bio.net Sun Jan 28 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.structural-nmr Subject: Re: ANNOUNCE: MOLMOL - Molecule Display and Analysis Date: 29 Jan 1996 10:43:47 -0000 Lines: 87 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4ei8d3$db8@mserv1.dl.ac.uk> Original-To: str-nmr@dl.ac.uk Note that the K.Wutrich's group URL for MOLMOL is: http://odin.ethz.ch/wuthrich/software/molmol/ I could not reach any http://www.mol.biol.ethz.ch/.... Bye Marco Tato' Pharmacia & Upjohn Structural Biochemistry - NMR lab via Giovanni XXIII n.23 20014 Nerviano (MI) Italy voice: xx39-331-583147,6,5 fax: 583100 e-mail: marco.tato@itner.pharmacia.se (P&U) marco_tato@rcm.inet.it (private) Hay que beber para recordar y comer para olvidar Pepe Carvalho ______________________________ Reply Separator _________________________________ Subject: ANNOUNCE: MOLMOL - Molecule Display and Analysis Author: server-daemon@dl.ac.uk at Internet Date: 96/01/26 00.53 We are proud to announce the free public availability of MOLMOL, a new program for display and analysis of macromolecular structures. MOLMOL was developed as a joint project between BRUKER/Spectrospin and the group of Prof. Wuthrich at the Institut fuer Molekularbiologie und Biophysik, ETH Zurich. The source code and precompiled binaries for some common UNIX workstations are available from the following URLs: ftp://ftp.mol.biol.ethz.ch/pub/software/MOLMOL ftp://ftp.spectrospin.ch/pub/sag/MOLMOL ftp://ftp.bruker.de/pub/bruker/MOLMOL ftp://ftp.bruker.com/pub/nmr/mirror.bruker.de/MOLMOL Please download the file README for further instructions. The legal information is in the file COPYING supplied with the program, you are required to read this file and agree with its contents before using the program. Further information can be found at: http://www.mol.biol.ethz.ch/wuthrich/software/molmol/ Following is the abstract from the paper (Journal of Molecular Graphics, in press): MOLMOL is a molecular graphics program for display, analysis, and manipulation of three-dimensional structures of biological macromolecules, with special emphasis on nuclear magnetic resonance (NMR) solution structures of proteins and nucleic acids. MOLMOL has a graphical user interface with menus, dialog boxes and on-line help. The display possibilities include conventional presentations, as well as novel schematic drawings, with the option of displaying different presentations in one view. The covalent molecular structures can be modified by addition or removal of individual atoms and bonds; the three-dimensional structure can be manipulated by interactive rotation about individual dihedral angles. Special efforts were made to allow for appropriate display and analysis of sets of (typically 20-40) conformers that are conventionally used to represent the result of a NMR structure determination, using functions for superimposing sets of conformers, calculation of root mean square distance (RMSD) values, identification of hydrogen bonds, checking and displaying violations of NMR constraints, and identification and listing of short distances between pairs of hydrogen atoms. -- Reto Koradi (kor@mol.biol.ethz.ch, http://www.mol.biol.ethz.ch/~kor) From owner-structural-nmr@net.bio.net Sun Jan 28 22:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!infobiogen.fr!sansgene.genethon.fr!julienas!news2.EUnet.fr!EU.net!Austria.EU.net!newsfeed.ACO.net!swidir.switch.ch!swsbe6.switch.ch!scsing.switch.ch!elna.ethz.ch!usenet From: Reto Koradi Newsgroups: bionet.structural-nmr Subject: Re: ANNOUNCE: MOLMOL - Molecule Display and Analysis Date: 29 Jan 1996 15:58:43 GMT Organization: Swiss Federal Institute of Technology (ETHZ) Lines: 16 Message-ID: <4eiqrj$fo2@elna.ethz.ch> References: <4ei8d3$db8@mserv1.dl.ac.uk> NNTP-Posting-Host: odin.ethz.ch Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12 (X11; I; SunOS 5.4 sun4d) To: marco.tato@itner.pharmacia.se X-URL: news:4ei8d3$db8@mserv1.dl.ac.uk wrote: >Note that the K.Wutrich's group URL for MOLMOL is: > >http://odin.ethz.ch/wuthrich/software/molmol/ > >I could not reach any > >http://www.mol.biol.ethz.ch/.... http://www.mol.biol.ethz.ch/ is correct, it works for me when I use it from another site. I also gave it to many other people, and nobody ever complained. The other one will work, too, but it's outdated and should not be used anymore. Reto From owner-structural-nmr@net.bio.net Sun Jan 28 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: "Dr. Michael Grzonka" Newsgroups: bionet.structural-nmr Subject: The JCAMP standard of spectroscopic data transfer - a summary Date: 29 Jan 1996 10:35:49 -0000 Lines: 137 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4ei7u5$d10@mserv1.dl.ac.uk> content-length: 6591 X-Sun-Charset: US-ASCII Original-To: str-nmr@dl.ac.uk, bionet-news@dl.ac.uk On the current status of JCAMP as data transmission standard for NMR,IR and MS ------------------------------------------------------------------------------ Michael T Grzonka, Weinheim, Germany, January 1996 Contents: --------- 0. Preface I. Historical Background II. The existing JCAMP standards (incl. references) III. JCAMP today IV. Future 0. PREFACE ---------- The famous IR activities in the early days of JCAMP have been covered earlier in this newsgroup, but there was serious further development since then. The general idea in that respect was always, that a fully developed JCAMP should cover more than just one spectroscopy. To the best of my knowledge I would like to summerize the current status below. I. HISTORICAL BACKGROUND ------------------------ It happened as early as 1990 that the German Federal Ministry of Research and Development had set-up a large funding programme covering specialised information in chemistry. Amongst the subjects funded was (and is still to the end of 1995) spectroscopy. The intentions of the German Government, however, were much broader than just this: beyond SpecInfo (covering the spectroscopy bit) the funding included Beilstein, Gmelin, and the Detherm Database. All four were developed from their ancient stages (e.g. books and paperwork for, say, Beilstein) into electronic form. All four databases are hosted and available to the public at STN International (the place were you get CAS Online). Please remember that in those days, WINDOWS and the like was virtually non-existent, and proprietory data formats were the credo of almost every instrument vendor (except for IR, of course). II. The existing JCAMP standards -------------------------------- Important for the further development of JCAMP was, that the generous funding of the German government fueled a inspiring discussion amongst the institutions and companies involved about all subjects releated to chemical information handling. Amongst these subjects was the exchange of chemical information. To many of us, the early JCAMP seemed to have shown an ideal way of how to approach this problem: - first non-binary approach ever - vendor independent, JCAMP is not owned by anybody - printable characters only (important for e-mail etc.) - reasonable compression rates (long before LHARC etc. did show up) - extendable and open definitions to allow further improvements Particulary the use of printables as the only valid characters has proven to be a very good move, since discussions on ASCII vs. EBCDIC, or: 8, 16, 32 bit vs. 64 bit were survived by all JCAMPs with considerable ease. However, there was a need for written definitions of JCAMP standards for more than just IR, and several people in the institutions and companies mentioned above have taken initative to push the subject. The following standards have been proposed and published since then: name : JCAMP-DX, subject covered: IR-spectra authors: R.S. McDonald and P.A. Wilks, Jr. journal: Appl.Spectroscopy, 42(1), 151-162 (1988) name : JCAMP-CS, subject covered: chemical structures authors: J.Gasteiger, B.M.P. Hendirks, P.Hoever,C.Jochum and H. Somberg journal: Appl. Spectroscopy, 45(1), 4-11 (1991) name : JCAMP-DX for NMR, subject covered: NMR FIDs and spectra authors: A.N. Davies and P. Lampen journal: Appl. Spectroscopy, 47(8), 1093-1099 (1993) name : JCAMP-DX for Mass Spectrometry authors: P. Lampen, H. Hillig, A. N. Davies and M. Linscheid journal: Appl. Spectroscopy, 48(12), 1545-1552 (1994) III. JCAMP today ---------------- The standards described in the above publications have been accepted and given free for publication by the Joint Commitee on Atomic and Molecular Physics Data (JCAMP). Meanwhile the usefulness has been recognised by such organisations as IUPAC and ASTM. As outlined in the most recent of the above papers, JCAMP has undergone several extensions and mutations to its current version 5.0. JCAMP version 5.0 is the only approved data exchange standard which allows you to keep chemical structure, raw and processed data of several spectroscopies, and (for NMR), signal assignments altogether in one file. According to the early principles, this file consists of printable ascii and is therefore suitable for transmission and storage under today's and tomorrow's conditions. (LHARC etc. can squize an additional 20-30% out of most spectra in JCAMP's DIFDUP format). Nowadays, a lot of NMR related products have picked up JCAMP as a format to exchange information. Although promised by all 3 big NMR instrument manufacturers on the 6th INUM Conference in Italy (1990), only Bruker has fully integrated JCAMP into their software. UXNMR/XWIN-NMR as well as 1D WINNMR employ export functions for JCAMP. According to Steve Patt, Varian can supply a macro to export their 1D NMR spectra into JCAMP. The current status for JEOL is not known to me at this time (January 1996). SpecInfo Online (STN International) allows downloading of NMR, IR and MS spectra from its 100,000+ documents including chemical structure and signal assignment where appropriate. And so does SpecInfo Inhouse. The WINDOWS-based NMR database called WIN-SpecEdit (developed by Bruker, BASF AG and Chemical Concepts) can import and export its inventory of NMR information (including assigned structures) and even email it by the press of a button - all using JCAMP as the underlying concept. IV. Future ---------- Other proposals, like ADISS or netCDF, were not yet able to convince the public in general because of various problems arising from their binary nature or some inherent assumptions on the binary structure of the data handled. However, some of the proposed features are worth considering for the future of data transmission standards. At the time of writing this, JCAMP is the only standard ready for application and its usefulness is out of question. The recent boost of e-mail and other net activites may well push forward JCAMP, because easy electronic transmission and the open, flexible nature of the assumptions underlying this idea of a standard are of the best available at this time. Michael Grzonka Facts and opinions as expressed above represent my own judgement based on my current knowledge. Chemical Concepts must not be held responsible, and Chemical Concepts may or may not agree with these statements. Your comments and suggestions on JCAMP are welcome at davies@helios.isas-dortmund.de (Dr A. N. Davies) and grzonka@cc.vchgroup.de (Dr M. T. Grzonka) From owner-structural-nmr@net.bio.net Mon Jan 29 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!nntp.coast.net!harbinger.cc.monash.edu.au!news.cs.su.oz.au!metro!metro!news.une.edu.au!metz.une.edu.au!not-for-mail From: cgarvey@metz.une.edu.au (gravityboy) Newsgroups: bionet.structural-nmr Subject: Dielectric Constants Of Solvents Date: 30 Jan 1996 01:00:51 GMT Organization: University of New England, NSW, Australia Lines: 35 Message-ID: <4ejqk3$mel@grivel.une.edu.au> NNTP-Posting-Host: metz.une.edu.au X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] While browsing I've seen question about this subject. Some dielectric constants of solvent mixture have been extensively studied. There are some references are contained in a series of papers (3 or 4) by Drummond et al. in J. Chem. Soc.., Faraday Trans. I., starting with vol 85, 521 (1989). You may have look around through the text. They have used solvent mixtures to investigate the non-electrostatic component of protonating an acid/base indicator at a micellar interface. There are other mixtures of solvents in other papers by Drummond. maybe this was some use feel free to get back with questions. chris -- >:)(:< ****APHORISMS FOR ALL OCCASIONS**** ______________________________________ ************************************** -------------------------------------- Christopher J. Garvey Tamworth Agricultural Research Centre AUSTRALIA email cgarvey@metz.une.edu.au ======================================= /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-structural-nmr@net.bio.net Mon Jan 29 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.structural-nmr Subject: E-mail adress Date: 30 Jan 1996 10:11:31 -0000 Lines: 16 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4ekqsj$863@mserv1.dl.ac.uk> X-Sender: terez@tome.cbs.univ-montp1.fr (Unverified) Original-To: str-nmr@dl.ac.uk Dear Netters, I would like to know the E-mail adress of Klaas Hallenga, who is working at the University of Chicago. Thank you in advance, Theresa Theresa E. Malliavin terez@tome.cbs.univ-montp1.fr Centre de Biochimie Structurale tel: (33) 67 04 34 36 Faculte de Pharmacie fax: (33) 67 52 96 23 15, av. Ch. Flahault F-34060 Montpellier From owner-structural-nmr@net.bio.net Mon Jan 29 22:00:00 1996 Newsgroups: bionet.structural-nmr,bionet.molbio.proteins Path: biosci!daresbury!is.bbsrc.ac.uk!bcc.ac.uk!davis From: davis@bsm.bioc.ucl.ac.uk (Ben Davis) Subject: Oxidised Met Message-ID: <1996Jan30.100702.37854@ucl.ac.uk> Date: Tue, 30 Jan 1996 10:07:02 GMT Organization: University College London X-Newsreader: TIN [version 1.2 PL2] Lines: 19 Xref: biosci bionet.structural-nmr:1069 bionet.molbio.proteins:6873 Hi, does anyone have any experience with the 13C & 1H shifts you'd expect for oxidised Met, especially the -Me shifts ? I've got a suspicious peak in an HMQC ... I dug out my old copy of Williams & Fleming, which predicts ~ 35 ppm in the C & ~ 2.5 ppm in the H, but I'd prefer to hear of an experimental value if possible. Thanks, Ben -- ______________________________________________________________________________ Ben Davis, | LICR NMR Group, Dept. of Biochemistry, http://www.biochem.ucl.ac.uk/~davis | University College London, UK "They can make me do it, but they can't make me do it with dignity." From owner-structural-nmr@net.bio.net Mon Jan 29 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!nntp.coast.net!news00.sunet.se!sunic!news99.sunet.se!nntp-trd.UNINETT.no!daresbury!not-for-mail From: Newsgroups: bionet.structural-nmr Subject: Re[2]: ANNOUNCE: MOLMOL - Molecule Display and Analysis Date: 30 Jan 1996 10:04:41 -0000 Lines: 36 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4ekqfp$7mf@mserv1.dl.ac.uk> Original-To: ruba@mol.biol.ethz.ch (Rudolf Baumann), str-nmr@dl.ac.uk I'm sorry for the problems caused by our DNS: now it's working. Regards Marco Tato' Pharmacia & Upjohn Structural Biochemistry NMR lab Nerviano (MI) Italy ______________________________ Reply Separator _________________________________ In bionet.structural-nmr you write: >Note that the K.Wutrich's group URL for MOLMOL is: >http://odin.ethz.ch/wuthrich/software/molmol/ >I could not reach any >http://www.mol.biol.ethz.ch/.... In this case something with your DNS is not working correctly! http://www.mol.biol.ethz.ch/ is the right address. R. Baumann System administrator of domain mol.biol.ethz.ch -- ----------------------------------------------------------------------------- Rudolf E. Baumann ruba@mol.biol.ethz.ch Institut fuer Molekularbiologie & Biophysik http://www.mol.biol.ethz.ch/ ETH Hoenggerberg (HPM G6) ,,, Tel. ++41 1 633 33 97 CH-8093 Zuerich/Switzerland (o o) Fax ++41 1 633 10 73 ----------------------------------oOO--(_)--OOo------------------------------ From owner-structural-nmr@net.bio.net Wed Jan 31 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!csn!nntp-xfer-2.csn.net!news-2.csn.net!csn!magnus.acs.ohio-state.edu!slip9-2.acs.ohio-state.edu!lboros From: lboros@magnus.acs.ohio-state.edu (Laszlo G. Boros) Newsgroups: bionet.structural-nmr Subject: HMP shunt metabolites on 31P NMR Date: Thu, 1 Feb 1996 00:07:09 GMT Organization: The Ohio State University Lines: 7 Message-ID: NNTP-Posting-Host: slip9-2.acs.ohio-state.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev B final beta #1] We are trying to track down some of the phosphate monoesther metabolites of the Hexose Monophosphate Shunt (HMPS) by 31P NMR spectroscopy. We are using human cells and the first try was unsuccessful. I would like to know if anyone on the list could suggest a method that would take us closer to the detection of glucose-6P, riboze-5P and fructose-1-6-DP by using cell extracts or living cells. Help is very much appreciated. Laszlo G. Boros, MD From owner-structural-nmr@net.bio.net Wed Jan 31 22:00:00 1996 Path: biosci!INDIANA.EDU!mpagel From: mpagel@INDIANA.EDU (Marty Pagel) Newsgroups: bionet.structural-nmr Subject: lines in postscript files Date: 1 Feb 1996 14:58:00 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 44 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net To InsightII users, Occasionally I get a thin horizontal line that stretches almost across the entire page in my postscript plots. This line usually appears just above my image (molecule), but sometimes it appears in the middle of my image. I generate these plots using Export_Image in InsightII version 95.0, selecting postscript, grayscale, a user-defined area of the screen, 300 dpi or 600 dpi, and printing to a file. I have NEVER seen a line in 72 dpi plots. I've tried "lp" and "lpr" printing to a number of different printing devices (300 dpi and 600 dpi) through different print-server platforms (or directly to the printer)---the horizontal line is still there. Displaying the postscript file in XV, xpsview, or ghostscript (running at 72 dpi) usually shows the line, but not always. I think the line is definitely part of the postscript file. I suspect that the 300 & 600 dpi options are picking up something on the screen. It might be the rubberband that defines the print region {which is just above my image}, or something underneath the InsightII window, etc? I've seen the line with XL 8-bit and 24-bit, XZ 24-bit , and Extreme 24-bit graphics on SGI workstations. However, I'm not sure if the Export_Image command is doing some sort of screen dump, so this is just my best guess. Has anyone else seen these horizontal lines? Any suggestions about how to get rid of these lines? Also, I often see others generate a plot with Export_Image using the "current window" option. The Export_Image menu (in the default position, the upper left corner of the InsightII window) overlaps their image. The final print-out has small, square blank regions. These blank regions are removed if the Export_Image menu and the InsightII window are positioned and resized so that they do not overlap. I'm guessing that the square "fields" in an overlapping Export_Image menu are incorporated in the image plot. If I have an extremely detailed plot (lots of graphs, moelcules, etc) and I want a full screen, is there a way to get a good plot, without these square blank areas, without moving the menu/InsightII window? Thanks, Marty Pagel mpagel@indiana.edu --- __o Department of Chemistry Phone: (812)-855-6492 --- \<, Indiana University Fax: (812)-855-8300 --- ()/ () Bloomington, IN 47405-4001 http://nmrsg1.chem.indiana.edu/~mpagel