From owner-structural-nmr@net.bio.net Sun Oct 01 23:00:00 1995 Path: biosci!CHEM.CHEM.ROCHESTER.EDU!krugh From: krugh@CHEM.CHEM.ROCHESTER.EDU (Thomas R. Krugh) Newsgroups: bionet.structural-nmr Subject: Biomolecular Structure Symposium (October 23-24, 1995) Date: 1 Oct 1995 19:05:02 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 54 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net A Biomolecular Structure Symposium will be held as part of the NorthEast Regional Meeting (NERM) of the American Chemical Society on Monday afternoon, October 23, and all day Tuesday, October 24, 1995 at the Rochester Convention Center in Rochester, New York. The NERM meeting is open to all interested scientists. Thomas R. Krugh, Presiding Speakers: G. Marius Clore (NIH) Herbert A. Hauptman (Hauptman-Woodward Medical Res. Inst.) Peter B. Moore (Yale) Thomas A. Steitz (Yale) Philip N. Borer (Syracuse) Jon Clardy (Cornell) William L. Duax (Hauptman-Woodward Medical Res. Inst.) Steven E. Ealick (Cornell) Thomas R. Krugh (Rochester) Linda Nicholson (Cornell) Byron Rubin (Medical College of Pennsylvania) John SantaLucia, Jr. (Wayne State) Ramaswamy H. Sarma (Albany) Ned Seeman (NYU) G. David Smith (Hauptman-Woodward Medical Res. Inst.) Michael P. Stone (Vanderbilt) A. Joshua Wand (Buffalo) The close of the symposium is followed by the Harrison Howe address by: Stuart Schreiber (Harvard) You may also be interested in the Monday morning symposium on Biological Electron Transfer. James Norris (Chicago) Leslie Dutton (Univ. of Pennsylvania) George McLendon (Princeton) Mitchell Mutz (Princeton) Amy Rosenzweig (Harvard) Please contact Arlene Bristol (716-275-4218; bristol@chem.rochester.edu) or Thomas Krugh for additional information on these programs, and/or registration and hotel information. _________________________________________________________________________ Thomas R. Krugh Krugh@chem.rochester.edu Department of Chemistry Phone: (716) 275-4224 University of Rochester FAX: (716) 473-6889 Rochester, NY 14627 _________________________________________________________________________ From owner-structural-nmr@net.bio.net Sun Oct 01 23:00:00 1995 Path: biosci!daresbury!bioftp.unibas.ch!citi2.fr!jussieu.fr!oleane!tank.news.pipex.net!pipex!uknet!bhamcs!news.ox.ac.uk!news From: "Simon M. Brocklehurst" Newsgroups: bionet.structural-nmr Subject: NAOMI Version 2.2 Date: 2 Oct 1995 13:55:56 GMT Organization: University of Oxford Lines: 68 Message-ID: <44or1c$ju5@news.ox.ac.uk> NNTP-Posting-Host: nmrz.ocms.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; IRIX 5.3 IP22) X-URL: news:bionet.structural-nmr 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 2.2 is available _now_ from the NAOMI Web site at: http://www.ocms.ox.ac.uk/~smb/Software/N_details/naomi.html or via anonymous ftp from: 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 : solvent accessibility, symmetry operations, disulphide bonds, new side-chain modelling commands, new molscript output options e.g. see the illustrations on the Cytokines Web: http://www.ocms.ox.ac.uk/~smb/cyt_web/ Fixes of minor bugs in key residues and molscript output commands. _____________________________________________________________________________ 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 Tue Oct 03 23:00:00 1995 Path: biosci!bcm.tmc.edu!pendragon.jsc.nasa.gov!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!news.sprintlink.net!howland.reston.ans.net!usenet.ins.cwru.edu!magnus.acs.ohio-state.edu!infoserver.bgsu.edu!dad.bgsu.edu!dychen From: dychen@dad.bgsu.edu (Deng-Ywan Chen) Newsgroups: bionet.structural-nmr Subject: pfg specification Date: 4 Oct 1995 14:12:36 GMT Organization: Bowling Green State Univ. Lines: 15 Distribution: world Message-ID: <44u4ok$7vt@infoserver.bgsu.edu> NNTP-Posting-Host: ernie.bgsu.edu hello everyone, we, bowling green state university, are fairly new into this techniques of pulsed-field-gradient nmr at our unity+400 instrument. we would like to ask for everyone's opinion/suggestion/experience on the following issue. our pfg system was installed and tested by varian's engineer and we did run couple pfg experiments with good results. the question we have is - are there ways of routinely checking at the performance of our pfg system? just like the line width/line shape specification, are there standard pfg experiments we can run (say, every 6 months) and check at its specification? (for example, the s/n ratio, or lines' separation of standard pfg experiment with standard sample.) we'll appreciate all of your responses and be glad to summarize the information we receive. chen ps. in order to spread out this request, i'll cross post it through couple news groups/email servers, i apologize if you receive multiple copies. From owner-structural-nmr@net.bio.net Thu Oct 05 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!howland.reston.ans.net!news.sprintlink.net!news00.sunet.se!sunic!sunic!sunic.sunet.se!columba.udac.uu.se!rigel.bmc.uu.se!gerard From: gerard@rigel.bmc.uu.se (Gerard Kleijwegt) Newsgroups: bionet.structural-nmr Subject: Re: What's happening here?! Date: 6 Oct 1995 17:56:00 GMT Organization: Uppsala University Lines: 20 Distribution: world Message-ID: <453qjg$1d6g@columba.udac.uu.se> References: NNTP-Posting-Host: rigel.bmc.uu.se In article , bijt@zeus.bris.ac.uk (DJ. Wood) writes: |> Dear NMR fellows: ... |> I want to read of my interest under appropriate newsgroups but not junk |> mails. I'm so pissed. ****** Don't drink & post ! |> |> Jiro |> |> J.Takei |> Dept. Biochem. |> Uni. Bristol |> UK |> *44-117-928-9000 x.4359 |> --cd From owner-structural-nmr@net.bio.net Thu Oct 05 23:00:00 1995 Newsgroups: bionet.structural-nmr Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!torn!utnut!oci!neptune!moverdui From: Michael Overduin Subject: POSTDOCTORAL POSITION IN NMR X-Sender: moverdui@neptune Content-Type: TEXT/PLAIN; charset=US-ASCII Message-ID: Sender: news@oci.utoronto.ca Organization: Ontario Cancer Institute - U of Toronto Mime-Version: 1.0 Date: Fri, 6 Oct 1995 19:31:25 GMT Lines: 35 I have an opening in my laboratory in the Department of Pharmacology at the University of Colorado Health Sciences Center. The position will involve protein expression and purification, and the application of multidimensional NMR and other biophysical techniques to characterize protein structure and function. Current research focuses on proteins involved in signal transduction and cell adhesion. The University of Colorado Health Sciences has begun building a multi-user NMR facility with new 600, 500, and 400 MHz spectrometers to be installed beginning next January. Silicon Graphics and Sun workstations will be available for data processing and analysis. A fermentation core facility is available for protein expression. The position will be available in early 1996. A competitive salary is available. The campus is located in a residential area a few miles from downtown Denver. Qualifications: Ph. D. in biochemistry, biophysics, biology, chemistry or equivalent is required. Skills heteronuclear NMR, protein biochemistry, and UNIX would be assets. Please send a letter, c.v. and 3 letters of reference to: Michael Overduin, Division of Molecular and Structual Biology, Ontario Cancer Institute 610 University Avenue, Toronto, Ontario, Canada M5G 2M9 FAX: (416) 946-6529, Phone: (416) 946-2000 ext 4930 moverdui@oci.utoronto.ca From owner-structural-nmr@net.bio.net Thu Oct 05 23:00:00 1995 Newsgroups: bionet.structural-nmr Path: biosci!bcm.tmc.edu!cs.utexas.edu!swrinde!tank.news.pipex.net!pipex!warwick!bsmail!zeus!bijt From: bijt@zeus.bris.ac.uk (DJ. Wood) Subject: What's happening here?! Message-ID: Sender: usenet@uns.bris.ac.uk (Usenet news owner) Nntp-Posting-Host: zeus.bris.ac.uk Organization: University of Bristol, England X-Newsreader: TIN [version 1.2 PL2] Date: Fri, 6 Oct 1995 11:11:00 GMT Lines: 18 Dear NMR fellows: Recently I've seen totally inrelevant articles posted to this news group. The first one was an advert for an erotic tape and today, another advert for a recipe book. They are found in other bionet or sci newsgroups. I'm really annoyed! I want to read of my interest under appropriate newsgroups but not junk mails. I'm so pissed. Jiro J.Takei Dept. Biochem. Uni. Bristol UK *44-117-928-9000 x.4359 From owner-structural-nmr@net.bio.net Sun Oct 08 23:00:00 1995 Path: biosci!SNEEZY.FHIS.NET!barry From: barry@SNEEZY.FHIS.NET ("Barry Schweitzer") Newsgroups: bionet.structural-nmr Subject: Post-doctoral Position Available Date: 9 Oct 1995 09:01:50 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 49 Sender: daemon@net.bio.net Distribution: world Message-ID: <9510091159.ZM13441@sneezy.fhis.net> NNTP-Posting-Host: net.bio.net POST-DOCTORAL POSITION AVAILABLE FOR PROTEIN NMR SPECTROSCOPIST A post-doctoral position is available starting January 1,1996 in the Laboratory of Structural Biology at the Walt Disney Memorial Cancer Institute (WDMCI) at Florida Hospital, a not-for-profit 1500-bed acute care research hospital in Orlando, Florida. Research in the Laboratory of Structural Biology is focused on the development of new anti-cancer agents through the use of Nuclear Magnetic Resonance (NMR) and computer modeling. Specific areas of interest include: (1) Structure- function relationships in proteins involved in blood coagulation and fibrinolysis; (2) Structure-function relationships in chemokines; (3) Effects of anti-cancer drugs on DNA-protein interactions. Candidates for postdoctoral fellows must have a Ph.D. degree in Chemistry or Biochemistry and have demonstrated experience in NMR spectroscopy and its use in protein structure determination. Experience with isotopically-labeled proteins, pulse sequence design, and/or molecular biology (PCR, cloning, protein over- expression/purification) is also desirable, but optional. Salary rate is negotiable and will be set commensurate with experience. The Laboratory of Structural Biology is located in a new 16,000 sq. ft. research facility that houses the Cancer Research Division of the WDMCI. Our laboratory has exclusive use of a Varian UnityPlus 600 MHz spectrometer with triple resonance and gradient capabilities and several SUN and SGI workstations. The Cancer Research Division also has excellent facilities for cellular and molecular biology, tissue culture, and protein chemistry. WDMCI is affiliated with the University of Central Florida, a 25,000-student research university located 2 minutes away. Send curriculum vitae and names of three references to: Dr. Barry Schweitzer Director, Division of Structural Biology Walt Disney Memorial Cancer Institute 12722 Research Parkway Orlando, FL 32826 email: barry@sneezy.fhis.net Applications will be accepted until the positions are filled. We thank all applicants for their interests, however, only those being considered will be contacted. From owner-structural-nmr@net.bio.net Sun Oct 08 23:00:00 1995 Path: biosci!daresbury!bioftp.unibas.ch!citi2.fr!jussieu.fr!oleane!plug.news.pipex.net!pipex!tank.news.pipex.net!pipex!newsfeed.internetmci.com!chi-news.cic.net!simtel!swidir.switch.ch!swsbe6.switch.ch!scsing.switch.ch!news.belwue.de!news.dfn.de!gina.zfn.uni-bremen.de!news From: "BrukerFan (tm)" Newsgroups: bionet.structural-nmr Subject: Re: pfg specification Date: 9 Oct 1995 16:09:59 GMT Organization: Zentrum fuer Netze, Universitaet Bremen Lines: 14 Message-ID: <45bhgn$de0@gina.zfn.uni-bremen.de> References: <44u4ok$7vt@infoserver.bgsu.edu> NNTP-Posting-Host: atair.chemie.uni-bremen.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 32bit) Hi, you should through away your (what's its name?) immediately and buy a Bruker instead! The technology is way ahead and they have it digital and on 800 MHz and all that... And they have all these requested Experiments pre-installed. If you can't do this, but I can't think of a reason, why not, contact your (what's its name?)-office and ask for help. Best wishes BrukerFan (tm) From owner-structural-nmr@net.bio.net Mon Oct 09 23:00:00 1995 Path: biosci!WWITCH.UNL.EDU!rshoe From: rshoe@WWITCH.UNL.EDU (Richard Shoemaker) Newsgroups: bionet.structural-nmr Subject: Re: nOe on hydroxy group Date: 10 Oct 1995 08:33:24 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 36 Sender: daemon@net.bio.net Distribution: world Message-ID: <9510101532.AA10850@wwitch.unl.edu.unl.edu> NNTP-Posting-Host: net.bio.net > >hi, >I wonder if anybody can help me. I'm trying to get the structure for >one of my sesquiterpens and on some stage I tried to get nOe from one >of the hydroxy groups (apparently there are two of them, probably next >to each other in the structure of the compound). >What's happend is that upon irradiation of the -OH signal I've got several >positive resonances as expected and one broad negative peak which might >correspond to the second hydroxy group. >Any ideas why this has happend? Does it really mean that the negative nOe >is due to the second -OH? > If you're doing NOE difference, and you get a "negative" peak from the OH that you presaturate _and_ from another peak, the most likely explanation is proton-exchange during the presaturation time. Anyone who's ever pre- saturated H2O in the presence of labile protons has seen this happen... i.e. if you saturate the water, and the water protons exchange with NH or OH protons, then they are subsequently saturated as well. If you do this in an NOE-Difference expt., the exchangeable protons will be negative (along with the peak that's being presaturated). We've used this to our advantage to determine exchange rates in the slow- exchange regime more than once. If the exchange rate is on the order of several seconds, you can adjust the pre-saturation time to monitor the rate of proton exchange. I hope this helps. Rich Shoemaker Richard Shoemaker, Ph.D. Phone--(402) 472-6255 Instrumentation Director, Chemistry FAX---- -6964 Research Associate Professor, Chemistry University of Nebraska-Lincoln URL: http://wwitch.unl.edu/nmrlab.html From owner-structural-nmr@net.bio.net Mon Oct 09 23:00:00 1995 Path: biosci!agate!news.ucdavis.edu!library.ucla.edu!info.ucla.edu!newsfeed.internetmci.com!chi-news.cic.net!simtel!swidir.switch.ch!scsing.switch.ch!news.dfn.de!gina.zfn.uni-bremen.de!news From: "BrukerFan(tm)" Newsgroups: bionet.structural-nmr Subject: Re: pfg specification Date: 10 Oct 1995 08:05:52 GMT Organization: Zentrum fuer Netze, Universitaet Bremen Lines: 21 Message-ID: <45d9h0$ilj@gina.zfn.uni-bremen.de> References: <44u4ok$7vt@infoserver.bgsu.edu> <45bhgn$de0@gina.zfn.uni-bremen.de> NNTP-Posting-Host: atair.chemie.uni-bremen.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 32bit) I wrote: > you should through away... ############ Yes, I see, I'm sorry, you couldn't knew that! It's Bruker-Slang. It means: "antimatter-annihilate" This can be simply achieved, buying a Bruker spectrometer, which has an anti-(what's its name?) in his extent of delivery. Throwing (now I mean throwing) this device at the (what's its name) you will get plenty of free space for new spectrometers. These anti-(what's its name?)s are also available separately from Bruker on request. BrukerFan(tm) From owner-structural-nmr@net.bio.net Mon Oct 09 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: Serge Iourine Newsgroups: bionet.structural-nmr Subject: nOe on hydroxy group Date: 10 Oct 1995 15:53:44 +0100 Lines: 15 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <45e1do$hrf@mserv1.dl.ac.uk> MIME-Version: 1.0 Original-To: str-nmr@dl.ac.uk hi, I wonder if anybody can help me. I'm trying to get the structure for one of my sesquiterpens and on some stage I tried to get nOe from one of the hydroxy groups (apparently there are two of them, probably next to each other in the structure of the compound). What's happend is that upon irradiation of the -OH signal I've got several positive resonances as expected and one broad negative peak which might correspond to the second hydroxy group. Any ideas why this has happend? Does it really mean that the negative nOe is due to the second -OH? Thnx. s.i. From owner-structural-nmr@net.bio.net Mon Oct 09 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.structural-nmr Subject: STOP THE STUPIDS Date: 10 Oct 1995 18:15:38 +0100 Lines: 23 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <45e9nq$t2b@mserv1.dl.ac.uk> Original-To: str-nmr@dl.ac.uk Is there any way to avoid stupid e-mail like the last replies to PFG-spec ? "I pirla" (ask some italian pepole to translate) are so brave to avoid their name and address. Marco Tato' PHARMACIA Biopharmaceuticals 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 (PHARMACIA) mtato@micronet.it (private) marco_tato@rcm.inet.it (private) Hay que beber para recordar y comer para olvidar Pepe Carvalho From owner-structural-nmr@net.bio.net Mon Oct 09 23:00:00 1995 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: nOe on hydroxy group Date: 10 Oct 1995 08:35:31 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 41 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <45e1do$hrf@mserv1.dl.ac.uk> NNTP-Posting-Host: net.bio.net What you see is most likely the saturation transfer (ST) effect. Irradiating one hydroxyl proton, this saturation will be transferred to the other OH by chemical exchange. Actually, this is one technique one can apply to find hidden resonances of exchangeable spins. Sincerely, Istvan =========================================================================== Istvan Pelczer, Ph.D. (ipelczer@mailbox.syr.edu) Res. Assist. Professor Visiting Assist. Professor Chemistry Department, CST Bldg. SUNY ESF, Chemistry Department Syracuse University One Forestry Drive Syracuse, NY 13244-4100 Syracuse, NY 13210-2778 ph: (315) 443 1023 or x-5932 ph# (315) 470 6596 or x-6855(Dept.) fax: x-1022 or x-4070(Dept.) On 10 Oct 1995, Serge Iourine wrote: > hi, > I wonder if anybody can help me. I'm trying to get the structure for > one of my sesquiterpens and on some stage I tried to get nOe from one > of the hydroxy groups (apparently there are two of them, probably next > to each other in the structure of the compound). > What's happend is that upon irradiation of the -OH signal I've got several > positive resonances as expected and one broad negative peak which might > correspond to the second hydroxy group. > Any ideas why this has happend? Does it really mean that the negative nOe > is due to the second -OH? > > Thnx. > > > s.i. > > From owner-structural-nmr@net.bio.net Tue Oct 10 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!vixen.cso.uiuc.edu!newsrelay.iastate.edu!news.iastate.edu!baker From: baker@iastate.edu (Wayne R. Baker) Newsgroups: bionet.biophysics,bionet.structural-nmr,sci.techniques.mag-resonance Subject: Stop The Whining (was Re: stop the idiotes) Date: 11 Oct 1995 19:29:34 GMT Organization: Biochemistry & Biophysics, Iowa State University Lines: 40 Message-ID: <45h5uu$s8j@news.iastate.edu> References: <9510101617.AA13749@rugmd9.chem.rug.nl> NNTP-Posting-Host: pv0a0b.vincent.iastate.edu Xref: biosci bionet.biophysics:1314 bionet.structural-nmr:809 sci.techniques.mag-resonance:1241 In bionet.biophysics and other groups, things similar to this have been said: :I have seen mail advertiseing for: :1) students reports :2) recipes :2) even a crazy chain letter for people with IQ < 10 : : :Is this biophysics??? : :Could someone please filter this newsgroup. Otherwise I will get out. While I don't like seeing specious posts in the newsgroups I read, the inevitable posts from people whining about how offended or outraged they are is even more annoying. In complaining about the dismal signal-to-noise levels, your post does nothing but reduce it even further. If a "filter" were installed, response times would be much slower and would require someone to invest a non-trivial amount of time and effort into moderating. Are you willing to volunteer? Garbage posts will always be a fact of life on the .net. The nature of the .net is such that the free and rapid exchange of information will invariably be accompanied by a certain level of dimwitted messages. You can either have a fecal hemorrhage over such off-topic posts or you can just chalk it up as part of the price we pay for this quite remarkable communication system. You can also forward a copy of the offending message to news, postmaster or root at the site of origin. This should also provide an incentive, for those who can, to move to newsreaders rather than mailing lists. You can construct killfiles to weed out garbage or just skip articles and not have things clogging up your mailbox. If you don't have access to a newsserver, then it is a personal decision as to whether you think it is worth it to continue reading a group. But make that decision in private so you don't compound the problem for everyone else. Wayne Baker (baker@iastate.edu) He who has a why to live for 4288 Molecular Biology Building can bear almost any how. Iowa State University --Nietzsche Ames IA 50011 (515) 294 0781 From owner-structural-nmr@net.bio.net Wed Oct 11 23:00:00 1995 Path: biosci!INDIANA.EDU!mpagel From: mpagel@INDIANA.EDU (Marty Pagel) Newsgroups: bionet.structural-nmr Subject: DelPhi Date: 11 Oct 1995 14:25:27 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: Biosym users, I have a colleague who would like to seach the surfaces of several protein structures in the PDB for regions of positive electostatic potential with a minimum square area meeting a minimum value (or density) of positive charge. I've calculated the electostatic potential of a protein surface before using DelPhi, but I've only visualized this surface. Is there a way to automatically evaluate the surface grid for electrostatics that have a minimum square area meeting a minimum positive value? Is there a way to generate an ascii file of the X,Y,Z coordinates of the surface along with the electostatic charge at this point? Thanks, Marty Pagel Chemistry Department mpagel@indiana.edu --- __o Indiana University Phone: (812)-855-6492 --- \<, Bloomington, IN 47405-4001 Fax: (812)-855-8300 --- ()/ () From owner-structural-nmr@net.bio.net Wed Oct 11 23:00:00 1995 Path: biosci!bcm.tmc.edu!pendragon.jsc.nasa.gov!news.msfc.nasa.gov!newsfeed.internetmci.com!EU.net!sun4nl!news.nic.surfnet.nl!ruu.nl!nmr!leef From: leef@nmr.chem.ruu.nl (Bas Leeflang) Newsgroups: bionet.structural-nmr Subject: Re: nOe on hydroxy group Date: 12 Oct 1995 15:23:58 GMT Organization: Academic Compter Centre Utrecht Lines: 25 Sender: leef@RUUCI9 (Bas Leeflang) Distribution: bionet Message-ID: <45jbue$56m@nic.cc.ruu.nl> References: <45e1do$hrf@mserv1.dl.ac.uk> NNTP-Posting-Host: ruuci9.chem.ruu.nl In article <45e1do$hrf@mserv1.dl.ac.uk>, Serge Iourine writes: |> hi, |> I wonder if anybody can help me. I'm trying to get the structure for |> one of my sesquiterpens and on some stage I tried to get nOe from one |> of the hydroxy groups (apparently there are two of them, probably next |> to each other in the structure of the compound). |> What's happend is that upon irradiation of the -OH signal I've got several |> positive resonances as expected and one broad negative peak which might |> correspond to the second hydroxy group. |> Any ideas why this has happend? Does it really mean that the negative nOe |> is due to the second -OH? |> This looks like a clasical example of chemical exchange to me. ---------------------------------------------------------------------- Bas R. Leeflang _/ _/ _/ _/ _/_/_/ Department of the Bijvoet Center _/_/ _/ _/_/ _/_/ _/ _/ for Biomolecular Research _/ _/ _/ _/ _/ _/ _/_/_/ Padualaan 8, 3584 CH Utrecht _/ _/_/ _/ _/ _/ _/ Tel. : int+31.30.533295 _/ _/ _/ _/ _/ _/ Fax : int+31.30.537623 Email: leef@nmr.chem.ruu.nl From owner-structural-nmr@net.bio.net Wed Oct 11 23:00:00 1995 Path: biosci!REN.ONYX-PHARM.COM!bkarlak From: bkarlak@REN.ONYX-PHARM.COM (Brian Karlak) Newsgroups: bionet.structural-nmr Subject: Re: **FREE Trial Pack of Middle School - College Essays** Date: 11 Oct 1995 14:39:08 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 25 Sender: daemon@net.bio.net Distribution: world Message-ID: <9510111354.ZM1932@ren.onyx-pharm.com> Does anyone happen to live near Scottsdale? Perhaps they could take a short trip over to this teenage dork's address and pound the living . . . um, uh, "convince" them to stop annoying us so. Brian Karlak > On Oct 10, 11:38am, foshay elena m wrote: > Subject: **FREE Trial Pack of Middle School - College Essays** > ****** 700+ Middle School - College Essays ****** > > ** For $1.00 you can order a sample of are 100 best Essays. > ** Use them for what ever you wish. Ahh, you want some uses > here are the top 3 uses of these Essays: > Address Envelope to: > > FreeStuff > 9393 N. 90th St. > Suite 102-289 > Scottsdale, AZ 85258 -------------- -- This .sig signifies nothing. From owner-structural-nmr@net.bio.net Thu Oct 12 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!EU.net!Germany.EU.net!nntp.gmd.de!news.rwth-aachen.de!news.rhrz.uni-bonn.de!aurelia!hartmann From: hartmann@physiogate.rhrz.uni-bonn.de (Dr. Rudolf Hartmann) Newsgroups: bionet.structural-nmr Subject: Re: nOe on hydroxy group Date: Fri, 13 Oct 1995 11:19:42 GMT Organization: meb.uni-bonn.de Lines: 32 Distribution: bionet Message-ID: References: <45e1do$hrf@mserv1.dl.ac.uk> NNTP-Posting-Host: frei1.meb.uni-bonn.de X-Newsreader: Trumpet for Windows [Version 1.0 Rev B] In article <45e1do$hrf@mserv1.dl.ac.uk> Serge Iourine writes: >From: Serge Iourine >Subject: nOe on hydroxy group >Date: 10 Oct 1995 15:53:44 +0100 >hi, >I wonder if anybody can help me. I'm trying to get the structure for >one of my sesquiterpens and on some stage I tried to get nOe from one >of the hydroxy groups (apparently there are two of them, probably next >to each other in the structure of the compound). >What's happend is that upon irradiation of the -OH signal I've got several >positive resonances as expected and one broad negative peak which might >correspond to the second hydroxy group. >Any ideas why this has happend? Does it really mean that the negative nOe >is due to the second -OH? >Thnx. >s.i. The protons of hydroxy groups can exchange very fast. (broad signals) You dont write about the solvent, (DMSO d6, or CDCl3, or CD3OD) the exchange-rate depends from the solvent. If you irradiate at one of your -OH group, the proton can exchange and the irradiated proton changed to the other -OH group. So you can see a negative signal. Try it with different irradiation times and/or other solvents. R.H. From owner-structural-nmr@net.bio.net Thu Oct 12 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!EU.net!Norway.EU.net!telepost.no!nntp-oslo.UNINETT.no!nntp-trd.UNINETT.no!daresbury!not-for-mail From: Serge Iourine Newsgroups: bionet.structural-nmr Subject: Absolute stereochemistry Date: 13 Oct 1995 12:05:31 +0100 Lines: 27 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <45lh5r$4ng@mserv1.dl.ac.uk> MIME-Version: 1.0 Original-To: str-nmr@dl.ac.uk hi, I am very grateful to those who answered my previous question - now that's another one... Do you think it is possible to find out the absolute stereochemistry at the C-2' atom CH-OH just by using the NMR techniques (see the partial structure below)? The wild guess is that hydrogen atom has an alpha orientation - but how to prove it? Me Me \ / / \ / 3' \____OH O 2'| | | | 1'| \ /\\ / \ / 4 \\ / | 3| | | | 2 | / \ / \\ / \1 / \\ O O Regards, s.i. From owner-structural-nmr@net.bio.net Thu Oct 12 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.sprintlink.net!EU.net!Germany.EU.net!news.dfn.de!gina.zfn.uni-bremen.de!news From: test Newsgroups: bionet.structural-nmr Subject: Re: Post-doctoral Position Available Date: 13 Oct 1995 13:52:27 GMT Organization: University of Bremen Lines: 2 Message-ID: <45lqur$gcn@gina.zfn.uni-bremen.de> References: <9510091159.ZM13441@sneezy.fhis.net> NNTP-Posting-Host: atair.chemie.uni-bremen.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 32bit) hfhfggdgd From owner-structural-nmr@net.bio.net Thu Oct 12 23:00:00 1995 Path: biosci!bcm.tmc.edu!pendragon.jsc.nasa.gov!news.msfc.nasa.gov!newsfeed.internetmci.com!news.sprintlink.net!EU.net!Germany.EU.net!news.dfn.de!gina.zfn.uni-bremen.de!news From: test Newsgroups: bionet.structural-nmr Subject: Re: pfg specification Date: 13 Oct 1995 13:54:09 GMT Organization: Wild in Hintertupfingen Lines: 2 Message-ID: <45lr21$gcn@gina.zfn.uni-bremen.de> References: <44u4ok$7vt@infoserver.bgsu.edu> <45bhgn$de0@gina.zfn.uni-bremen.de> <45lqqv$gcn@gina.zfn.uni-bremen.de> NNTP-Posting-Host: atair.chemie.uni-bremen.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 32bit) hhdhh From owner-structural-nmr@net.bio.net Thu Oct 12 23:00:00 1995 Path: biosci!bcm.tmc.edu!pendragon.jsc.nasa.gov!news.msfc.nasa.gov!newsfeed.internetmci.com!news.sprintlink.net!EU.net!Germany.EU.net!news.dfn.de!gina.zfn.uni-bremen.de!news From: test Newsgroups: bionet.structural-nmr Subject: Re: pfg specification Date: 13 Oct 1995 13:50:23 GMT Organization: University of Bremen Lines: 2 Message-ID: <45lqqv$gcn@gina.zfn.uni-bremen.de> References: <44u4ok$7vt@infoserver.bgsu.edu> <45bhgn$de0@gina.zfn.uni-bremen.de> NNTP-Posting-Host: atair.chemie.uni-bremen.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 32bit) ndsjfh From owner-structural-nmr@net.bio.net Fri Oct 13 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!Germany.EU.net!news.dfn.de!fu-berlin.de!zrz.TU-Berlin.DE!cs.tu-berlin.de!informatik.uni-bremen.de!Altair From: test@versuch.it (Tester) Newsgroups: bionet.structural-nmr Subject: Just a short try Date: Fri, 13 Oct 95 16:38:41 GMT Organization: Universitaet Bremen, Germany Lines: 1 Message-ID: <45ltlk$1v7@p235.informatik.uni-Bremen.de> NNTP-Posting-Host: atair.chemie.uni-bremen.de Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: News Xpress Version 1.0 Beta #4 testing From owner-structural-nmr@net.bio.net Fri Oct 13 23:00:00 1995 Path: biosci!bcm.tmc.edu!pendragon.jsc.nasa.gov!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!torn!nott!crc-news.doc.ca!netfs.dnd.ca!ub!newserve!bingsun1!schulte From: Juergen Schulte Newsgroups: bionet.structural-nmr Subject: Re: Absolute Stereochemistry Date: Sat, 14 Oct 1995 12:36:42 -0400 Organization: Binghamton University, Binghamton, NY Lines: 42 Message-ID: NNTP-Posting-Host: 128.226.1.2 Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: schulte@bingsun1 In article <45lh5r$4ng@mserv1.dl.ac.uk> you wrote: : Do you think it is possible to find out the absolute stereochemistry at : the C-2' atom CH-OH just by using the NMR techniques (see the partial : structure below)? The wild guess is that hydrogen atom has an alpha : orientation - but how to prove it? : Me Me : \ / : / \ : / 3' \____OH : O 2'| : | | | 1'| : \ /\\ / : \ / 4 \\ / : | 3| : | | : | 2 | : / \ / \\ : / \1/ \\ : O O You could start with determining the C,H coupling constant between the methyl carbons and the proton at C-2'. If both J's are similar, the dihedral angle C-C-C-H2'should be the same for both methyl-C's. If one J is much larger than the other one, then the proton is likely to be in a anti position to one and on a gauche position to the other methyl. Provided that the conformation of the ring is known (the double bond doesn't leave many possibilities), this should give you at least the relative configuration. A simple proton coupled C-13 spectrum (Gated Decoupling) should do the trick. Otherwise a proton selective 2D-INEPT should give the result. Hope this helps! Juergen Schulte SUNY Binghamton From owner-structural-nmr@net.bio.net Fri Oct 13 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!newsfeed.internetmci.com!news.compuserve.com!newsmaster From: Dirk Friedrich <73742,2243@compuserve.com> Newsgroups: bionet.structural-nmr Subject: Re: nOe on hydroxy group Date: 14 Oct 1995 15:13:36 GMT Organization: CompuServe Incorporated Lines: 6 Message-ID: <45ok30$5a8@dub-news-svc-1.compuserve.com> References: <45e1do$hrf@mserv1.dl.ac.uk> NNTP-Posting-Host: ad42-147.compuserve.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) X-URL: news:45e1do$hrf@mserv1.dl.ac.uk The second negative resonance is just caused by chemical exchange of the target OH proton with other exchangeables in the sample during the preirradiation period (NOED) or the mixing time (NOESY). These other exchangeables may be other OH's in the same molecule, but may also just represent H2O present in the sample (e.g., ca. 1.6 ppm in CDCl3, ca. 3.3 ppm in DMSO-d6 etc.). From owner-structural-nmr@net.bio.net Sun Oct 15 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!torn!news.bc.net!rover.ucs.ualberta.ca!unixg.ubc.ca!news From: Lawrence McIntosh Newsgroups: bionet.structural-nmr Subject: backup hardware Date: Mon, 16 Oct 1995 13:12:44 -0700 Organization: The University of British Columbia Lines: 17 Message-ID: <3082BCBC.41C6@otter.biochem.ubc.ca> NNTP-Posting-Host: otter.biochem.ubc.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0b1J (X11; I; IRIX 5.2 IP12) Hello: We use a Tahati 2 and an Exabyte 8500 drive for NMR data backup from our SGI's. However, we seem to have had no end of bad luck with these drives (everything from software to hardware failures). I am curious (i) if others have had similar hassels, and (ii) is it worth sticking with these systems or are there better alternatives (ZIP drives, WORM drives)? Thanks! Lawrence McIntosh UBC From owner-structural-nmr@net.bio.net Sun Oct 15 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.sprintlink.net!in1.uu.net!newsfeed.pitt.edu!dsinc!netnews.upenn.edu!news.tju.edu!usenet From: James Varnum Newsgroups: bionet.structural-nmr Subject: DIANA Date: 16 Oct 1995 16:19:27 GMT Organization: Thomas Jefferson University Lines: 3 Message-ID: <45u0mf$h89@mail.TJU.EDU> NNTP-Posting-Host: watson.jci.tju.edu I need the source for the program DIANA Thanks jim v. From owner-structural-nmr@net.bio.net Sun Oct 15 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!info.ucla.edu!nnrp.info.ucla.edu!usenet From: Flint Smith Newsgroups: bionet.structural-nmr Subject: Re: backup hardware Date: 16 Oct 1995 23:24:29 GMT Organization: UCLA Lines: 21 Message-ID: <45upjd$ndh@saba.info.ucla.edu> References: <3082BCBC.41C6@otter.biochem.ubc.ca> NNTP-Posting-Host: holmes.mbi.ucla.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12 (X11; I; IRIX 5.2 IP22) X-URL: news:3082BCBC.41C6@otter.biochem.ubc.ca Lawrence McIntosh wrote: >We use a Tahati 2 and an Exabyte 8500 drive >for NMR data backup from our SGI's. However, we >seem to have had no end of bad luck with >these drives (everything from software to >hardware failures). We too have had numerous problems with our Tahiti Drives (from Introl). One thing that really kills one is to let it warm up. The fans were (are?) inadequate. We haven't had any software problems, other than having the file system marked "dirty", but that's easily fixed. It seems our most frequent problem is caused by bad power supplies. The light comes on but the disk never reaches full speed. Now that the price of harddrives has come down, we tend to buy more harddrives and backup large chunks onto DAT tape. Flint Smith flint@ucla.edu From owner-structural-nmr@net.bio.net Mon Oct 16 23:00:00 1995 Path: biosci!UNITY.NCSU.EDU!idshin From: idshin@UNITY.NCSU.EDU ("Dan Shin") Newsgroups: bionet.structural-nmr Subject: Re: backup hardware Date: 17 Oct 1995 10:59:12 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 42 Sender: daemon@net.bio.net Distribution: world Message-ID: <9510171348.ZM16015@152.1.38.71> References: NNTP-Posting-Host: net.bio.net Lawrence, we've installed writable optical drive 3 years ago from ARTECON (with 1GB erasable optical diskettes available at that time). We have had no problems at all since then and we're enjoying it. I've heard they have improved capacities and speed, also price has been lowered too. You can contact to: ARTECON, INC. 6305 El Camino Real Carlsbad, CA 92009 (800) USA-ARTE Hope this helps. Dan NMR Facility, NCSU On Oct 16, 1:12pm, Lawrence McIntosh wrote: > Subject: backup hardware > Hello: > > We use a Tahati 2 and an Exabyte 8500 drive > for NMR data backup from our SGI's. However, we > seem to have had no end of bad luck with > these drives (everything from software to > hardware failures). > > I am curious (i) if others have had similar > hassels, and (ii) is it worth sticking with > these systems or are there better alternatives > (ZIP drives, WORM drives)? > > Thanks! > > Lawrence McIntosh > UBC > > >-- End of excerpt from Lawrence McIntosh -- Dan Shin dan_shin@ncsu.edu (919) 515-2248 From owner-structural-nmr@net.bio.net Mon Oct 16 23:00:00 1995 Path: biosci!WWITCH.UNL.EDU!rshoe From: rshoe@WWITCH.UNL.EDU (Richard Shoemaker) Newsgroups: bionet.structural-nmr Subject: Re: backup hardware Date: 17 Oct 1995 08:06:10 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 51 Sender: daemon@net.bio.net Distribution: world Message-ID: <9510171505.AA18920@wwitch.unl.edu.unl.edu> NNTP-Posting-Host: net.bio.net > >Lawrence McIntosh wrote: >>We use a Tahati 2 and an Exabyte 8500 drive >>for NMR data backup from our SGI's. However, we >>seem to have had no end of bad luck with >>these drives (everything from software to >>hardware failures). > >We too have had numerous problems with our Tahiti Drives >(from Introl). One thing that really kills one is to let >it warm up. The fans were (are?) inadequate. We haven't >had any software problems, other than having the file system >marked "dirty", but that's easily fixed. It seems our most >frequent problem is caused by bad power supplies. The light >comes on but the disk never reaches full speed. > >Now that the price of harddrives has come down, we tend to buy >more harddrives and backup large chunks onto DAT tape. > >Flint Smith >flint@ucla.edu I originally wrote back directly to Lawrence McIntosh, but the above response from F. Smith might indicate that the entire group might be interested. My Tahiti-3 drive (1.2 MB, 512 Byte/Sector) drive was purchased from Falcon Systems, and I've used it for over a 1 1/2 years without a single error of any kind. It's on 24 hours/day, 7 days/week. For the past 5 years, I'm purchased ALL of my drives from Falcon: External Hard-drives, DAT-Tape drives, Tahiti-Drive, Sun-CD-ROM drive. They have EXTREMELY robust power supplies, cases, fans, ...etc., and they back everything with the best warranty, and knowledgeable technical people. This may sound like a shameless plug, but I certainly don't get anything for saying this. If Flint is correct, and his problems were related to cases/fans/power-supplies, this could explain why I've never had a R/W error on any Falcon product. (I'm sure someday one of the hard-drives will fail, but it hasn't happened yet). For the record, our Tahiti-3 drive is on a Sun-Sparc 1+, and is NFS mounted on up to 7 other systems simultaneously at any given time...so when I say it's "on" 24 hours/day, it's actually being _used_ 24 hours/day. Rich Shoemaker Richard Shoemaker, Ph.D. Phone--(402) 472-6255 Instrumentation Director, Chemistry FAX---- -6964 Research Associate Professor, Chemistry University of Nebraska-Lincoln URL: http://wwitch.unl.edu/nmrlab.html P.S. What good is a shameless plug w/o a phone number...800-326-1002 From owner-structural-nmr@net.bio.net Mon Oct 16 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!bronze.ucs.indiana.edu!jverburg From: jverburg@ucs.indiana.edu (John M. VerBurg) Newsgroups: bionet.biophysics,bionet.structural-nmr,sci.techniques.mag-resonance Subject: Re: Stop The Whining (was Re: stop the idiotes) Followup-To: bionet.biophysics,bionet.structural-nmr,sci.techniques.mag-resonance Date: 17 Oct 1995 17:02:13 GMT Organization: Indiana University Lines: 13 Message-ID: <460nil$mvr@usenet.ucs.indiana.edu> References: <9510101617.AA13749@rugmd9.chem.rug.nl> <45h5uu$s8j@news.iastate.edu> NNTP-Posting-Host: nickel.ucs.indiana.edu X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.biophysics:1329 bionet.structural-nmr:825 sci.techniques.mag-resonance:1248 Wayne R. Baker (baker@iastate.edu) wrote: [snip] : But make that decision in private so you don't compound the problem : for everyone else. I agree completely. I too hate spams, but I believe the best way to protest them is to reply to the original poster and feign interest in their scam and do nothing. They will waste their time following up on a false lead. Imagine if 10,000 people did this. To save time, I usually just write "me too" in the relpy, along with their post. jverburg From owner-structural-nmr@net.bio.net Mon Oct 16 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.uoregon.edu!news.corpcomm.net!newstand.syr.edu!syr.edu!dkiemle From: dkiemle@syr.edu (David Kiemle) Newsgroups: bionet.structural-nmr Subject: Calibration of D2O samples Date: Tue, 17 Oct 1995 14:30:21 UNDEFINED Organization: Syracuse University Lines: 4 Message-ID: NNTP-Posting-Host: 149.119.4.19 X-Newsreader: Trumpet for Windows [Version 1.0 Rev B final beta #1] When doing variable temperature studies in D2O without an internal or external reference compound, how do you calibrate chemical shifts? Thanks in advance for any help. From owner-structural-nmr@net.bio.net Tue Oct 17 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!tank.news.pipex.net!pipex!warwick!news.ncl.ac.uk!usenet From: j.d.swarbrick@ncl.ac.uk Newsgroups: bionet.structural-nmr Subject: Peptides in TFE Date: 18 Oct 1995 13:10:41 GMT Organization: Newcastle University, UK Lines: 45 Message-ID: <462uch$42d@whitbeck.ncl.ac.uk> Reply-To: j.d.swarbrick@ncl.ac.uk NNTP-Posting-Host: fernwood.ncl.ac.uk X-Newsreader: WinVN 0.91.6 AGGREGATION IN NEAT TFE (1H NMR 500MHz) I have been looking at several linear peptides by NMR using the srandard 2D techniques (ROESY,NOESY etc) in various solvent systems e.g H2O, DMSO and TFE. For my peptides of length 5-12 residues in H2O the tumbling rate is close to WTc=1 and so ROESY experiments yield the NOEs and structural info.In DMSO for the peptides >6 residues the NOESY experiments yield sufficiently good spectra because of the favourable viscosity of the solvent. In this case WTc>1 and the NOEs are negative enhancements (spin diffusion regime). The problem arrises when I look at the peptides in neat TFE. For example: A)at T=295k for a 7 residue peptide of low concentration the typical NH line width is about 15Hz. For a more conc. sample the width is about 25 Hz and some small chem. shift changes are observed. B)I ran most of my exp. at lower temperature to increase my chance of observing any secondary structure (very slim for linear peps I know!) and at 270K very good NOESY spectra are observed for this peptide. This peptide indeed shows a high population of B turn. The amide coeff. are in agreement with this showing a 1-4 hydrogen bond across the turn. However the linewidths are typically large and overlap is (almost) a problem! C)The same sequence but with the 2 N terminal residue removed (i.e. 5 res peptide) shows the same B turn over the same residues in TFE. The line widths are narrower and the peptide less concentrated. The temp. coeffs. are in agreement again D)In general, the peptides do give good NOESY spectra at room temp in neat TFE,when the conc. is low but suffer from large linewidths as the conc is increased. When only a small amount of H2O is added the tmbling regime tends to that of say the peptide in H2O (i.e poor NOESY and OK ROESY) and the line widths are narrower (say about 8-10Hz). Question: a) Is the tumbling regime almost certainly a result of aggregation? (I think so). b) Does anyone have the viscosity of TFE at R.T. just out of interest to compare with DMSO. c) If it is a result of aggregation, then is there any way I can separate direct NOEs between a single peptide unit and those between two or more different units in the aggregated state. (Can I use the ROESY here like transfered NOEs to do this etc) d) has anybody out there come across this before? Well many thanks see you, James. (j.d.swarbrick@ncl.ac.uk) From owner-structural-nmr@net.bio.net Tue Oct 17 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.sprintlink.net!in2.uu.net!news.compuserve.com!newsmaster From: Dirk Friedrich <73742,2243@compuserve.com> Newsgroups: bionet.structural-nmr Subject: Re: Absolute Stereochemistry Date: 18 Oct 1995 09:15:25 GMT Organization: CompuServe Incorporated Lines: 9 Message-ID: <462gjd$gjh@dub-news-svc-3.compuserve.com> References: NNTP-Posting-Host: dd05-003.compuserve.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) X-URL: news:Pine.SOL.3.91.951013213035.362A-100000-100000@bingsun2-gw To determine the absolute stereochemistry via NMR would require to introduce some sort of chiral environment with known absolute configuration as a "reference". For example by derivatizing the alcohol separately with both enantiomers of a chiral derivatizing agent and examining the two diastereomeric derivatives by NOE experiments. Of course, determination of relative stereochemistry would be a prerequisite, as Juergen Schulte noted. It may be more straightforward to derive the absolute stereochemistry surrounding the unsaturated lactone chromophor from CD spectroscopy. From owner-structural-nmr@net.bio.net Tue Oct 17 23:00:00 1995 Path: biosci!prius.jnj.com!PMCDONNELL From: PMCDONNELL@prius.jnj.com (PMCDONNELL) Newsgroups: bionet.structural-nmr Subject: subscribe Date: 18 Oct 1995 06:08:26 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 3 Sender: daemon@net.bio.net Distribution: world Message-ID: <8940000818101995.A23188.DELPHI.119A92001800*@MHS.prius.jnj.com> NNTP-Posting-Host: net.bio.net subscribe pmcdonnell@prius.jnj.com From owner-structural-nmr@net.bio.net Wed Oct 18 23:00:00 1995 Path: biosci!ggr.co.uk!rhf23484 From: rhf23484@ggr.co.uk (Dr R H Fogh) Newsgroups: bionet.structural-nmr Subject: Problem - bacterial growth in labelling media Date: 19 Oct 1995 10:40:20 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <324.199510191222@mailhub.ggr.co.uk> NNTP-Posting-Host: net.bio.net Dear netters We are trying to grow E. Coli JM109 in celtone soulution (a hydrolysed algae medium for isotope labelling). Unfortunately we are getting lag phases of around 11 hours. Once the cells start growing they get up to O.D. around 2.0, but the long lag time makes it impossible to schedule the work (we do not have the option of having people come to start induction in the middle of the night). Has anyone got experience with a similar problem? any helpful suggestions? a protocol for this or a similar medium? Send answers direct to me (please) and I will post a resume. Thanks, Rasmus Fogh Glaxo SpA, Via Fleming 4, 37125 Verona, Italy. Email: RHF23484@GGR.CO.UK (yes, UK). From owner-structural-nmr@net.bio.net Wed Oct 18 23:00:00 1995 Path: biosci!ggr.co.uk!rhf23484 From: rhf23484@ggr.co.uk (Dr R H Fogh) Newsgroups: bionet.structural-nmr Subject: Problem - bacterial growth in labelling media Date: 19 Oct 1995 10:40:45 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <2420.199510191259@mailhub.ggr.co.uk> NNTP-Posting-Host: net.bio.net Dear netters We are trying to grow E. Coli JM109 in celtone soulution (a hydrolysed algae medium for isotope labelling). Unfortunately we are getting lag phases of around 11 hours. Once the cells start growing they get up to O.D. around 2.0, but the long lag time makes it impossible to schedule the work (we do not have the option of having people come to start induction in the middle of the night). Has anyone got experience with a similar problem? any helpful suggestions? a protocol for this or a similar medium? Send answers direct to me (please) and I will post a resume. Thanks, Rasmus Fogh Glaxo SpA, Via Fleming 4, 37125 Verona, Italy. Email: RHF23484@GGR.CO.UK (yes, UK). From owner-structural-nmr@net.bio.net Wed Oct 18 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!uwm.edu!msunews!harbinger.cc.monash.edu.au!newshost.anu.edu.au!surya From: Jill.Gready@anu.edu.au (Jill Gready) Newsgroups: bionet.structural-nmr Subject: RESEARCH FELLOW - BIOLOGICAL NMR Date: Fri, 20 Oct 95 12:36:19 GMT Organization: JCSMR, ANU Lines: 56 Distribution: world Message-ID: <466kej$neq@manuel.anu.edu.au> NNTP-Posting-Host: 150.203.7.194 X-Newsreader: News Xpress Version 1.0 Beta #4 RESEARCH FELLOW POSITION AVAILABLE IN BIOLOGICAL NMR AT THE AUSTRALIAN NATIONAL UNIVERSITY, CANBERRA AUSTRALIA UNIVERSITY NMR CENTRE (UNMRC) JOHN CURTIN SCHOOL OF MEDICAL RESEARCH (JCSMR) RESEARCH SCHOOL OF BIOLOGICAL SCIENCES (RSBS) Research Fellow in Biological NMR [Academic Level B (research-only equiv. to teaching/research Lecturer level)] As part of a planned upgrade of the University's high-field NMR capabilities, applications are invited for a Research Fellow position to facilitate the use of biological NMR within research programs in the ANU. The duties of the position include advising researchers on appropriate use of NMR techniques for their biological problems, undertaking research on collaborative projects, and co-supervising or assisting researchers, including students and postdoctoral workers. Applicants should have a PhD in biological NMR or cognate discipline, with experience in 3-D structure solution of proteins or peptides, or other large biomolecules. Experience in an area of non-structural biological NMR such as study of ligand binding, transport or metabolism may be an advantage. Demonstrated interest in the problem-oriented application of NMR to studying biomolecular and biological systems and success in undertaking such studies are essential. Ability and willingness to interact with other researchers and technical staff, and assist researchers in use of NMR techniques and data analysis are essential. The successful applicant will have the ability to work efficiently and with initiative, and also possess good oral and written communication skills. The appointee will have office space and data processing facilities in the UNMRC, JCSMR and RSBS. The JCSMR will be the area of primary academic responsibility. The position is available from March 1996 for an initial period of three years with the possibility of extension for a further two years. Enquiries: Dr Jill Gready, JCSMR, telephone 61 6 279 8304, fax 61 6 249 0415, email Jill.Gready@anu.edu.au Further particulars on the position and biological NMR research programs, which include the Selection Criteria, should be obtained from the School Secretary, JCSMR, telephone 61 6 249 2580, fax 61 6 249 3955, email school.secretary@jcsmr.anu.edu.au Closing date: 30 November 1995 Ref: JC9512. Salary range: Research Fellow $42,198 - $50,111 pa APPLICATIONS ADDRESSING THE SELECTION CRITERIA should be submitted in duplicate to The Secretary, The Australian National University, Canberra ACT 0200, Australia, quoting reference number and including curriculum vitae, list of publications and names and addresses, and preferably fax and email addresses, of at least three referees. An additional copy of the application should be sent directly to the School Secretary, JCSMR, by fax 61 6 249 3955 or email school.secretary@jcsmr.anu.edu.au The University has a "no smoking" policy in all University buildings and vehicles. From owner-structural-nmr@net.bio.net Wed Oct 18 23:00:00 1995 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: Calibration of D2O samples Date: 19 Oct 1995 16:31:52 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 36 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net Dave is practically next door, so we could talk about this in person, but I believe the following could be interesting for others on the net, too. The chemical shift of the residual water signal can be used for reference, and it is a linear function of the temperature. Actually, there is a recent paper in J. Biomol. NMR (Wishart, D. S., et al., 6, 1995, 135-140; 1H, 13C and 15N chemical shift referencing in biomolecular NMR), about this issue (and more) and gives valuable guidelines. In Table 1. of this paper they give the teperature coefficient of HDO as -11.9 ppb/oC. Cheers, 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 Tue, 17 Oct 1995, David Kiemle wrote: > When doing variable temperature studies in D2O without an internal or external > reference compound, how do you calibrate chemical shifts? > > Thanks in advance for any help. > > From owner-structural-nmr@net.bio.net Thu Oct 19 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: Antxon Ilarduia Newsgroups: bionet.structural-nmr Subject: subscribe Date: 20 Oct 1995 12:20:54 +0100 Lines: 1 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4680mm$l3v@mserv1.dl.ac.uk> Original-To: str-nmr@dl.ac.uk (Receipt Notification Requested) (Non Receipt Notification Requested) subscribe From owner-structural-nmr@net.bio.net Thu Oct 19 23:00:00 1995 Path: biosci!bcm.tmc.edu!pendragon.jsc.nasa.gov!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!uwm.edu!math.ohio-state.edu!magnus.acs.ohio-state.edu!infoserver.bgsu.edu!dad.bgsu.edu!dychen From: dychen@dad.bgsu.edu (Deng-Ywan Chen) Newsgroups: bionet.structural-nmr,sci.techniques.mag-resonance Subject: summary of pfg specification Date: 20 Oct 1995 18:20:58 GMT Organization: Bowling Green State Univ. Lines: 262 Distribution: world Message-ID: <468paa$2dv@infoserver.bgsu.edu> NNTP-Posting-Host: ernie.bgsu.edu Xref: biosci bionet.structural-nmr:836 sci.techniques.mag-resonance:1254 hello everyone, i have posted the question of pfg specification awhile back and received quitea few of response. we are grateful to all of whom spending time on replying this question. since this is sort of an opinion poll, i'll summarize all of the response 'as is' with minimal editing and ask you to read them with your own judgement. again, i have to cross post this message through couple news groups/email lists and apologize if you receive multiple copies. later!! chen *********************original question************************************* hello everyone, we, bowling green state university, are fairly new into this techniques of pulsed-field-gradient nmr at our unity+400 instrument. we would like to ask for everyone's opinion/suggestion/experience on the following issue. our pfg system was installed and tested by varian's engineer and we did run couple pfg experiments with good results. the question we have is - are there ways of routinely checking at the performance of our pfg system? just like the line width/line shape specification, are there standard pfg experiments we can run (say, every 6 months) and check at its specification? (for example, the s/n ratio, or lines' separation of standard pfg experiment with standard sample.) we'll appreciate all of your responses and be glad to summarize the information we receive. chen **********From jwg4@slc10.INS.CWRU.Edu Wed Oct 4 10:41:55 1995********** I am moving and have all my journal papers in boxes..., but there was an interesting paper in the journal "Magnetic Resonance Imaging" where in Europe, there they tried to compared different machines. Sorry I do not have the reference, but it was in 85-88 (approx). They detailed the experiments which were used on a whole body scanner. jim **********From cgregory@uiuc.edu Wed Oct 4 10:53:45 1995********** Three standard tests are "gradient amplitude", "settling time", and "stability". For 3-axis system, run gradient amplitude on each axis, and settling time and stability on all 3 axes at once (to save time, if possible). Gradient amplitude: Run a sequence (on our VXR-500S it is called "profile") that applies a gradient during the acquisition. Measure the width of the line with a standard sample - this should not change. (This is the same procedure used to calibrate the gradient in gauss/cm). Settling time (also called "eddy current" test): Run an arrayed experiment with variable delays between a longish gradient pulse (e.g. 50ms at 25% maximum amplitude) and an rf pulse/acquisition (e.g. "g2pul" sequence). Look at the peak amplitude and linewidth vs delay (typically a multiexponential decay) and the frequency vs. delay. There should be a spec for your probe (e.g. linewidth with no gradient = x% of linewidth with gradient at y msec after pulse). Stability: Run any favorite pfg sequence, with a dummy array (e.g. array d1 but make all the steps the same). A 2dft should show all of the signal along the center in f1. Any sidebands along f1 indicate instability. Measure their amplitude and keep a record. The first two of these at least should have been run by the factory rep when the pfg accessory was installed. Hope this helps. Carl Gregory Biomedical Magnetic Resonance Laboratory College of Medicine University of Illinois 1307 W Park St Urbana, IL 61801 (217)-244-2350 **********From hilton@ncifcrf.gov Wed Oct 4 11:04:16 1995********** Well, I would run the gradient calibration to check the gradient strength (doped water) and the gradient recovery test. Both of these are quite fast, and are a stand--ard part of the Varian psglib. If you want more, get a concentrated sample of say 2,3 dibomoproprionic acid and set up conditions so you can run an hmqc in 10 minutes (very narrow narrow SW) or less. Run a gradient hmqc under a uniform set of conditions and keep the spectra. This will allow a fairly demanding test in under 30 minutes. But the tests above are important because they concentrate on gradient preformance. Dr. Bruce D. Hilton NCI-FCRDC hilton@ncifcrf.gov 301-846-1226 **********From kfw@lubrizol.com Wed Oct 4 12:56:49 1995********** Chen: I have had PFG for over 2 years on my Bruker AMX500 and routinely use various PFG experiments.Typicall, I do very little as far as calibrations or standard experiments besides tweeking the gradient amplitudes with 1D exp before doing a 2D exp. All the experiments that I typically use run as expected. I would be interested in the replys that you get back to see what others have to say in about this subject matter. I guess you could run the typical installation experiments to check gradient strengths and linearity of the gradients but I would be interested to see if others are doing more elaborate tests to check their PFG systems. Thanks in advance, Kurt Kurt Wollenberg e-mail:kfw@lubrizol.com Research Chemist ph#:(216)943-1200 ext2026 fax:(216)943-9022 NMR Spectroscopy Lubrizol Corporation **********From nieman@asu.edu Wed Oct 4 13:11:16 1995********** Varian provides two tests, which start with the p2pul sequence: profile and grecovery. Profile will give you a very good indication of whether the efficiency of the gradients has changed over time (look at the macro 'setgcal' and the parameter 'gcal'. the grecovery test will tell you about any problems with degredation of the coils. Another set of tests involves using "real" pulse-sequences. We use the ghmqc sequence, which is exquisitely sensitive to gradient strength (array 'gzlvl3' by 10 to 20 with ni=1, nt=32 on a 10-20mg/ml sample). We have found the gradients on our 400 and 500 to be rock solid. We tested them routinely each week. They just don't change. These tests every few months will ensure that the gradients are working. --------------------------------------------------------------------- Ron Nieman, Director Nuclear Magnetic Resonance Facility Department of Chemistry and Biochemistry Arizona State University Tempe, Arizona 85287-1604 (602) 965-3613 Fax (602) 965-2747 email: nieman@asu.edu **********From scott@iastate.edu Wed Oct 4 14:34:13 1995********** chen, We had the same trouble when specifying gradient performance in our rfp but settled on: After a 0.0002 second 10 gauss/cm gradient pulse followed by a .001 second delay, the residual signal should be 95% of the signal obtained without a gradient pulse. The lineshape specifications of the probe must be obtained with the gradient amplifier blanked at zero current. Fast 2D gradient experiments (3 min hmqc and 20min hmbc) must produce spectra of similar quality. You might want to talk to Paul Keifer (415-424-6609) at Varian because he knows a lot about gradients and the tests you could perform. I just tend to run a quick gradient experiment on a stable standard sample. good luck, dave scott iowa state university 515-294-4057 **********From drethwis@icaen.uiowa.edu Wed Oct 4 17:29:48 1995********** We spend a fair amount of our research on PFG. We are using it to measure the diffusion coefficient of gases dissolved in polymers. We are using an MSL300 and our probe is a Doty probe (high field gradient and up to 300 C). In terms of a standard, we have used 50/50 H2O/D2O for our calibrations. We don't really spec the line width (our probe doesn't give the sharpest lines since it was optimized for other things) or the S/N but look more at the gradient strength. If you want more details let me know. Also, please let me know what you find out. Thanks. Professor David Rethwisch Dept of Chemical Engineering University of Iowa Iowa City IA drethwis@icaen.uiowa.edu **********From JSCARSDALE@Gems.VCU.EDU Wed Oct 4 20:39:14 1995********** In response to your questions concerning pfg specifications, the Varian engineer should have run two tests, a gradient recovery test and a gradient profile test both of which should be in the appropriate subdirectory. It is my understanding that the gradient profile test is a good test of both the pfg current amplifier and the gradient coils in the probe. The gradient recovery test is a good test of the pfg amplifier and its ability to deliver gradient pulses as well as insuring that there are not other problems which interfere with the systems ability to recover after a gradient pulse. Both of these tests should be run on the doped D2O sample. If you run these tests every two months, as you suggested, and compare the results to those obtained after the initial installation, you should be able to obtain at least a rough idea of gradient performance. I believe these tests are documented in the accessory installation guide, if I remember correctly, as I have only run them once when we had a problem with our pfg amplifier after our upgrade to vnmr 5.1. I find that I use the gradients often enough (whenever possible) that I can generally note any changes in experimental performance, and if I noted any such changes would run these gradient tests to try to isolate any system fault. J. Neel Scarsdale Assistant Professor Biochemistry and Molecular Biophysics, Virginia Commonwealth University *******From thio@johann.chemie.mu-luebeck.de Thu Oct 5 12:10:41 1995******* Hi Deng-Ywan (hope that's your first name), I would be very interested in getting a copy of the resonces of your question about the calibration of pgf's. We just got a new drx500 and will face the same problem. Many thanks in advance, thomas /\ /Thomas Weimar / \ _ / Institut of Chemistry / \ _| |_ / Medical University of Luebeck / \_| o |_/ Ratzeburger Allee 160 / oOOOo 23538 Luebeck | _______ OOOOO ______ | | Tel. x451 500 4231 | _______ ______ Fax. x451 500 4241 | /C-O\ | |_________ C C_____thio@johann.chemie.mu-luebeck.de \C-C/ **********From gsr3g@avery.med.virginia.edu Sun Oct 8 21:08:24 1995**********--Your should check the gradient strength and gradient recovery time on a semi-regular basis. Just follow the test procedures that are given in the Varian install manual. x-----------------------------------------------------------x | | | Gordon S. Rule gsr3g@Virginia.EDU | | Department of Biochemistry (804) 924-2683 (office) | | University of Virginia (804) 924-1337 (NMR lab) | | Charlottesville, VA | | | x-----------------------------------------------------------x **********From bantalek@Kodak.COM Mon Oct 9 10:22:38 1995********** Dr. Chen, We have had a pfg (and diffusion) package on our Unity 500 for over a year now. We calibrate the gradients in our coherence transfer experiments regularly and save the values. Usually they are very consistent. As far as specifications are concerned, we usually are satisfied with two tests: 1) eddy current ringdown time, 2) gradient strength. Both tests are described sufficiently in the Varian manuals. We generally see a ringdown time between 300 and 400 microseconds. We can achieve 33 gauss/cm for a maximum gradient strength. These have not changed during the time we have had the system. We generally check them every 3-6 months. Let me know if you have any additional questions. /) . /) /^ / (/ /) Magnetic Resonance Analytical Technology **********From: "BrukerFan (tm)" ********** Hi, you should through away your (what's its name?) immediately and buy a Bruker instead! The technology is way ahead and they have it digital and on 800 MHz and all that... And they have all these requested Experiments pre-installed. If you can't do this, but I can't think of a reason, why not, contact your (what's its name?)-office and ask for help. Best wishes BrukerFan (tm) **********From west@qtp.ufl.edu Tue Oct 10 08:42:29 1995********** Please summarize what you learn. John West west@qtp.ufl.edu **********From: "BrukerFan(tm)" ********** I wrote: > you should through away... ############ Yes, I see, I'm sorry, you couldn't knew that! It's Bruker-Slang. It means: "antimatter-annihilate" This can be simply achieved, buying a Bruker spectrometer, which has an anti-(what's its name?) in his extent of delivery. Throwing (now I meanthrowing) this device at the (what's its name) you will get plenty of freespace for new spectrometers. These anti-(what's its name?)s are also available separately from Bruker on request. BrukerFan(tm) ************************************************************* From owner-structural-nmr@net.bio.net Fri Oct 20 23:00:00 1995 Path: biosci!ihnp4.ucsd.edu!scripps.edu!usenet From: Christoph Weber Newsgroups: bionet.structural-nmr Subject: Re: Problem - bacterial growth in labelling media Date: Fri, 20 Oct 1995 17:57:38 -0700 Organization: The Scripps Research Institute, La Jolla, CA Lines: 15 Message-ID: <30884582.570B@scripps.edu> References: <324.199510191222@mailhub.ggr.co.uk> NNTP-Posting-Host: haddock.scripps.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0b1N (X11; I; SunOS 5.3 sun4m) You might want to grow a preculture in unlabelled Celtone to condition your cells. Or even grow them on Celtone plates. I've grown JM109 cells in Celtone myself a few years ago with no problems whatsoever. I wonder what's going on in your system. I did eventually switch hosts to BL21, simply because this gave me higher yield and less proteolytic damage. Good luck, Christoph -- | Christoph Weber weber@scripps.edu | Dept.of Molecular Biology, MB2 619-554-8754 (phone) | The Scripps Research Institute 619-554-3757 (FAX) | La Jolla CA 92037 From owner-structural-nmr@net.bio.net Fri Oct 20 23:00:00 1995 Path: biosci!daresbury!bioftp.unibas.ch!citi2.fr!univ-lyon1.fr!dsi.unimi.it!sirio.cineca.it!nmrlab.ciam.unibo.it!mauro From: "M.A. Cremonini" Newsgroups: bionet.structural-nmr Subject: Re: Calibration of D2O samples Date: Sat, 21 Oct 1995 09:24:26 +0100 Organization: Cineca Lines: 24 Message-ID: References: NNTP-Posting-Host: nmrlab.ciam.unibo.it Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In-Reply-To: > On Tue, 17 Oct 1995, David Kiemle wrote: > > > When doing variable temperature studies in D2O without an internal or external > > reference compound, how do you calibrate chemical shifts? > > > > Thanks in advance for any help. There is an article by Bertini et al. somewhere (sorry, I don't remember where...) which states that the HDO signal can be calibrated according to: (5.11 - 0.012 * t (centigrade)) ppm. Hope it helps. Ciao Mauro ============================================ Dr. Mauro Andrea Cremonini Institute of Agricultural Chemistry University - Bologna - Italy FAX:+39.51.243362 e-mail: m.a.cremonini@nmrlab.ciam.unibo.it 73 de IK4QIX ============================================ From owner-structural-nmr@net.bio.net Sat Oct 21 23:00:00 1995 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.structural-nmr Subject: IMPORTANT: BIOSCI miniFAQ Date: 22 Oct 1995 02:02:39 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 196 Sender: daemon@net.bio.net Distribution: world Message-ID: <199510220900.CAA04819@net.bio.net> NNTP-Posting-Host: net.bio.net This is a new "miniFAQ" 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) What to do about "spams," i.e., junk mail, ads, etc. 2) Examples of subscribing and unsubscribing to the mailing lists. 3) How to access BIOSCI/bionet newsgroup archives. 4) The BIOSCI user address and research interest directory. 1) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups) and mailing lists. The same postings are distributed on both 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 newsgroups from about 95% of the spams that are being sent to date. This means 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. Unfortunately there are easy ways for determined spammers to override the moderation mechanism. We are working on new systems to provide access to our newsgroups over the WWW. These should be available soon, probably November 1995, and will allow you to use your Web browser to look at the news postings. While this 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. 2) 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. 3) How to access BIOSCI/bionet newsgroup archives. -------------------------------------------------- Back postings of all BIOSCI/bionet newsgroups can be found on the World Wide Web at URL http://www.bio.net/. There are several searchable newsgroup indices at this site. E-mail users can search the BIOSCI archives by using our waismail e-mail server. For instructions send the message help to waismail@net.bio.net. Leave the Subject: line blank (anything entered on the Subject: line is ignored). 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 Oct 22 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.sprintlink.net!news.interserv.net!usenet From: 100073.1514@compuserve.com Newsgroups: bionet.structural-nmr Subject: New Method for Poly A+ isolation Date: 23 Oct 1995 13:13:14 GMT Organization: My Org. Lines: 10 Message-ID: <46g4da$a14@data.interserv.net> NNTP-Posting-Host: dd43-140.compuserve.com X-Newsreader: AIR News 3.X (SPRY, Inc.) A new method for the isolation of Poly A+ has been developed on the basis of controlled pore glass (CPG). No further need to waste time with cellulose. There is the possibility to get a free isolation kit for trial purposes. Further details can be seen in http://www.webcom.com/~eppendrf. Guenther Mohr This message might appear twice, as there were server problems. From owner-structural-nmr@net.bio.net Tue Oct 24 22:00:00 1995 Path: biosci!URANO.MIA.UV.MX!fmontes From: fmontes@URANO.MIA.UV.MX (Fernando M. Montes Gonzalez) Newsgroups: bionet.structural-nmr Subject: Positions on protein analysis on immune recognition available in Mexico Date: 24 Oct 1995 10:04:55 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 54 Sender: daemon@net.bio.net Distribution: world Message-ID: <9510241707.AA13707@urano.mia.uv.mx> Two positions are available for research in protein sequences and structure analysis applied to the Study of the Immune Molecular Recognition Process. Our group in Molecular Bioinformatics and Immune Recognition are opening a new laboratory in protein modeling and sequence analysis. We are seeking for two Ph.D. with experience in sequence and/or structure analysis of proteins or in the the study of the molecular mechanism of immune recognition. Our area of research is the study of the molecular basis of immune recognition. This problem is studied from a wide spectrum that goes from the analysis of the structural diversity of the germline repertoire, the comparison of the immune molecular recognition strategies in vertebrates, the construction of a 3-d specialized database of Igs, Mhc and Tcr and it analysis, molecular dynamics studies of the Fv, etc. We try to integrate these studies in the context of theoretical models and the general theory of the immune response. We are planing to extend in the future our studies to other recognition models like those of the endocrine or nervous systems. The two positions available are for a period of three years of renewal. After this period, if the work is evaluated as satisfactory the position will come permanent. The new laboratory is the result from an agreement between the National University of Mexico and the Veracruzana University. The seat of the laboratory will be the City of Xalapa at the state of Veracruz. Xalapa (1500 m. over the sea level) is a medium size city (300,000) and is the capital of the state of Veracruz. For information about the Veracruzana University please see at: http://www.coacade.uv.mx/ For information about our Molecular Biology Laboratory here in Xalapa please see at: http://uv4.ivest.uv.mx/ The candidates must send their curriculum vitae with all its publications to the e-address indicated at the end of this message. You can find information about our research in: J. Mol. Evol. (1994) 38:100 J. Mol. Evol. (1995) 41:41 Biosystems (1995) 32:25 J. Mol. Biol. (1995) 246:74 Int. J. Pept. Prot. Res. (1995) 45:180 Prot. Sci. (1995) oct. issue. Immunogenenics (1995) in press. J. Mol. Biol. (1995) in press. Please contact with Dr. Enrique Vargas-madrazo at: evargas@uv4.invest.uv.mx or evargas@speedy.coacade.uv.mx From owner-structural-nmr@net.bio.net Tue Oct 24 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!info.ucla.edu!nnrp.info.ucla.edu!usenet From: Flint Smith Newsgroups: bionet.structural-nmr Subject: Re: Wanted: Recommendations for 3-D processing software. Date: 25 Oct 1995 20:51:13 GMT Organization: UCLA Lines: 21 Message-ID: <46m801$12h2@saba.info.ucla.edu> References: <46m05b$sn0@nntp3.u.washington.edu> NNTP-Posting-Host: holmes.mbi.ucla.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12 (X11; I; IRIX 5.2 IP22) X-URL: news:46m05b$sn0@nntp3.u.washington.edu tomasz@u.washington.edu (John Tomaszewski) wrote: >Hi all, > I'm just getting started running some 3-D spectra and would like >to hear other peoples recommendations and experiences with a few of the >processing packages out there. We use Felix 2.0 for our 2-D work and I >find that fairly useful but it doesn't seem to lend itself to 3-D spectra >(I find myself switching between the menus and command line modes a >lot). Why don't you write a macro to do exactly what you want? We found the stock menus to be a pain even for 2D processing. >Any opinions (especially from anyone who's used both)? Thanks. I haven't used either. I heard that Pronto was poorly designed in that it opened too many windows. Closing the windows became tiresome. File this under "unsubstantiated rumor". Flint (FELIX CZAR) Smith flint@ucla.edu From owner-structural-nmr@net.bio.net Tue Oct 24 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!news.u.washington.edu!tomasz From: tomasz@u.washington.edu (John Tomaszewski) Newsgroups: bionet.structural-nmr Subject: Wanted: Recommendations for 3-D processing software. Date: 25 Oct 1995 18:37:31 GMT Organization: University of Washington, Seattle Lines: 18 Sender: tomasz@u.washington.edu Message-ID: <46m05b$sn0@nntp3.u.washington.edu> NNTP-Posting-Host: mead1.u.washington.edu NNTP-Posting-User: tomasz Keywords: NMR,3D,Felix,GIFA,Pronto Hi all, I'm just getting started running some 3-D spectra and would like to hear other peoples recommendations and experiences with a few of the processing packages out there. We use Felix 2.0 for our 2-D work and I find that fairly useful but it doesn't seem to lend itself to 3-D spectra (I find myself switching between the menus and command line modes a lot). The 2 programs I'm thinking of trying are GIFA and Pronto. I think the former, and know the latter can process 3-D spectra, but I don't know which I should spend my time downloading, installing, and learning. Any opinions (especially from anyone who's used both)? Thanks. Sincerely, -- ******************************************************************** ** ** ** ** * ** DEPARTMENT OF CHEMISTRY ** ** ** ** ** * ** tomasz@helix.chem.washington.edu ** ** ***** ***** JOHN TOMASZEWSKI ** From owner-structural-nmr@net.bio.net Wed Oct 25 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!oleane!jussieu.fr!pasteur.fr!univ-lyon1.fr!dsi.unimi.it!sirio.cineca.it!nmrlab.ciam.unibo.it!mauro From: "M.A. Cremonini" Newsgroups: bionet.structural-nmr Subject: bruker floating point numbers Date: Thu, 26 Oct 1995 19:14:47 +0100 Organization: Cineca Lines: 18 Message-ID: NNTP-Posting-Host: nmrlab.ciam.unibo.it Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Can anybody please tell me how I can convert an ASPECT 48 bits floating point number into a more 'human' real*8 number? This means: how are bruker floating point number coded? I looked for this piece of information througout the manual but I was not able to find the solution... Thanks for your help. Mauro ============================================ Dr. Mauro Andrea Cremonini Institute of Agricultural Chemistry University - Bologna - Italy FAX:+39.51.243362 e-mail: m.a.cremonini@nmrlab.ciam.unibo.it 73 de IK4QIX ============================================ From owner-structural-nmr@net.bio.net Wed Oct 25 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: Serge Iourine Newsgroups: bionet.structural-nmr Subject: Postdoc position Date: 26 Oct 1995 16:11:52 -0000 Lines: 12 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <46oc08$q1s@mserv1.dl.ac.uk> MIME-Version: 1.0 Original-To: str-nmr@dl.ac.uk Dear netters, May be this question is not quite relevant to this group, but anyhow. Does anybody know of postdoc or research positions in NMR spectroscopy starting next year? At the moment I'm doing PhD in Natural Products Chemistry, working on structure elucidation of novel compounds, mostly on the basis of the NMR data. I'm going to submit my thesis in Dec-Jan and will be available afterwards. Any info will be appreciated. Regards, s.i. From owner-structural-nmr@net.bio.net Wed Oct 25 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!EU.net!Belgium.EU.net!chaos.kulnet.kuleuven.ac.be!news.belnet.be!infoserv.rug.ac.be!bionmr1!kris From: kris@bionmr1.bionmr1.rug.ac.be (Kris Boulez) Newsgroups: bionet.structural-nmr Subject: Re: Wanted: Recommendations for 3-D processing software. Date: 26 Oct 1995 10:17:22 GMT Organization: University of Ghent, Belgium Lines: 23 Message-ID: <46nn7i$gta@infoserv.rug.ac.be> References: <46m05b$sn0@nntp3.u.washington.edu> <46m801$12h2@saba.info.ucla.edu> NNTP-Posting-Host: bionmr1.rug.ac.be X-Newsreader: TIN [version 1.2 PL2] Flint Smith (flint@ucla.edu) wrote: : tomasz@u.washington.edu (John Tomaszewski) wrote: [ both in the next sentence is about GIFA and Pronto ] : >Any opinions (especially from anyone who's used both)? Thanks. : I haven't used either. I heard that Pronto was poorly designed in that : it opened too many windows. Closing the windows became tiresome. : File this under "unsubstantiated rumor". First of all this: the original poster asked for NMR processing software. Pronto does the analysis and assignment of spectra, but not processing. The Carlsberg laboratories, where Pronto is developed, also have an procesing package called MNMR which I haven't used. As a regular user I must say that I find Pronto very easy to use and very powerfull. It does indeed create quite a lot of windows and a big monitor with a high resolution is certainly needed. Kris, -- Kris Boulez (Kris.Boulez@rug.ac.be) Biomolecular NMR unit University of Ghent, Belgium From owner-structural-nmr@net.bio.net Wed Oct 25 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!btnet!dispatch.news.demon.net!demon!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: kalle@RUUCI9.chem.ruu.nl (Karl Hard) Newsgroups: bionet.structural-nmr Subject: NMR position in Utrecht Date: 26 Oct 1995 09:46:42 -0000 Lines: 59 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <46nle2$645@mserv1.dl.ac.uk> Original-To: str-nmr@dl.ac.uk 750 MHz NMR SON NMR Large Scale Facility Bijvoet Center, the Netherlands The 750 MHz NMR spectrometer at Utrecht University is part of the SON NMR Large Scale Facility, which is operated in the framework of the Bijvoet-NSR Research Alliance (BNRA). The BNRA is a joint initiative of the Netherlands Foundation for Chemical Research (SON), the Bijvoet Center for Biomolecular Research at Utrecht University and the Nijmegen SON Research Center (NSR) at the University of Nijmegen. The 750 MHz NMR spectrometer, and a range of other advanced NMR spectrometers in this institute, are part of an European Union supported Large Scale Facility, under the terms of the Training and Mobility of Researchers Programme, which is operated as a facility for European scientists. For this facility a vacancy exists for the post of Supervising Scientist This scientist will provide the scientific expertise and will be responsible for training, assisting and advising visiting scientists from European laboratories. A suitable candidate will have the opportunity to start an NMR research project in structural biology of his own, within the context of the Bijvoet/NSR research programme. In addition there will be ample opportunities to collaborate with visiting scientists using the 750 MHz and other NMR spectrometers of the NMR Large Scale Facility. Together with a specialist for applications and instrumentation, the scientist will be responsible for the day to day management, operation and reporting of the Large Scale Facility. The applicant will have a Ph.D. degree, a good theoretical knowledge of advanced NMR techniques, extensive research experience in modern high field NMR spectroscopy as applied to problems in structural biology, a good working knowledge of modern NMR spectrometers and the associated NMR software packages. Experience with NMR based structure calculations will be an advantage. The applicant should have good interpersonal skills and flexibility and be willing to operate in close cooperation with users of the facility. The appointment will be for the duration of the project (at least three years), with a salary indication of NLG 65,000 - NLG 100,000 per year (government scales BBRA 10 - 12), depending on experience. The position is available from January 1st, 1996. Applications, including a full CV with list of publications and the names, phone numbers and addresses of three possible referees, should be sent within three weeks to: Prof.dr. Robert Kaptein Dept. NMR Spectroscopy Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8 NL-3584 CH Utrecht, the Netherlands. FAX: +31 30 253 76 23; Phone: +31 30 253 37 87 More information about the NMR group in Utrecht can be obtained from http://www-nmr.chem.ruu.nl From owner-structural-nmr@net.bio.net Wed Oct 25 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: mad@tome.cbs.univ-montp1.fr (Marc-Andre Delsuc) Newsgroups: bionet.structural-nmr Subject: Re: Wanted: Recommendations for 3-D processing software. Date: 26 Oct 1995 14:16:14 -0000 Lines: 38 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <46o57e$k1a@mserv1.dl.ac.uk> Original-To: str-nmr@dl.ac.uk To all my fellow NMR spectroscopists, >Hi all, > I'm just getting started running some 3-D spectra and would like >to hear other peoples recommendations and experiences with a few of the >processing packages out there. We use Felix 2.0 for our 2-D work and I >find that fairly useful but it doesn't seem to lend itself to 3-D spectra >(I find myself switching between the menus and command line modes a >lot). The 2 programs I'm thinking of trying are GIFA and Pronto. I >think the former, and know the latter can process 3-D spectra, but I don't >know which I should spend my time downloading, installing, and learning. >Any opinions (especially from anyone who's used both)? Thanks. I take the oportunity of this discussion to announce the new version of our NMR processing programme, Gifa : v4.06b Most notably this version includes a complete user interface for processing 3D files. 3D processing has always been present in Gifa, but a Graphics User Interface was not available up to now. Other salient new features are : Motif port finally completed (all dialog and control boxes; customisation of fonts and colors), automatic 1D phase correction, much better zoom control, etc... And of course, many bug removed ;-) This new version should be available by the end of the week, at least for the SGI and HP versions, on our server : ftp:/tome.cbs.univ-montp1.fr/pub/gifa_v4 the SUN and RS6000 versions should come later. Marc A. Delsuc, _________________________________________________________________________ Marc-Andre' Delsuc Centre de Biochimie Structurale mad@cbs.univ-montp1.fr Faculte de Pharmacie tel : (33) 67 04 34 36 34060 Montpellier cedex fax : (33) 67 52 96 23 FRANCE From owner-structural-nmr@net.bio.net Wed Oct 25 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!dispatch.news.demon.net!demon!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!bioc.cam.ac.uk!arcr1 From: arcr1@bioc.cam.ac.uk (Andrew Raine) Newsgroups: bionet.structural-nmr Subject: Re: Wanted: Recommendations for 3-D processing software. Date: 26 Oct 1995 13:47:46 GMT Organization: Somewhere in the University of Cambridge Lines: 33 Distribution: world Message-ID: <46o3i2$af8@lyra.csx.cam.ac.uk> References: <46m05b$sn0@nntp3.u.washington.edu> NNTP-Posting-Host: giza.bioc.cam.ac.uk Keywords: NMR,3D,Felix,GIFA,Pronto In article <46m05b$sn0@nntp3.u.washington.edu>, tomasz@u.washington.edu (John Tomaszewski) writes: > Hi all, > I'm just getting started running some 3-D spectra and would like > to hear other peoples recommendations and experiences with a few of the > processing packages out there. We use Felix 2.0 for our 2-D work and I > find that fairly useful but it doesn't seem to lend itself to 3-D spectra > (I find myself switching between the menus and command line modes a > lot). The 2 programs I'm thinking of trying are GIFA and Pronto. I > think the former, and know the latter can process 3-D spectra, but I don't > know which I should spend my time downloading, installing, and learning. > Any opinions (especially from anyone who's used both)? Thanks. > > Sincerely, > > -- > ******************************************************************** > ** ** ** ** * ** DEPARTMENT OF CHEMISTRY ** > ** ** ** ** * ** tomasz@helix.chem.washington.edu ** > ** ***** ***** JOHN TOMASZEWSKI ** You could always try the Azara suite of programs developed here. You can get the distribution file by anonymous ftp from ftp.bio.cam.ac.uk:/pub/azara Andrew -------------------------------------------------------------------------------- Dr. Andrew Raine, Cambridge Centre for Molecular Recognition, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, United Kingdom. Telephone: +44 1223 333744 or 333499, FAX +44 1223 333345 email: A.R.C.Raine@bioc.cam.ac.uk -------------------------------------------------------------------------------- From owner-structural-nmr@net.bio.net Thu Oct 26 22:00:00 1995 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: Wanted: Recommendations for 3-D processing software. Date: 27 Oct 1995 09:36:29 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 63 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <46m05b$sn0@nntp3.u.washington.edu> NNTP-Posting-Host: net.bio.net In fact, there are a relatively large number of programs available, both for processing and visualization/analysis. In my opinion none offers a fully satisfactory solution in terms of capabilities, flexibility, communication to other software formats and environments at the time. Several of these programs are available for free over ftp, some others for a nominal license fee (no, or minimal customer support). For processing I would definitely consider NMRPipe which can be downloaded from the NIH site (MSI has licensed it and is about to release user interface to it in their software package). For visulaization/analysis NMRView could be a good option or PIPP (from NIH again). I guess John is looking for inexpensive solutions, but let me name the commercial packages here: beside Felix Sybyl/Triad from Tripos, and MSI's software are available. Bruker's XWIN-NMR with Aurelia for analysis is an alternative, too. Varian offers 3D processing tools, but I am not aware of any specific analysis module at the time (others may give some hints on it). By the way, let me use this message for a little self-advertisment: our review with Brian Carter on nD NMR data processing is on its way to print (I have the proofs already) and is expected to be out early nest year as part of the Techniques in Protein NMR (Methods in Molecular Biology, Ed.: D. G. Reid, Humana Press, NJ). Hope it will not be outdated in terms of available software packages at that time. Sincerely, 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 25 Oct 1995, John Tomaszewski wrote: > Hi all, > I'm just getting started running some 3-D spectra and would like > to hear other peoples recommendations and experiences with a few of the > processing packages out there. We use Felix 2.0 for our 2-D work and I > find that fairly useful but it doesn't seem to lend itself to 3-D spectra > (I find myself switching between the menus and command line modes a > lot). The 2 programs I'm thinking of trying are GIFA and Pronto. I > think the former, and know the latter can process 3-D spectra, but I don't > know which I should spend my time downloading, installing, and learning. > Any opinions (especially from anyone who's used both)? Thanks. > > Sincerely, > > -- > ******************************************************************** > ** ** ** ** * ** DEPARTMENT OF CHEMISTRY ** > ** ** ** ** * ** tomasz@helix.chem.washington.edu ** > ** ***** ***** JOHN TOMASZEWSKI ** > > From owner-structural-nmr@net.bio.net Thu Oct 26 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!howland.reston.ans.net!torn!news.bc.net!news.sfu.ca!ian From: gay@sfu.ca (Ian Gay) Newsgroups: bionet.structural-nmr Subject: Re: bruker floating point numbers Date: Fri, 27 Oct 95 18:10:18 GMT Organization: Simon Fraser University Lines: 23 Message-ID: <46r3sd$ni9@morgoth.sfu.ca> References: NNTP-Posting-Host: ian.chem.sfu.ca X-Newsreader: News Xpress Version 1.0 Beta #4 In article , "M.A. Cremonini" wrote: >Can anybody please tell me how I can convert an ASPECT 48 bits floating >point number into a more 'human' real*8 number? >This means: how are bruker floating point number coded? I looked for this >piece of information througout the manual but I was not able to find the >solution... >Thanks for your help. >Mauro The Bruker floating point format has 37 bit mantissa and an 11 bit exponent. The first 24 bit word contains the most significant 24 bits of the mantissa. The second word contains the exponent in its most significant 11 bits, and the bottom of the mantissa in the least significant 13 bits. Both mantissa and exponent are in 2's complement notation. I can send you a routine in C for making the conversion, if you wish. Ian From owner-structural-nmr@net.bio.net Thu Oct 26 22:00:00 1995 Path: biosci!IRIS108.BIOSYM.COM!ssz From: ssz@IRIS108.BIOSYM.COM ("Sa'ndor Szalma") Newsgroups: bionet.structural-nmr Subject: Re:Wanted: Recommendations for 3-D processing software. Date: 27 Oct 1995 09:33:21 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 29 Sender: daemon@net.bio.net Distribution: world Message-ID: <199510271631.JAA09173@iris108.biosym.com> NNTP-Posting-Host: net.bio.net Hi, >> JOHN TOMASZEWSKI writes: >> We use Felix 2.0 for our 2-D work and I find that fairly >> useful but it doesn't seem to lend itself to 3-D spectra Felix 2.0 was released quite a few years ago, and since then there have been several releases (2.05, 2.1, 2.3 and next week Felix 95.0 will be delivered to customers). So while it is probably true that Felix 2.0 was not ideal for multidimensional processing (N > 2), this has changed. You might want to try Felix 95.0 which has a much improved EZ interface for the most common 3D processing schemes, and has a wide variety of visualization and analysis tools, too. Sincerely, \~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/ * , * * Sandor Szalma, Ph.D. * * Manager, Felix NMR Data Processing, * * Analysis and Assignment * * Biosym/MSI * * 9685 Scranton Rd, San Diego, CA 92121-2777 * * e-mail:ssz@biosym.com, Tel.: 619-546-5503 * * * /~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\ From owner-structural-nmr@net.bio.net Sun Oct 29 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!dish.news.pipex.net!pipex!news00.sunet.se!sunic!news99.sunet.se!news.uni-c.dk!news From: Mogens Kjaer Newsgroups: bionet.structural-nmr Subject: Re: Wanted: Recommendations for 3-D processing software. Date: Mon, 30 Oct 1995 08:03:32 +0100 Organization: News Server at UNI-C, Danish Computing Centre for Research and Education. Lines: 34 Message-ID: <309478C4.41C6@unidhp.uni-c.dk> References: <46m05b$sn0@nntp3.u.washington.edu> <46m801$12h2@saba.info.ucla.edu> NNTP-Posting-Host: lgbppp31.uni-c.dk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0b1 (X11; I; IRIX 5.3 IP22) Flint Smith wrote: > > tomasz@u.washington.edu (John Tomaszewski) wrote: > >Hi all, > > I'm just getting started running some 3-D spectra and would like > >to hear other peoples recommendations and experiences with a few of the > >processing packages out there. > > I haven't used either. I heard that Pronto was poorly designed in that > it opened too many windows. Closing the windows became tiresome. > File this under "unsubstantiated rumor". > We developed Pronto here at the Carlsberg Lab... Well, this is correct if you watch someone using Pronto, and not using it yourself, it could look like a mess of windows. However, after a few days of actually using the program, most people learn to manage the windows, even on a 1024x768 screen. The program Pronto and the processing software MNMR is available for free, both for academic and commercial institutions. Pronto comes precompiled for SGI's and Sun's, MNMR only as source code: You need a C and a FORTRAN compiler and at least one UNIX guru to install it... Please Email me if you're interested in the software. Mogens -- Mogens Kjaer, Carlsberg Laboratory, Dept. of Chemistry Gamle Carlsberg Vej 10, DK-2500 Valby, Denmark Phone: +45 33 27 53 25, Fax: +45 33 27 47 08 Email: carlmk@unidhp.uni-c.dk From owner-structural-nmr@net.bio.net Sun Oct 29 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!usenet.eel.ufl.edu!tank.news.pipex.net!pipex!lade.news.pipex.net!pipex!news00.sunet.se!sunic!psinntp!psinntp!psinntp!psinntp!pfizergate!holly.sandwich.pfizer.com!siris7!jpo From: jpo@siris7 (John Overington) Newsgroups: bionet.molec-model,bionet.molbio.proteins,bionet.xtallography,bionet.structural-nmr,bionet.biophysics,sci.chem,sci.comp-aided Subject: Internet Drug Design Course Date: 30 Oct 1995 08:57:28 GMT Organization: Pfizer Central Research, Sandwich, Kent, UK Lines: 27 Message-ID: <47241o$1r3@holly.sandwich.pfizer.com> NNTP-Posting-Host: siris7.sandwich.pfizer.com Keywords: Internet Drug Design Course X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.molec-model:639 bionet.molbio.proteins:6132 bionet.xtallography:2130 bionet.structural-nmr:857 bionet.biophysics:1372 sci.chem:42204 sci.comp-aided:926 We (Peter Murray-Rust of Glaxo Wellcome, and John Overington of Pfizer) would like to announce an initiative in industrial training for medicinal chemists interested in applying protein structure-based drug design (SBDD) techniques as part of their jobs. Additionally, skills in effectively using the internet as a scientific resource will also be developed. The course will use self-paced, internet-based training, coupled to close contact with course 'tutors', working in the pharmaceutical industry. We are currently looking for further partners to offer financial support, and course material. Partners need to have a presence in the UK to qualify for potential funding under a Technology Foresight grant; although the basic course material will be generally accessible over the internet to the wider community. Further details, and a draft prospectus can be found at http://www.cryst.bbk.ac.uk/SBDD/course.html If you have any further questions, we would be pleased to answer them. John Overington jpo@guitar.rockefeller.edu Peter Murray-Rust ubcg09q@cryst.bbk.ac.uk -- Dr. John Overington email: overingtonj@pfizer.com Pfizer Central Research phone: +44-(0)1304-618467 Sandwich, Kent, CT13 9NJ fax: +44-(0)1304-618422 United Kingdom cc-mail: overington_j@sandwich.pfizer.com From owner-structural-nmr@net.bio.net Sun Oct 29 22:00:00 1995 Path: biosci!ggr.co.uk!bgc0829 From: bgc0829@ggr.co.uk (Dr B G Carter) Newsgroups: bionet.structural-nmr Subject: unsubscribe Date: 30 Oct 1995 07:06:31 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <14890.199510301444@mailhub.ggr.co.uk> NNTP-Posting-Host: net.bio.net unsubscribe str-nmr bgc0829@ggr.co.uk From owner-structural-nmr@net.bio.net Sun Oct 29 22:00:00 1995 Path: biosci!biophy.jussieu.fr!michel From: michel@biophy.jussieu.fr (Michel SEIGNEURET) Newsgroups: bionet.structural-nmr Subject: Re:Wanted: Recommendations for 3-D processing software. Date: 30 Oct 1995 01:26:11 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 29 Sender: daemon@net.bio.net Distribution: world Message-ID: <9510300935.AA07075@mood.biophy.jussieu.fr> NNTP-Posting-Host: net.bio.net Here is my contribution to this most stimulating discussion on 3D software: Here are the ones we use or used routinely: 1) NMRPipe: in my opinion the best and smartest software for processing 3D data. It provides highly sophisticated and very flexible processing facilities including a very stable linear prediction routine. Processing is very fast if you have sufficient memory. 2) NMRView: very good for manual analysis of NMRPipe or Felix 3D matrices (simultaneous tracking of several planes in several 3D matrices, etc...). Also importantly, it allows one to make an optimal use of screen space. 3) PIPP: very powerful automated pick-peacking of 3D data processed with NMRPipe. 4) Felix 2.3: was slow and severely bugged for 3D processing and display. Here are the ones we have tried or are currently trying: 1) Gifa: probably the most comprehensive academic processing program. Has very advanced processing facilities (lp, me). There is also a rather creative analysis software called Cindy that uses the same data format (available from the same ftp site). 2) Pronto: nice for simultaneous tracking and semi-automated assignments in several 2D planes. The problem is that you cannot spend your life testing software. So you finally make a choice, often arbitrary... Best regards. Michel M. Seigneuret Universite Paris 7 Lab. de Biophysique Cellulaire Paris, France. From owner-structural-nmr@net.bio.net Mon Oct 30 22:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!plug.news.pipex.net!pipex!tank.news.pipex.net!pipex!soap.news.pipex.net!pipex!usenet From: M J Geisow Newsgroups: bionet.structural-nmr Subject: PERSPECTIVES ON PROTEIN ENGINEERING: Early registration deadline Date: 31 Oct 1995 08:10:31 GMT Organization: BIODIGM Ltd. Lines: 9 Message-ID: <474lln$qim@soap.news.pipex.net> NNTP-Posting-Host: am189.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) -- BIODIGM Tel: +44 (0) 1949 839077 Fax: +44 (0) 1949 831886 Email: biodigm@dial.pipex.com From owner-structural-nmr@net.bio.net Mon Oct 30 22:00:00 1995 Newsgroups: bionet.xtallography,bionet.structural-nmr Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!ix.netcom.com!netcom.com!misrael From: misrael@scripps.edu (Mark Israel) Subject: Re: General Questions re NMR Message-ID: Sender: misrael@netcom14.netcom.com Organization: The Scripps Research Institute, La Jolla, California, USA References: Date: Tue, 31 Oct 1995 13:01:56 GMT Lines: 20 Xref: biosci bionet.xtallography:2132 bionet.structural-nmr:861 In article , mdabl@cc.newcastle.edu.au (Allen Black) writes: > I'll bet this is the wrong newsgroup but maybe you can help me. What is > the newsgroup for people using NMR to solve protein structures, if any? bionet.structural-nmr -- I've crossposted this for you. > Next question: I am an immunologist by trade but am interested in learning > about NMR, especially NOESY, in the field of biochemistry. Is there a > semi-lucid text out there that anyone can recommend. My old Organic Chem > text is useless for learning about how to solve protein structures, and > what methods are available to modern biochemists. > > Cheers, > Allen Black > Dept. of Pathology > Univ. of Newcastle -- misrael@scripps.edu Mark Israel From owner-structural-nmr@net.bio.net Mon Oct 30 22:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!tank.news.pipex.net!pipex!soap.news.pipex.net!pipex!usenet From: M J Geisow Newsgroups: bionet.structural-nmr Subject: PERSPECTIVES ON PROTEIN ENGINEERING:early registrations(correction) Date: 31 Oct 1995 08:11:38 GMT Organization: BIODIGM Ltd. Lines: 24 Message-ID: <474lnq$qim@soap.news.pipex.net> NNTP-Posting-Host: am189.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) PERSPECTIVES ON PROTEIN ENGINEERING MONTPELLIER, FRANCE March 2-6 1996 Reduced (early) registration ends 31.10.95 Information and on-line registration: http://www.cryst.bbk.ac.uk/CEC/pope5.html Main scientific programme published: http://www.cryst.bbk.ac.uk/CEC/program.html List of planned EU Framework III Structural Biology satellite meetings now available: http://www.cryst.bbk.ac.uk/CEC/networks.html Proceedings from the 1994 Oxford Perspectives on Protein Engineering conference now published: http://www.cryst.bbk.ac.uk/CEC/book.html -- BIODIGM Tel: +44 (0) 1949 839077 Fax: +44 (0) 1949 831886 Email: biodigm@dial.pipex.com From owner-structural-nmr@net.bio.net Tue Oct 31 22:00:00 1995 Path: biosci!bcm.tmc.edu!pendragon.jsc.nasa.gov!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!uwm.edu!lll-winken.llnl.gov!fnnews.fnal.gov!nntp-server.caltech.edu!rickert From: rickert@cco.caltech.edu (Keith Warren Rickert) Newsgroups: bionet.structural-nmr Subject: Re: Wanted: Recommendations for 3-D processing software. Date: 1 Nov 1995 17:47:00 GMT Organization: California Institute of Technology, Pasadena Lines: 33 Message-ID: <478bqk$2kd@gap.cco.caltech.edu> References: <46m05b$sn0@nntp3.u.washington.edu> <46m801$12h2@saba.info.ucla.edu> <309478C4.41C6@unidhp.uni-c.dk> NNTP-Posting-Host: accord.cco.caltech.edu X-Newsreader: NN version 6.5.0 #12 (NOV) In <309478C4.41C6@unidhp.uni-c.dk> Mogens Kjaer writes: >Flint Smith wrote: >> >> tomasz@u.washington.edu (John Tomaszewski) wrote: >> >Hi all, >> > I'm just getting started running some 3-D spectra and would like >> >to hear other peoples recommendations and experiences with a few of the >> >processing packages out there. >> >> I haven't used either. I heard that Pronto was poorly designed in that >> it opened too many windows. Closing the windows became tiresome. >> File this under "unsubstantiated rumor". >> >We developed Pronto here at the Carlsberg Lab... Well, this is correct >if you watch someone using Pronto, and not using it yourself, it >could look like a mess of windows. However, after a few days of >actually using the program, most people learn to manage the windows, >even on a 1024x768 screen. Having obtained Pronto this summer, I learned to use it pretty well and fairly quickly, and found it very useful. I would say that it's not that it opens too many windows, its just that it points out to you that your screen is too small ;-). I would give it a high recommendation as an analysis tool. Keith -- Keith Rickert | "The time is now. The chains of Fenric have keith@imppig.caltech.edu | shattered. The gods have lost the final battle. rickert@cco.caltech.edu | Dead men's ship has slipped its moor, and the | great ash itself trembles to its roots." From owner-structural-nmr@net.bio.net Tue Oct 31 22:00:00 1995 Path: biosci!GATE.SINICA.EDU.TW!ccchuang From: ccchuang@GATE.SINICA.EDU.TW (Chyh-chong Chuang) Newsgroups: bionet.structural-nmr Subject: molecular topology and parameter in xplor Date: 1 Nov 1995 02:10:17 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 27 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net To Xplor experts: how to creat a topology and parameter for a residue not appear on standard xplor topology and parameter file? I had read the inp file for generate cyclosporin A, and tried to learn some there. But I had problem in assigning the charge of atoms. Do there are some "rules" when do this? (I mean assigning the parameters) I also had problem in assignment of a improper group. How and when to assign a impropers? Any help will be great appreciated. Thanks all ============================================ Chyh-Chong Chuang Institude of Biological Chemistry, Academia Sinica,Taipei, Taiwan -------------------------------------------- P.O. BOX 23-106, Phone: 886-2-362-0261 ext 2021 Taipei, Taiwan, Fax: 886-2-363-5038 R.O.C. E-Mail: ccchuang@gate.sinica.edu.tw ============================================