From owner-structural-nmr@net.bio.net Thu Feb 01 22:00:00 1996 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: labeled sample Date: 2 Feb 1996 06:25:10 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Netters, An old question: I'd need a good isotope labeled (13C, or 15N, and both) test sample. I know ubiquitin was available commercially, but I lost the address, ph, fax#s. I recall an oligopeptide labeled only for few residues in the middle only, from Johathan Lee/CIL(?). Any suggestions? Thanks, best regards, Istvan wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww Istvan Pelczer, Ph.D. ipelczer@chemvax.princeton.edu (or: ipelczer@syr.edu) Senior NMR Spectroscopist Princeton University Department of Chemistry ph# (609) 258 1633 Frick Laboratory fax# (609) 258 6746 Washington Road Princeton, NJ 08544 From owner-structural-nmr@net.bio.net Thu Feb 01 22:00:00 1996 Newsgroups: bionet.structural-nmr Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!torn!utnut!oci!bloch.med.utoronto.ca!gardner From: gardner@bloch.med.utoronto.ca (Kevin Gardner) Subject: Re: labeled sample Message-ID: Sender: news@oci.utoronto.ca Organization: Ontario Cancer Institute - U of Toronto X-Newsreader: TIN [version 1.2 PL2] References: Date: Fri, 2 Feb 1996 16:11:21 GMT Lines: 29 Istvan Pelczer (ipelczer@MAILBOX.SYR.EDU) wrote: : An old question: I'd need a good isotope labeled (13C, or 15N, and both) : test sample. I know ubiquitin was available commercially, but I lost the : address, ph, fax#s. Here's some info re: the doubly-labelled ubiquitin, provided with the caveats that a). I haven't used this company's product and b). these numbers are potentially out-of-date: ----- Vendor: VLI Research (Pennsylvania) (610) 650-0264 voice (610) 666-7549 fax 15N and/or 13C labeled (99%) human ubiquitin (76 amino acids) 10 mg of the 15N label -> $2000 10 mg of the 15N/13C label -> $7500 ----- Enjoy, Kevin -- ************************************************************************* Kevin Gardner gardner@redfield.med.utoronto.ca University of Toronto http://abragam.med.utoronto.ca/~gardner Dept. of Medical Genetics phone: 416-978-0642/FAX: -6885 From owner-structural-nmr@net.bio.net Thu Feb 01 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!EU.net!news.eunet.fi!newsmaster From: piero pollesello Newsgroups: bionet.structural-nmr Subject: Re: HMP shunt metabolites on 31P NMR Date: 2 Feb 1996 13:35:23 GMT Organization: POLYbios, Area Science Park, Trieste, Italy Lines: 28 Message-ID: <4et3ur$ac3@idefix.eunet.fi> References: NNTP-Posting-Host: protein.orion.fi Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12(Macintosh; I; 68K) To: lboros@magnus.acs.ohio-state.edu X-URL: news:lboros.22.3110042D@magnus.acs.ohio-state.edu >>> Look up at the WWW-URL site http://poly01.tbs.trieste.it/figpp.html and select the poster on quantification of minor phosphorus metabolites in crude perchloric extracts by 31P-1H NMR spectroscopy. The list of references could be useful. Regards Piero ****************************************************************** Piero Pollesello, PhD senior lecturer of medical chemistry at the University of Helsinki (docent i medicinsk kemi vid Helsingfors Universitet) actual position: research scientist at the Nuclear magnetic resonance spectroscopy Unit Chemical research department Orion Research Center (Mankaa, Espoo) Orion-Farmos, Orion Corporation P.O.box 65 FIN-02101 Espoo, Finland Tel.:int-358-0-429-4191 Fax.:int-358-0-429-2924 e-mail: piero.pollesello@rd.orion.orion.mailnet.fi www-URL: http://poly01.tbs.trieste.it/figpp.html ******************************************************************** From owner-structural-nmr@net.bio.net Thu Feb 01 22:00:00 1996 Path: biosci!BIOC01.UTHSCSA.EDU!sudha From: sudha@BIOC01.UTHSCSA.EDU (Sudha Veeraraghavan) Newsgroups: bionet.structural-nmr Subject: Re: lines in postscript files Date: 2 Feb 1996 05:32:25 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <9602021329.AA05919@bioc01.uthscsa.edu> References: NNTP-Posting-Host: net.bio.net I have experienced this problem as well. Usually when a line appears in the print out, it corresponds with a screen imperfection and snapshot picks it up along with the model. For skeleton structures, I find the use of export_plot fast and trouble free. However, one needs to view the ps file that is generated then go back and adjust the positioning of the image on the screen before printing the final version. Sudha V. -- !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Sudha Veeraraghavan sudha@bioc01.uthscsa.edu Department of Biochemistry sveerara@opal.med.tufts.edu Tufts University School of Medicine [Tel] (617) 636-6873 136 Harrison Ave. [Fax] (617) 636-6409 Boston, MA 02111 U.S.A. !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! From owner-structural-nmr@net.bio.net Thu Feb 01 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!news.emi.com!pauling.wadsworth.org!trimble From: trimble@news.wadsworth.org (Robert B. Trimble) Newsgroups: bionet.structural-nmr Subject: Internal ppm std? Date: 2 Feb 1996 15:25:42 GMT Organization: Wadsworth Center, NY Health Dept. Lines: 20 Message-ID: <4etadm$8uu@pauling.wadsworth.org> NNTP-Posting-Host: alcor.wadsworth.org Summary: Internal chemical shift marker for D2O spectra: acetone? X-Newsreader: TIN [version 1.2 PL2] Dear Netters: We have been performing high-field nmr on oligosaccharides in D2O for sometime and have routinely used acetone as an internal chemical shift standard. Recently our NMR Facility came on line at the Wadsworth Center, and after a series of temperature calibration runs using methanol, we realized that some of our earlier "fee for service" spectra taken at other institutions were probably not at the advertised temp. Can someone point me to a reference that shows the effect of temp on the chemical shift of acetone? Also, what would be the expected exchange rate for the methyl protons of acetone in 99.996% D2O? WE are seeing broadening and side peaks around the 2.225 (296K) protons after only 4 to 5 days at room temp that I don't recall seeing previously. Thanks for any insights provided: Robert B. Trimble Wadsworth Labs C-535 NYSDOH, Albany, NY 12202-0509 From owner-structural-nmr@net.bio.net Fri Feb 02 22:00:00 1996 Path: biosci!GATE.SINICA.EDU.TW!ccchuang From: ccchuang@GATE.SINICA.EDU.TW (Chyh-chong Chuang) Newsgroups: bionet.structural-nmr Subject: convert brucker ADVANCE's data to felix Date: 2 Feb 1996 21:55:11 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Netters: I am curious whether thare is any program can convert brucker's ADVANCE data (DMX, DRX) to felix format for off-line processing? Any comment will be appreciated. Thanks all ccchuang ============================================ Chyh-Chong Chuang Institude of Biological Chemistry, Academia Sinica,Taipei, Taiwan -------------------------------------------- Phone: 886-2-7858981 ext 7091 Fax: 886-2-7883473 E-Mail: ccchuang@gate.sinica.edu.tw ============================================ From owner-structural-nmr@net.bio.net Fri Feb 02 22:00:00 1996 Path: biosci!CMGM.STANFORD.EDU!zzheng From: zzheng@CMGM.STANFORD.EDU (Zhiwen Zheng, olegj) Newsgroups: bionet.structural-nmr Subject: Cost of Protein Structures Date: 2 Feb 1996 16:14:50 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 36 Sender: daemon@net.bio.net Distribution: world Message-ID: <199602030012.QAA07438@cmgm.Stanford.EDU> NNTP-Posting-Host: net.bio.net Dear Netters, Could anybody help me to get information on the average cost of solving a mid-size protein tertiary structure using NMR? There is a pharmaceutical company who had an interesting protein (8KDa,purified) and asked us if we can solve the solution structure for them. This is going to be a contract work. They provide sample and pay us to solve the structure and they get the result. So I am very interested in knowing the average cost of a structure in order to have a common sense on this matter. I would appreciate any information or comments on the related subjects. -David ----------------------------------------------------------------------- Zhiwen (David) Zheng, Ph.D. E-mail zzheng@cmgm.stanford.edu Stanford Magnetic Resonance Laboratory Phone: (415) 725-1811 Staford University Fax: (415) 723-2253 Stanford, CA 94305-5055 ----------------------------------------------------------------------- From owner-structural-nmr@net.bio.net Sat Feb 03 22:00:00 1996 Path: biosci!EDUSERV.ITS.UNIMELB.EDU.AU!s_jws From: s_jws@EDUSERV.ITS.UNIMELB.EDU.AU (Julian Salerno) Newsgroups: bionet.structural-nmr Subject: data acquisition + drivers Date: 4 Feb 1996 15:33:55 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Is anyone out there using Igor/Nidaq (or similar combination) to drive their Varian or Bruker instruments during acquisition ?? This would in essence be an alternative to the Tecmag options currently available. All comments most welcome. Many thanks in advance. Julian Salerno (j.salerno@pgrad.unimelb.edu.au) University of Melbourne Chemistry Department Phone: +61 3 9344 4125 Kinetics Laboratory Fax: +61 3 9347 5180 or 11 Bellevue Street RICHMOND 3121 VIC Private: +61 3 9428 4883 From owner-structural-nmr@net.bio.net Sat Feb 03 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!nntp.coast.net!torn!nott!nrcnet0.nrc.ca!BRI.NRC.CA!Feng.Ni From: Feng.Ni@BRI.NRC.CA (Feng Ni) Newsgroups: bionet.structural-nmr Subject: POST-DOCTORAL POSITIONS IN PROTEIN NMR Date: 4 Feb 1996 20:20:24 GMT Organization: Institut de recherche en biotechnologie, Montréal Lines: 34 Distribution: world Message-ID: <4f34e8$qng@nrcnet0.nrc.ca> NNTP-Posting-Host: indy.bri.nrc.ca POST-DOCTORAL POSITIONS IN BIOPHYSICAL AND PROTEIN NMR SPECTROSCOPY There are one or two postdoctoral positions available in the NMR laboratory of the Biotechnology Research Institute (BRI). Our research centers on proteins in blood coagulation, protease regulation and ligand-receptor interactions. Candidates must have a Ph.D. degree in chemistry, biochemistry or a related area and have demonstrated abbilities in carrying out creative research. Knowledge of high-resolution NMR spectroscopy is desirable and experience in protein/pep- tide purification is an important asset. Through their work at BRI, postdoc- toral fellows obtain experience in the use of NMR spectroscopy to characterize the structures and the biophysical properties of proteins and protein-protein complexes. Postdoctoral fellows are paid an annual salary of $23,000-$28,000 according to the MRC guidelines. Exceptional candidates may be promoted to more senior posi- tions offerred by the National Research Council of Canada. Qualified individuals are invited to forward your resume to: Feng Ni, Ph.D. Head of Biomolecular NMR Biotechnology Research Institute 6100 Royalmount Avenue Montreal, Quebec, H4P 2R2 Canada phone: (514)-496-6729 fax: (514)-496-5143 e_mail: fengni@bri.nrc.ca Applications will be accepted until the 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 Sat Feb 03 22:00:00 1996 Path: biosci!CMGM.STANFORD.EDU!zzheng From: zzheng@CMGM.STANFORD.EDU (Zhiwen Zheng, olegj) Newsgroups: bionet.structural-nmr Subject: Re: Cost of Protein Structures Date: 3 Feb 1996 21:12:11 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <199602040510.VAA23914@cmgm.Stanford.EDU> NNTP-Posting-Host: net.bio.net Dear Netter, In order to avoid some misunderstanding that may occur regarding to my recent inquiry "Cost of Protein Structures". I would like to make one thing clear. The inquiry is only my own personal curiousity, not at all representing the lab that I am currently associated with. The "contract work" was a make-up story. Please don't take it seriously. -David zzheng@cmgm.stanford.edu From owner-structural-nmr@net.bio.net Sat Feb 03 22:00:00 1996 Path: biosci!CMGM.STANFORD.EDU!zzheng From: zzheng@CMGM.STANFORD.EDU (Zhiwen Zheng, olegj) Newsgroups: bionet.structural-nmr Subject: "Cost of Protein Structures" Please Disregard It,a Bad Joke Date: 3 Feb 1996 20:35:29 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 4 Sender: daemon@net.bio.net Distribution: world Message-ID: <199602040433.UAA23555@cmgm.Stanford.EDU> NNTP-Posting-Host: net.bio.net From owner-structural-nmr@net.bio.net Sun Feb 04 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!gatech!concert!bigblue.oit.unc.edu!mmlds1.pha.unc.edu!iiv From: Iosif Vaisman Newsgroups: bionet.biophysics,bionet.molec-model,bionet.xtallography,bionet.molbio.proteins,bionet.structural-nmr Subject: Gordon Conference on Water and Aqueous Solutions Date: Mon, 5 Feb 1996 11:36:42 -0500 Organization: The University of North Carolina at Chapel Hill Lines: 158 Message-ID: NNTP-Posting-Host: mmlds1.pha.unc.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Xref: biosci bionet.biophysics:1679 bionet.molec-model:804 bionet.xtallography:2352 bionet.molbio.proteins:6937 bionet.structural-nmr:1088 Crossposted from Water Science Network (water@listserv.unc.edu) Gordon Research Conference PHYSICS AND PHYSICAL CHEMISTRY OF WATER AND AQUEOUS SOLUTIONS Aug 4 - Aug 9, 1996 ------------------------------------------------------ ------------------------------------------------------ George E. Walrafen, Chair H. Eugene Stanley, Vice Chair ------------------------------------------------------ ------------------------------------------------------ WATER IN PROTEINS--------------(Sunday evening, 4 Aug) A. Parsegian-------------------(Session chair) P. Nicholls/P. Kahn/R. Wolfenden ------------------------------------------------------ AMORPHOUS ICE TO HOT WATER----(Monday morning, 5 Aug) J. Teixeira--------------------(Session chair) G. Johari/O. Mishima/ A. Geiger/M. Neumann/ P. Debenedetti-----------------(Commentator) SCATTERING: X-RAY, NEUTRON-----(Monday evening, 5 Aug) M.-C. Bellissent-Funel---------(Session chair) T. Yamaguchi/A. Soper PLENARY POSTER SESSION #1 H. E. Stanley------------------(Poster chair) ------------------------------------------------------ ULTRAFAST DYNAMICS/HOLE BURNING-(Tuesday morning, 6 Aug) A. Laubereau-------------------(Session chair) E. Castner/R. J. Dwayne-Miller/ G. J. Small/H. Graener/ W. T. Lotshaw------------------(Commentator) LOW-FREQUENCY RAMAN SPECTROSCOPY--(Tuesday evening, 6 Aug) Y. Tominaga--------------------(Session chair) Y. C. Chu/Y. Kameda/ O. Faurskov-Nielsen------------(Commentator) ------------------------------------------------------- HYDRATION OF BIOMOLECULES------(Wednesday morning, 7 Aug) B. Schoenborn------------------(Session chair) S. Leikin/H. Berman/ A. Gronenborn/E. Mayer ICES AND CAGES-----------------(Wednesday evening, 7 Aug) P. Kusalik---------------------(Session chair) I. Svishchev/S.-H. Chen PLEANARY POSTER SESSION #2 H. E. Stanley------------------(Poster chair) ------------------------------------------------------- STRUCTURE AND DYNAMICS OF H-BONDED SYSTEMS---------------(Thursday morning, 8 Aug) C. A. Angell-------------------(Session chair) A. Luzar/T. Head-Gordon/ R. Saykally/N. Agmon THURSDAY EVENING: BANQUET, BUSINESS SESSION, ELECTION OF VICE CHAIR, ETC. CRITICAL PHENOMENA-------------(Thursday evening, 8 Aug) G. E. Walrafen-----------------(Session chair) B. Widom-----------------------(45 minute special speaker) Professor Widom's lecture will be a wide overview of the developments in CRITICAL PHENOMENA from the early days of the subject to the most recent exciting developments, such as renormalization group theory, etc. ----------------END OF CONFERENCE------------------------ THE POSTERS WILL BE ON DISPLAY ALL WEEK LONG!!! INFORMATION: Tentative poster titles for Gene Stanley's PLENARY POSTER SESSIONS, should be sent by E-mail or FAX directly to Gene (HES@BU.EDU, 617-353-3783). These poster sessions will be held on Monday and Wednesday evenings. The posters will be on display all week long, and they will be displayed in the big, well-lighted, red school house. The poster boards are 4 ft. X 8 ft., so there will be plenty of room for your material. More than one poster per person is also possible. We also want to emphasize as strongly as we can that EARLY REGISTRATION is absolutely essential. No applicants will be accepted by the GRC after about 135 people have registered!!!! Contact the GRC office; phone (401)-783-4011 or -3372; FAX (401)-783-7644; E-MAIL grc@grcmail.grc.uri.edu to obtain your registration forms. The GRC has streamlined the registration procedures. For example, they can take registration payments by FAX if you give your credit card number on their form, sign it, and FAX it back. We will also mail out some registration forms to people who are definitely attending, or to people who attended in 1994. However, it is best to get your materials yourself from the GRC people. We plan mini- or ground-zero review for most sessions. These will be presented by the session chairs. The ground-zero reviews will involve overviews of the talks to follow in each session. The ground- zero reviews WILL NOT involve talks by the session chairs about their own work. The ground-zero reviews are intended to introduce each session for people in the audience who may not be familiar with the previous work in the area of the session. We will also have two micro-reviews Monday evening and Wednesday evening to save time for the poster sessions to follow. In addition we will have commentators (about 5 minutes) following the sessions on Monday morning, Tuesday morning, and Wednesday evening. The purpose of the commentators is to present a summing up, as well as to indicate problems, or regions of work which should be exploited in the future. Our Thusday evening speaker, after the banquet, will be Professor Ben Widom from Cornell University. This will really be a special treat for all of us. Professor Widom will tell us about developments in "CRITICAL PHENOMENA" from the past to the present. Our mixer will be held Sunday afternoon starting roughly at 4:30 or 5:00 p.m. before the full dinner on Sunday evening. This year you will get a dinner, and not a mini-dinner, on Sunday evening. Gene Stanley and I hope to greet all of you in person at the mixer. Adrian Parsegian is helping us with the reception, and he is also the first session chair, Sunday night. We could hardly have gotten a better person for both assignments. He has assured me that he will pick up the liquid refreshments for us on his way to the conference. Remember, REGISTER SOON. We hope to see you in August. Sincerely yours, George Walrafen Chair Ph:(202)-806-6897 Fax:(202)-806-5475 e-mail:YCC@SCS.HOWARD.EDU H. Eugene Stanley Vice Chair Ph:(617)-353-2617 FAX:(617)-353-3783 e-mail:HES@BU.EDU From owner-structural-nmr@net.bio.net Tue Feb 06 22:00:00 1996 Newsgroups: bionet.structural-nmr Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!primus.ac.net!news.cais.net!xara.net!peer-news.britain.eu.net!newsfeed.ed.ac.uk!leeds.ac.uk!news From: a.g.booth@leeds.ac.uk (Andrew Booth) Subject: recent JCAMP messages Message-ID: <1996Feb7.155315.28650@leeds.ac.uk> NNTP-Posting-Host: bmb_pc112.leeds.ac.uk Date: Wed, 7 Feb 1996 15:53:14 +0000 (GMT) X-Newsreader: News Xpress Version 1.0 Beta #3 Lines: 10 A friend in Jamaica is having trouble receiving news. In particular, he is interested in the message(s) about JCAMP that appeared recently on this list. I tried to find them, but I think I got here too late. Could some kind soul send him a copy? He is Dr Robert Lancashire in the Department of Chemistry at the University of the West Indies (Mona). His email address is rjlanc@uwimona.edu.jm Thank you. Andrew Booth From owner-structural-nmr@net.bio.net Wed Feb 07 22:00:00 1996 Newsgroups: bionet.structural-nmr Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!usenet.eel.ufl.edu!warwick!bradford.ac.uk!leeds.ac.uk!news From: a.g.booth@leeds.ac.uk (Andrew Booth) Subject: JCAMP messages - Thank you Message-ID: <1996Feb8.094016.5285@leeds.ac.uk> NNTP-Posting-Host: bmb_pc112.leeds.ac.uk Date: Thu, 8 Feb 1996 09:40:16 +0000 (GMT) X-Newsreader: News Xpress Version 1.0 Beta #3 Lines: 4 Just a message to relay Bob Lancashire's thanks to everyone who posted him a copy of the JCAMP article. Andrew Booth From owner-structural-nmr@net.bio.net Wed Feb 07 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.sprintlink.net!shore4.intercom.net!usenet From: raydavis@shore.intercom.net Newsgroups: bionet.structural-nmr Subject: Varian FT80 FT80A or CFT20 Disk Conversions Date: 8 Feb 1996 06:03:27 GMT Organization: ICNet, Salisbury, MD Lines: 8 Message-ID: <4fc3nf$psv@shore4.intercom.net> Reply-To: raydavis@shore.intercom.net NNTP-Posting-Host: modem208.intercom.net X-Newsreader: AIR News 3.X (SPRY, Inc.) We have a package which will allow to the replacing of the 8" floppies used by the Varian FT80, FT80A, and CFT20 NMRs with an IBM compatible PC. We also can reduce the 8" floppies to MS-DOS compatible files. The DOS compatible files are supplied with a file extractor and viewer. Current technology replacement processors are also available for the systems. These processors are single board items which plug directly into the existing I/O chassis. They include 32k of ROM in which operational software can be stored, eliminating the tedious booting procedure and a PC interface. From owner-structural-nmr@net.bio.net Wed Feb 07 22:00:00 1996 Path: biosci!ns1.faseb.org!lamarck.sura.net!newsfeed.internetmci.com!usenet.eel.ufl.edu!warwick!leicester!usenet From: B S Hickman Newsgroups: bionet.structural-nmr,sci.techniques.mag-resonance Subject: Re: convert brucker ADVANCE's data to felix Date: Thu, 08 Feb 1996 19:36:20 +0000 Organization: Leicester univesity Lines: 26 Message-ID: <311A50B4.1BF0@le.ac.uk> References: NNTP-Posting-Host: sun3.chem.le.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0b6a (X11; I; SunOS 5.4 sun4m) Xref: biosci bionet.structural-nmr:1093 sci.techniques.mag-resonance:1475 Chyh-chong Chuang wrote: > > Dear Netters: > > I am curious whether thare is any program can convert brucker's > ADVANCE data (DMX, DRX) to felix format for off-line processing? > > Any comment will be appreciated. Thanks all > > ccchuang > If you are using the latest version of felix (felix95) a facility for this conversion is included in the programme but I don't think the older versions (e.g. felix 2.3) include one. It might be worth asking biosym if they can help if you use the older versions of felix. The other option is to upgrade. Also have you tried asking in the sci.techniques.mag-resonance group I've added it the list if you haven't -- Benjamin Hickman Chemistry Dept. NMR Spectroscopy & Imaging University of Leicester Leicester LE1 7RH Elm: BSH2@le.ac.uk U.K. From owner-structural-nmr@net.bio.net Wed Feb 07 22:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!infobiogen.fr!jussieu.fr!univ-lyon1.fr!dsi.unimi.it!galileo.polito.it!usenet From: Mauro Fasano Newsgroups: bionet.structural-nmr Subject: New NMR Courses Date: 8 Feb 1996 17:46:15 GMT Organization: University of Torino, NMR Laboratory Lines: 8 Distribution: world Message-ID: <4fdct7$88k@galileo.polito.it> NNTP-Posting-Host: chpc07.ch.unito.it X-Newsreader: Dear NMR Spectroscopists, the European Initiative for Training in NMR is presenting now the program of activities in 1996. Interested people can find the programs of three new courses at the URL http://chpc07.ch.unito.it/announce.htm Mauro From owner-structural-nmr@net.bio.net Thu Feb 08 22:00:00 1996 Path: biosci!LAPLACE.CSB.YALE.EDU!abonvin From: abonvin@LAPLACE.CSB.YALE.EDU ("Alexandre Bonvin") Newsgroups: bionet.structural-nmr Subject: Re: quantitative analysis of populations Date: 9 Feb 1996 11:15:44 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 49 Sender: daemon@net.bio.net Distribution: world Message-ID: <9602091913.AA17529@laplace.csb.yale.edu> NNTP-Posting-Host: net.bio.net Ramkrishna, > dear netters, > i would like to know the latest state of art of the quatitative analysis > of populations of conformers sampled by linear peptides in aq.solution, > based on the information obtianed by the observed NOEs. any references > in this context will be greatly appreciated. > Thanks in advance > This is pretty difficult problem. I have been working on this and an communication has been accepted for publication in the Journal of Biomolecular NMR on this subject. In short our finding (for proteins) are the following: it is very difficult if possible to estimate relative populations of multi-conformer structures from NOE data only. We used cross-validation to estimate populations of multi-conformer structures and found that you can basically refine any population ratio to similar quality of the fit! You will need other information like J-couplings and/or chemical shifts. You can get some information on side-chain dynamics and conformation from long range homonuclear and heteronuclear scalar couplings (Bax et al. Methods in Enzymol. 239, 79 (1994)) Some work has also been done for small molecules and again it was not really clear that you can obtain accurate information from NOEs only. It seems easier to identify multiple conformations than to quantify them. Here are a couple of references you might want to check: - J. Am. Chem. Soc. 94, 2561 (1972) - J. Am. Chem. Soc. 107, 5435 (1985) - J. Biomol. NMR 1, 3 (1991) - J. Am. Chem. Soc. 116, 1042 (1994) - J. Mol. Biol. 250, 80 (1995) - J. Biomol. NMR 6, 163 (1995) - J. Magn. Reson. B 109, 44 (1995) Cheers, Alexandre ========================================================================== | Alexandre Bonvin PhD | Phone: (203) 432-5066 | | Mol. Biophys. & Biochemistry | Fax: (203) 432-3923 | | Yale University | Email: abonvin@laplace.csb.yale.edu | | New Haven CT 06520-8114, USA | http://xplor.csb.yale.edu | ========================================================================== From owner-structural-nmr@net.bio.net Thu Feb 08 22:00:00 1996 Newsgroups: bionet.structural-nmr Path: biosci!agate!howland.reston.ans.net!newsfeed.internetmci.com!in1.uu.net!sangam!iitb!powai!n1403305 From: n1403305@powai.cc.iitb.ernet.in (ramakrishna) Subject: quantitative analysis of populations Message-ID: Date: Fri, 9 Feb 1996 16:04:01 GMT Organization: Computer Centre, Indian Institute of Technology, Bombay X-Newsreader: TIN [version 1.2 PL2] Lines: 16 dear netters, i would like to know the latest state of art of the quatitative analysis of populations of conformers sampled by linear peptides in aq.solution, based on the information obtianed by the observed NOEs. any references in this context will be greatly appreciated. Thanks in advance Ramkrishna ______________________________________________________________________ Ramkrishna Molecular Biophysics lab Department of Chemistry Indian Institute of Technology Bombay 400 076 INDIA email: rama@ether.chem.iitb.ernet.in _____________________________________________________________________ From owner-structural-nmr@net.bio.net Thu Feb 08 22:00:00 1996 Path: biosci!lhc.nlm.nih.gov!crick.sura.net!lamarck.sura.net!newsfeed.internetmci.com!howland.reston.ans.net!nntp.coast.net!torn!nott!nrcnet0.nrc.ca!BRI.NRC.CA!Feng.Ni From: Feng.Ni@BRI.NRC.CA (Feng Ni) Newsgroups: bionet.structural-nmr Subject: POSITIONS IN PROTEIN NMR - SECOND ANOUNCEMENT Date: 9 Feb 1996 18:57:03 GMT Organization: Institut de recherche en biotechnologie, Montréal Lines: 39 Distribution: world Message-ID: <4fg5dv$77f@nrcnet0.nrc.ca> NNTP-Posting-Host: indy.bri.nrc.ca POSTDOCTORAL AND RESEARCHER POSITIONS IN BIOPHYSICAL AND PROTEIN NMR SPECTROSCOPY Postdoctoral and researcher positions are available in the NMR laboratory of the Biotechnology Research Institute (BRI). Our research centers on proteins in blood coagulation, protease regulation and ligand-receptor interactions. Candidates must have a recent Ph.D. degree in chemistry, biochemistry or a related field and have demonstrated abilities (e.g. through publications) in carrying out creative research. Knowledge of high-resolution NMR spectroscopy is desirable and experience in protein/peptide purification is an important asset. Through their work at BRI, postdoctoral fellows obtain experience in the use of NMR spectroscopy to determine the structures and the biophysical properties of proteins and protein-protein complexes. Postdoctoral fellows are paid an annual salary of $23,000-$28,000 according to the MRC guidelines. Exceptional candidates may be promoted to senior research positions offerred by the National Research Council of Canada. Our institute is equipped with one Bruker AMX-500 NMR spectrometer and shares a second with members of the Montreal Joint Centre for Structural Biology. Funds are secured for a state-of-the-art higher field NMR instrument to be installed within the coming months. Qualified individuals are invited to forward your resume to: Feng Ni, Ph.D. Head of Biomolecular NMR Biotechnology Research Institute 6100 Royalmount Avenue Montreal, Quebec, H4P 2R2 Canada phone: (514)-496-6729 fax: (514)-496-5143 e_mail: fengni@bri.nrc.ca Applications will be accepted until the positions are filled. We thank all applicants for their interests, however, only those being considered will be contacted. From owner-structural-nmr@net.bio.net Fri Feb 09 22:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!news-e1a.megaweb.com!newstf01.news.aol.com!newsbf02.news.aol.com!not-for-mail From: nalorac@aol.com (Nalorac) Newsgroups: bionet.structural-nmr Subject: Nalorac NMR Symposium Date: 9 Feb 1996 19:52:29 -0500 Organization: America Online, Inc. (1-800-827-6364) Lines: 53 Sender: root@newsbf02.news.aol.com Message-ID: <4fgq8d$nv5@newsbf02.news.aol.com> Reply-To: nalorac@aol.com (Nalorac) NNTP-Posting-Host: newsbf02.mail.aol.com You are invited to attend a special symposium prior to ENC ADVANCES IN NMR APPLICATIONS S Y M P O S I U M Featuring the Latest Developments in Experimental Techniques at The Inn at Spanish Bay Pebble Beach, California Sunday, March 17, 1:30 to 5:00 p.m. AGENDA INCLUDES: Resolving Ambiguities in NOESY Data for Larger Proteins. David P. Cistola, Michael E. Hodsdon, and Jay W. Ponder, Washington University School of Medicine Practical Aspects of Diffusional Filters in Protein NMR. J. Prestegard, M. Andrec, J. Lim-Weaver, and E. Sayers, Yale University Structures of Protein-Nucleic Acid Complexes. Angela Gronenborn, National Institute of Health Exploring the Submicro World. Ron Crouch and Toby Zens, Nalorac Corporation Applications of 1H/13C/X Triple Resonance NMR In Polymer Science. Peter Rinaldi, University of Akron Long-Range Gradient Enhanced 1H/15N Correlation Spectroscopy at Natural Abundance. Gary Martin, Pharmacia & Upjohn, Inc.; Ron Crouch, Nalorac Corporation Combinatorial Chemistry - Fad or Future - A Personal Perspective. Michael Shapiro, Sandoz Research Laboratories Helium-3 NMR Spectroscopy - Inside and Outside of Molecules. M. Saunders, H.A. Jimenez-Vasquez, and R.J. Cross, Yale University This NMR Symposium will be held Sunday afternoon prior to the start of ENC. The Symposium site is located approximately one mile from the Asilomar Conference Center, site of the 1996 ENC. Please RSVP by contacting our ENC Coordinator via our E-Mail address: sales@nalorac.com. N A L O R A C 841A Arnold Drive, Martinez, CA 94553 Phone: (510) 229-3501 FAX: (510) 229-1651 E-mail: sales@nalorac.com From owner-structural-nmr@net.bio.net Sun Feb 11 22:00:00 1996 Newsgroups: bionet.software.x-plor,bionet.structural-nmr Path: biosci!daresbury!bioftp.unibas.ch!infobiogen.fr!jussieu.fr!oleane!nntp.coast.net!news.sprintlink.net!rockyd!notes From: Ajay Royyuru Subject: [Q] Engh+Huber like force field for NMR refinement? X-Nntp-Posting-Host: rockyj.rockefeller.edu Content-Type: text/plain; charset=us-ascii Message-ID: <311F91F6.41C67EA6@mskcc.org> Sender: notes@rockyd.rockefeller.edu (News Administrator) Content-Transfer-Encoding: 7bit Organization: Sloan-Kettering Institute, MSKCC, New York Mime-Version: 1.0 Date: Mon, 12 Feb 1996 19:16:06 GMT X-Mailer: Mozilla 2.0b5 (X11; I; SunOS 4.1.3_U1 sun4m) Lines: 17 Xref: biosci bionet.software.x-plor:333 bionet.structural-nmr:1100 Hi X-plor-ers, Is there/will there be an effort to construct an "all atom" force field on the lines of Engh+Huber (Acta Cryst. A47, 392-400, 1991) for proteins, or Parkinson et al. (Acta Cryst. D52, 57-64, 1996) for nucleic acid structure refinement from NMR data ? Many thanks in anticipation. +-----------------------------------------------------------------------------+ | Ajay Kumar Royyuru, PhD | Tel +1 (212) 639 7225 | | Memorial Sloan-Kettering Cancer Center | Fax +1 (212) 717 3066 | | Box 557 | | | 1275 York Avenue | ajay@sbnmr1.mskcc.org | | New York NY 10021 | | +-----------------------------------------------------------------------------+ From owner-structural-nmr@net.bio.net Sun Feb 11 22:00:00 1996 Newsgroups: bionet.molec-model,bionet.software,bionet.structural-nmr,bionet.xtallography,bionet.software.source,bionet.molbio.proteins Path: biosci!daresbury!bioftp.unibas.ch!infobiogen.fr!jussieu.fr!oleane!nntp.coast.net!news.sprintlink.net!rockyd!notes From: Andrej Sali Subject: ANNOUNCEMENT: MODELLER-3 AVAILABLE (HOMOLOGY PROTEIN MODELING) X-Nntp-Posting-Host: guitar.rockefeller.edu Content-Type: text/plain; charset=us-ascii Message-ID: Sender: notes@rockyd.rockefeller.edu (News Administrator) Content-Transfer-Encoding: 7bit Organization: Rockefeller University Mime-Version: 1.0 Date: Mon, 12 Feb 1996 18:41:34 GMT X-Mailer: Mozilla 1.1N (X11; I; IRIX 5.3 IP22) X-Url: news:bionet.molec-model Lines: 89 Xref: biosci bionet.molec-model:814 bionet.software:14699 bionet.structural-nmr:1099 bionet.xtallography:2379 bionet.molbio.proteins:7041 ANNOUNCEMENT: A NEW VERSION OF MODELLER, A PROGRAM FOR COMPARATIVE PROTEIN STRUCTURE MODELING, IS RELEASED. ------------------------------------------------------------------------------- MODELLER PROTEIN MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS MODELLER 3, December 31, 1995 Copyright(c) 1989-1995 Andrej Sali All Rights Reserved Written by Andrej Sali Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Andrej Sali, Box 270, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA. Tel: +1-212-327-7550. Fax: +1-212-327-7540. E-mail: sali@rockvax.rockefeller.edu. ** DESCRIPTION: MODELLER is most frequently used for homology or comparative modeling of protein three-dimensional structure: the user provides an alignment of a sequence to be modeled with known related structures and MODELLER will automatically calculate a full-atom model. More generally, MODELLER models protein 3D structure by satisfaction of spatial restraints (A. Sali & T.L. Blundell. J.Mol.Biol. 234, 779-815, 1993). In principle, the restraints can be derived from a number of different sources. These include homologous structures (comparative modeling), NMR experiments (NMR refinement), rules of secondary structure packing (combinatorial modeling), cross-linking experiments, fluorescence spectroscopy, image reconstruction in electron microscopy, site-directed mutagenesis, intuition, residue-residue and atom-atom potentials of mean force, etc. The output of MODELLER is a 3D structure of a protein that satisfies these restraints as well as possible. The optimization is carried out by the variable target function procedure employing methods of conjugate gradients and molecular dynamics with simulated annealing. MODELLER can also do several other tasks, including multiple comparison of protein sequences and/or structures, clustering, and searching of sequence databases. The program is described in a 120-page manual. MODELLER is written in Fortran and is meant to run on a UNIX system. ** DISTRIBUTION: MODELLER is available free of charge to academic non-profit institutions. First, please use the anonymous ftp account on guitar.rockefeller.edu (IP 129.85.13.198) to copy at least the following files from the pub/modeller directory to your computer: the license form (PostScript file academic-license.ps), the distribution file that contains the data files necessary to run MODELLER (modeller3-data.tar.Z), and an executable for each machine type that you need (described in file INSTALLATION). Next, please sign and mail (or fax) the license form to Andrej Sali. You will then receive the key (MODELLER_KEY) that has to be assigned to the environment variable KEY_MODELLER3 in your login script (.cshrc). See file INSTALLATION for installation instructions. There is also a MODELLER home page on World Wide Web at URL http://guitar.rockefeller.edu that can be used to ftp the program and view the manual. A graphical interface to MODELLER is available as part of QUANTA and INSIGHT, interactive molecular modeling programs with many tools for protein modeling and structural analysis. QUANTA and INSIGHT facilitate preparation of input files for MODELLER (eg, alignment file) as well as an analysis of results (eg, an evaluation of the models). If you are interested in QUANTA or INSIGHT, please contact Ms. Brenda Pfeiffer, BIOSYM / Molecular Simulations Inc., 9685 Scranton Road, San Diego, CA 92121-3752, tel: +1-619-546-5319, fax: +1-619-458-0136, email: blp@biosym.com. ** CONTENTS: src\ sources or executables for MODELLER; modlib\ libraries and data files for the programs; scripts\ script files used to compile and use MODELLER; doc\ MODELLER documentation; Makefile Makefile for compiling/installing MODELLER modules; modeller3.README this file; INSTALLATION how to install MODELLER; Install compilation and installation script relying on Makefile; tests\ tests and examples; From owner-structural-nmr@net.bio.net Mon Feb 12 22:00:00 1996 Path: biosci!ns1.faseb.org!lamarck.sura.net!newsfeed.internetmci.com!uwm.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!rana!wombats From: wombats@rana (Mark E. Anderson) Newsgroups: bionet.structural-nmr,sci.techniques.mag-resonance Subject: Re: convert brucker ADVANCE's data to felix Followup-To: bionet.structural-nmr,sci.techniques.mag-resonance Date: 13 Feb 1996 19:09:46 GMT Organization: University of Wisconsin, Madison Lines: 9 Message-ID: <4fqnlq$2fsi@news.doit.wisc.edu> References: <311A50B4.1BF0@le.ac.uk> NNTP-Posting-Host: rana.nmrfam.wisc.edu X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.structural-nmr:1102 sci.techniques.mag-resonance:1492 as soon as if fix the links there is a program we've been using for converting the uxnmr/xwinnmr/avance files to felix available on our website. -- mark anderson * Incorrigible punster. * wombats@nmrfam.wisc.edu * Please do not incorrige. * http://www.nmrfam.wisc.edu From owner-structural-nmr@net.bio.net Mon Feb 12 22:00:00 1996 Path: biosci!biophy.jussieu.fr!michel From: michel@biophy.jussieu.fr (Michel SEIGNEURET) Newsgroups: bionet.structural-nmr Subject: diagonal suppression software Date: 13 Feb 1996 03:46:26 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <199602131156.MAA06483@mood.biophy.jussieu.fr> NNTP-Posting-Host: net.bio.net Dear Collegues, A diagonal suppression scheme for COSY spectra was described a few years ago by Friedrichs et al. (JMR 95, 178-183 1991) and Pelczer (JACS 113,3211-3212 1991). It involves performing a linear phase correction on each experiment in order to bring the diagonal signal to zero frequency and then removing the diagonal by convolution. Up to now, I have been too dumb to implement anything that works. Would someone have written down such a scheme (e.g. as a Felix or NMRPipe macro or as a separate fortran or c program) and be so kind as to mail me a copy ? Thanks in advance. With best regards. Michel Seigneuret Universite Paris 7 Lab. de Biophysique Cellulaire et RMN France From owner-structural-nmr@net.bio.net Tue Feb 13 22:00:00 1996 Path: biosci!UBACLU.UNIBAS.CH!WILTSCHECK From: WILTSCHECK@UBACLU.UNIBAS.CH (Ronald Wiltscheck) Newsgroups: bionet.structural-nmr Subject: conversion of spectra from VNMR to FELIX Date: 14 Feb 1996 00:11:44 -0800 Organization: University of Basel, Switzerland Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: <01I1755BQD388ZJGH1@ubaclu.unibas.ch> NNTP-Posting-Host: net.bio.net Dear netter, does anyone of you know how to trnasfer already processed VNMR-spectra ('/datdir/data' file) into a Felix *.mat format? I'm greatful for any kind of suggestions, ============================================================================= Ronald Wiltscheck e-mail: wiltscheck@ubaclu.unibas.ch University of Basel phone: ++41-61/267-2091 Biozentrum/Structural Biology fax: ++41-61/267-2190 CH-4053 Basel/Switzerland home: ++41-61/361-8605 ============================================================================= From owner-structural-nmr@net.bio.net Tue Feb 13 22:00:00 1996 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: diagonal suppression software Date: 13 Feb 1996 17:58:19 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 55 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <199602131156.MAA06483@mood.biophy.jussieu.fr> NNTP-Posting-Host: net.bio.net Dear Michel, It is my pleasure to see that diagonal supression through data processing (instead of expensive experimental approaches) is making its way to real life applications. In fact, major data processing software packages have neglected this opportunity (so far), although you may find something in Aurelia now, and I am sure macros will be available both for Felix and NMRPipe. Mark Roggenbuck wrote a nice standalone routine which does the job in cooperation with NMRZ (from the late NMRi, now taken over by Tripos), which is the fastest and most efficient routine at the time to my best knowledge. Unfortunately, NMRZ is not available any more, although you may find some users who have it still. Frank Delaglio, the engine behind NMRPipe knows NMRi software more than I do (he used to be the main developer of it back in time...), and Luciano Mueller's group has developed the routine which works in time domain for the spectral rearrangement in Felix -- so you have a good chance to get a working routine. My original, so called Simple-COSY presented the alternative do to this in the frequency domain in combination with Hilbert transform for rephasing, but the time domain version is better in general. Some new, enhanced applications of the same idea we present with Brian Carter in our review (Chapter for Protocols in Protein NMR, in press) and in a "to be submitted" (very soon) publication. Good luck, all the best, Istvan wwww,wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww Istvan Pelczer, Ph.D. ipelczer@chemvax.princeton.edu Senior NMR Spectroscopist Princeton University Department of Chemistry ph# (609) 258 2342 Frick Laboratory fax# (609) 258 6746 Washington Road Princeton, NJ 08544 On 13 Feb 1996, Michel SEIGNEURET wrote: > > Dear Collegues, > A diagonal suppression scheme for COSY spectra was described a few > years ago by Friedrichs et al. (JMR 95, 178-183 1991) and Pelczer > (JACS 113,3211-3212 1991). It involves performing a linear phase > correction on each experiment in order to bring the diagonal signal > to zero frequency and then removing the diagonal by convolution. Up > to now, I have been too dumb to implement anything that works. Would > someone have written down such a scheme (e.g. as a Felix or NMRPipe > macro or as a separate fortran or c program) and be so kind as to > mail me a copy ? Thanks in advance. > With best regards. > Michel Seigneuret > Universite Paris 7 > Lab. de Biophysique Cellulaire et RMN > France > From owner-structural-nmr@net.bio.net Tue Feb 13 22:00:00 1996 Path: biosci!fmp.fta-berlin.de!schultz From: schultz@fmp.fta-berlin.de (Johan Schultz) Newsgroups: bionet.structural-nmr Subject: pKa value determination of Histidines Date: 14 Feb 1996 09:06:12 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Netters, I would like to know the pKa value of a histidine (actually there is only one) in my 15N-labelled, not fully assigned protein. How do I determine this pKa value easiest? I imagine that recording 1H-15N HSQC:s at a number of different pH-values and determining the volume of the Histidine imidazole ring "epsilon NH" peak would be a good method. If so, does anyone know what a typical (or random coil) 15N chemical shift for this nitrogen would be? All suggestions are highly appreciated! Thanks in advance Johan Schultz From owner-structural-nmr@net.bio.net Tue Feb 13 22:00:00 1996 Path: biosci!fmp.fta-berlin.de!peter From: peter@fmp.fta-berlin.de (Peter Schmieder) Newsgroups: bionet.structural-nmr Subject: (none) Date: 14 Feb 1996 04:24:06 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: Reply-To: schmieder@fmp.fta-berlin.de NNTP-Posting-Host: net.bio.net subscribe ################################################################## # # # ******* ** ** ******* Dr. Peter Schmieder # # * * * * * * * Forschungsinstitut fuer # # * * * * * * * molekulare Pharmakologie # # ***** * * * ******* Alfred-Kowalke-Str. 4 # # * * * * D-10315 Berlin # # * * * * Tel. (030) 5163-214 # # * * * * Fax (030) 5163-235 od. 512 8014 # # E.Mail peter@fmp.fta-berlin.de # # # # "Il faut imaginer Sisyphe heureux" # # A. Camus # # # ################################################################## From owner-structural-nmr@net.bio.net Wed Feb 14 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!usenet.eel.ufl.edu!gatech!swrinde!news.uh.edu!news.uth.tmc.edu!bmb155.med.uth.tmc.edu!user From: tliang@utmmg.med.uth.tmc.edu (T. Chyau Liang) Newsgroups: bionet.structural-nmr Subject: Re: pKa value determination of Histidines Date: 14 Feb 1996 20:22:47 GMT Organization: UT Medical School at Houston Lines: 34 Distribution: world Message-ID: References: NNTP-Posting-Host: bmb155.med.uth.tmc.edu Mime-Version: 1.0 Content-Type: text/plain;charset=US-ASCII Content-Transfer-Encoding: 7bit You may be albe to do this with simple 1D spin-echo experiments without isotope enrichment. The hydrogen attached to ring C-2 of His appears between 8.5-7.5 ppm depending on pH. In this region, you also have signals from aromatic and amide hydrogens. Aromatic signals will not titrate in the pH range that you are interested in (pH 6-8). The amide signals tend to have broader lines (shorter T2) and can be suppressed by spin-echo sequence. We have successfully monitored the titration of His in unlabeled chymotrypsin with this method (Bioorganic Chem. 22, 268-275). Good luck. Chyau Liang ---------------------- In article , schultz@fmp.fta-berlin.de (Johan Schultz) wrote: > Dear Netters, > > I would like to know the pKa value of a histidine (actually there is only > one) in my 15N-labelled, not fully assigned protein. How do I determine > this pKa value easiest? I imagine that recording 1H-15N HSQC:s at a number > of different pH-values and determining the volume of the Histidine > imidazole ring "epsilon NH" peak would be a good method. If so, does > anyone know what a typical (or random coil) 15N chemical shift for this > nitrogen would be? > > All suggestions are highly appreciated! > > Thanks in advance > > Johan Schultz From owner-structural-nmr@net.bio.net Wed Feb 14 22:00:00 1996 Path: biosci!agate!howland.reston.ans.net!gatech!swrinde!newsfeed.internetmci.com!uwm.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!news From: xia@nmrfam.wisc.edu (Bin Xia) Newsgroups: bionet.structural-nmr Subject: Re: pKa value determination of Histidines Date: 15 Feb 1996 05:04:41 GMT Organization: UW-Madison Lines: 16 Message-ID: <4fuet9$1lio@news.doit.wisc.edu> References: NNTP-Posting-Host: f183-056.net.wisc.edu X-Newsreader: WinVN 0.92.6+ Hi, You can monitor the chemical shift ( either H or N) change of the histidine. Plot the chemical shift vs. pH, and you can get the pKa from it. You can do HMBC expt to observe multi-bond H-N coupling peaks of histidine imidazole ring. It has a very unique pattern. You may read my paper on Biochemistry 34, 180-187 (1995). Good luck! Bin In article , schultz@fmp.fta-berlin.de (Johan Schultz) says: > >I would like to know the pKa value of a histidine (actually there is only ... From owner-structural-nmr@net.bio.net Wed Feb 14 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!uwm.edu!msunews!netnews.upenn.edu!dsinc!news.icubed.com!babe.lglobal.com!grumpy.insinc.net!magic-toronto!avernus15.magic.ca!user From: auriel@astral.magic.ca (Alex Singer) Newsgroups: bionet.structural-nmr Subject: Re: pKa value determination of Histidines Date: 15 Feb 1996 16:54:47 GMT Organization: Private Lines: 31 Distribution: world Message-ID: References: NNTP-Posting-Host: avernus15.magic.ca In article , schultz@fmp.fta-berlin.de (Johan Schultz) wrote: > Dear Netters, > > I would like to know the pKa value of a histidine (actually there is only > one) in my 15N-labelled, not fully assigned protein. How do I determine > this pKa value easiest? I've been recently involved in determination of His pKa's of an SH2/phospho- peptide complex, and am presently writing up the paper. As a how to guide for His titrations, I strongly recommend a paper from Dennis Torchia's group (Pelton et al., 1993, Protein Science 2: 543). The technique as Bin Xia suggested previously is an 15N/1H HMBC -- 2- or 3-bond correlation, not a 1-bond correlation as the 15N-attached protons on the imidizole ring are rarely observed due to rapid exchange with water. > If so, does > anyone know what a typical (or random coil) 15N chemical shift for this > nitrogen would be? As described in a figure in the Pelton et al paper I mentioned, the 15N chemical shifts for the histidine imidazole are quite unusual, 170-180 ppm if protonated, 240-250 ppm if unprotonated. As you proceed through the titration, intermediate values will appear for one of these 15N nucleii, and you can fit these values as a function of pH to a sigmoidal curve. Because of the large chemical shift range being covered (70 ppm), you should be able to determine a pKa value to +/- .02 pH units. E-mail me if you have any more questions or problems Alex U. Singer From owner-structural-nmr@net.bio.net Wed Feb 14 22:00:00 1996 Path: biosci!B.PSC.EDU!HECKATHO From: HECKATHO@B.PSC.EDU Newsgroups: bionet.structural-nmr Subject: Pittsburgh Supercomputing Center 1996 Biomed Workshops Date: 15 Feb 1996 15:12:21 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 137 Sender: daemon@net.bio.net Distribution: world Message-ID: <960215181054.20402d62@B.PSC.EDU> NNTP-Posting-Host: net.bio.net ************************************************************************** PITTSBURGH SUPERCOMPUTING CENTER BIOMEDICAL SUPERCOMPUTING INITIATIVE Biomedical Workshops offered by the Pittsburgh Supercomputing Center typically consist of theoretical lectures taught by leaders in the respective scientific discipline, and extensive hands-on computer sessions. During the computer sessions, participants are able to work on the examples provided or on their own experimental data. Attendance is limited to 20 participants to allow one-on-one instruction and encourage scientific interactions and discussions. Application deadlines are six weeks prior to the workshop. Researchers nationwide are invited to apply. For additional information, please refer to http://www.psc.edu/biomed/workshops.html CONTACT INFORMATION: Nancy Blankenstein, Biomedical Program Assistant, (412)268-4960, blankens@psc.edu TO APPLY FOR A WORKSHOP, please fill out the application form. The following four workshops will be offered during 1996: SUPERCOMPUTING TECHNIQUES FOR BIOMEDICAL RESEARCHERS; May 5-9. The purpose of this workshop is to introduce attendees to the concepts of supercomputing. The main goal is to provide researchers with a firm basis from which to analyze their applications for implementation in a supercomputing environment. After a brief introduction to PSC's supercomputing environment, including the architectures of the CRAY C90 and T3E, various vector and massively parallel programming models will be discussed. Message passing, performance monitoring, optimization techniques, and heterogeneous supercomputing will be introduced with emphasis on practical considerations. Specific real-world biomedical supercomputing applications will be presented to illustrate these concepts. Finally, a panel discussion will attempt to address researchers' individual application questions. NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS; June 9-14. Emphasis will be on alignment of and pattern extraction from multiple sequences. Topics to be discussed include Comparing and aligning sequences Identifying informative patterns in a set of sequences Using extracted informative patterns to identify related sequences. Leaders are Dr. Gary Churchill, Cornell University; Dr. Michael Gribskov, San Diego Supercomputing Center and Dr. Hugh B. Nicholas, Jr., Pittsburgh Supercomputing Center. METHODS AND APPLICATIONS OF MOLECULAR MECHANICS AND DYNAMICS TO MOLECULES OF BIOLOGICAL INTEREST; August 7-10. Instructors include Dr. David Case, the Scripps Research Institute, Thomas Cheatham III, UCSF; Prof. Peter A. Kollman, UCSF, Dr. David A. Pearlman, Vertex Pharmaceuticals; and Bill Ross, UCSF. General aspects of molecular mechanics and dynamics theory and software will be discussed. The program AMBER will be utilized extensively in demonstrations. ADVANCED NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS; Dates TBA; subject to funding availability. Open to researchers who have previously attended one of the PSC's annual "Nucleic Acid and Protein Sequence Analysis" workshops or who have appreciable experience with computerized sequence analysis. The workshop will build on previous experience to teach techniques for analyzing families and superfamilies of genes and proteins. Please fill out the following application form. APPLICATION FORM - Biomedical Workshop Application Deadline: six weeks prior to each workshop. PITTSBURGH SUPERCOMPUTING CENTER BIOMEDICAL SUPERCOMPUTING INITIATIVE WORKSHOP APPLICATION FORM Workshop I am interested in attending:_____________________________________ Name: ________________________________________________________________ Affiliation: ________________________________________________________________ Address: ________________________________________________________________ (Business) ________________________________________________________________ ________________________________________________________________ (Home) ________________________________________________________________ Telephone: ____________________________ ______________________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship:___________________ Electronic Mail Address:_______________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) Please indicate specifically any special housing, transportation or dietary arrangements you will need: ___________________________________________________ How did you learn about this workshop:_________________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, your current research, and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vitae. Graduate students must have a letter of recommendation from a faculty member. Please return all application materials six weeks before the workshop you are applying for to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From owner-structural-nmr@net.bio.net Thu Feb 15 22:00:00 1996 Path: biosci!sfu.ca!nglover From: nglover@sfu.ca (Nicholas Ronald Glover) Newsgroups: bionet.structural-nmr Subject: (none) Date: 15 Feb 1996 16:22:07 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: <199602160019.AAA14006@fraser.sfu.ca> NNTP-Posting-Host: net.bio.net Nick Glover Dept. of Chemistry Simon Fraser University Vancouver Canada nglover@sfu.ca From owner-structural-nmr@net.bio.net Thu Feb 15 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!gatech!newsfeed.pitt.edu!bb3.andrew.cmu.edu!andrew.cmu.edu!mm6n+ From: Marcella Madrid Newsgroups: bionet.structural-nmr Subject: Pittsburgh Supercomputer Center 1996 Biomedical Workshops Date: Fri, 16 Feb 1996 17:19:14 -0500 Organization: Pittsburgh Supercomputing Center, Carnegie Mellon, Pittsburgh, PA Lines: 127 Message-ID: <8l9E=WS00YUr8YV8dG@andrew.cmu.edu> NNTP-Posting-Host: po7.andrew.cmu.edu ************************************************************************** PITTSBURGH SUPERCOMPUTING CENTER BIOMEDICAL SUPERCOMPUTING INITIATIVE Biomedical Workshops offered by the Pittsburgh Supercomputing Center typically consist of theoretical lectures taught by leaders in the respective scientific discipline, and extensive hands-on computer sessions. During the computer sessions, participants are able to work on the examples provided or on their own experimental data. Attendance is limited to 20 participants to allow one-on-one instruction and encourage scientific interactions and discussions. Application deadlines are six weeks prior to the workshop. Researchers nationwide are invited to apply. For additional information, please refer to http://www.psc.edu/biomed/workshops.html CONTACT INFORMATION: Nancy Blankenstein, Biomedical Program Assistant, (412)268-4960, blankens@psc.edu TO APPLY FOR A WORKSHOP, please fill out the application form. The following four workshops will be offered during 1996: SUPERCOMPUTING TECHNIQUES FOR BIOMEDICAL RESEARCHERS; May 5-9. The purpose of this workshop is to introduce attendees to the concepts of supercomputing. The main goal is to provide researchers with a firm basis from which to analyze their applications for implementation in a supercomputing environment. After a brief introduction to PSC's supercomputing environment, including the architectures of the CRAY C90 and T3E, various vector and massively parallel programming models will be discussed. Message passing, performance monitoring, optimization techniques, and heterogeneous supercomputing will be introduced with emphasis on practical considerations. Specific real-world biomedical supercomputing applications will be presented to illustrate these concepts. Finally, a panel discussion will attempt to address researchers' individual application questions. NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS; June 9-14. Emphasis will be on alignment of and pattern extraction from multiple sequences. Topics to be discussed include Comparing and aligning sequences Identifying informative patterns in a set of sequences Using extracted informative patterns to identify related sequences. Leaders are Dr. Gary Churchill, Cornell University; Dr. Michael Gribskov, San Diego Supercomputing Center and Dr. Hugh B. Nicholas, Jr., Pittsburgh Supercomputing Center. METHODS AND APPLICATIONS OF MOLECULAR MECHANICS AND DYNAMICS TO MOLECULES OF BIOLOGICAL INTEREST; August 7-10. Instructors include Dr. David Case, the Scripps Research Institute, Thomas Cheatham III, UCSF; Prof. Peter A. Kollman, UCSF, Dr. David A. Pearlman, Vertex Pharmaceuticals; and Bill Ross, UCSF. General aspects of molecular mechanics and dynamics theory and software will be discussed. The program AMBER will be utilized extensively in demonstrations. ADVANCED NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS; Dates TBA; subject to funding availability. Open to researchers who have previously attended one of the PSC's annual "Nucleic Acid and Protein Sequence Analysis" workshops or who have appreciable experience with computerized sequence analysis. The workshop will build on previous experience to teach techniques for analyzing families and superfamilies of genes and proteins. Please fill out the following application form. APPLICATION FORM - Biomedical Workshop Application Deadline: six weeks prior to each workshop. PITTSBURGH SUPERCOMPUTING CENTER BIOMEDICAL SUPERCOMPUTING INITIATIVE WORKSHOP APPLICATION FORM Workshop I am interested in attending:_____________________________________ Name: ________________________________________________________________ Affiliation: ________________________________________________________________ Address: ________________________________________________________________ (Business) ________________________________________________________________ ________________________________________________________________ (Home) ________________________________________________________________ Telephone: ____________________________ ______________________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship:___________________ Electronic Mail Address:_______________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) Please indicate specifically any special housing, transportation or dietary arrangements you will need: ___________________________________________________ How did you learn about this workshop:_________________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, your current research, and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vitae. Graduate students must have a letter of recommendation from a faculty member. Please return all application materials six weeks before the workshop you are applying for to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From owner-structural-nmr@net.bio.net Fri Feb 16 22:00:00 1996 Newsgroups: bionet.structural-nmr Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!swrinde!howland.reston.ans.net!torn!utnut!oci!news From: Michael Overduin Subject: POSTDOCTORAL POSITION Content-Type: text/plain; charset=us-ascii Message-ID: Sender: news@oci.utoronto.ca Content-Transfer-Encoding: 7bit Organization: Ontario Cancer Institute - U of Toronto Mime-Version: 1.0 Date: Fri, 16 Feb 1996 19:30:25 GMT X-Mailer: Mozilla 1.1N (X11; I; SunOS 4.1.4 sun4c) X-Url: news:bionet.structural-nmr Lines: 56 WHAT? I have a postdoctoral position in my laboratory that 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 signal transducing proteins and cell adhesion molecules. WHERE? The University of Colorado Health Sciences Center has begun building a multi-user NMR facility. The campus is located in a residential area a few miles from downtown Denver, and is an hour's drive from the Rocky Mountains. HOW? Two Varian INOVA spectrometers (600 and 500 MHz) have been purchased and will be installed next June. Silicon Graphics and Sun workstations will be available for data processing and analysis. A fermentation core facility is available for protein expression. WHO? You will be joining me in the Department of Pharmacology and become part of a community of NMR spectroscopists that spans several departments in the University of Colorado Health Sciences Center as well as in the nearby Boulder campus of the University of Colorado. WHEN? The position will be available in the spring of 1996. A competitive salary is available. Qualifications: 1) a recent Ph.D. in chemistry, biochemistry or a related field, and solid training in protein structure and protein biochemistry 2) research experience in the structural study of proteins/peptides by multidimensional NMR spectroscopy. Please send a letter, c.v. and 3 letters of reference to: Michael Overduin Department of Pharmacology University of Colorado Health Sciences Center 4200 East Ninth Avenue, Denver Colorado 80262 (303) 270-8774; (303) 270-7097 (fax) overduin@essex.uchsc.edu Applications will be accepted until the position is filled. I thank all applicants for their interests, however, only those being considered will be contacted. _____ ---------- / o \ ____ | / \ |\ |\_____/| //||\\ || || | | | ______________ ____||||||||_|| || |_ | | / / /| / O||||||O | \ / |/ \ | | /------/------/ | / |||||||| ---------- \ | |\ | |||| | |||| | | / \ / / 8888888 // \ |\_____/| \ ___ | | | | / __| |__----///--- \ || | | || \ /__/| | | | | =======/ \==/ /============ || | | || |ooo|| | | | | || | |_/ / || || | | || |ooo||====| | | ===||====| |__/ || ~~ | | ~~ |___|/ |______|______|/ || | | || ~~~ || | | || From owner-structural-nmr@net.bio.net Fri Feb 16 22:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!infobiogen.fr!pasteur.fr!jussieu.fr!oleane!plug.news.pipex.net!pipex!tube.news.pipex.net!pipex!dish.news.pipex.net!pipex!wave.news.pipex.net!pipex!soap.news.pipex.net!pipex!usenet From: ohm.dial.pipex.com (William Payne) Newsgroups: bionet.structural-nmr Subject: Next door neighbours. Date: Sat, 17 Feb 1996 13:52:40 GMT Organization: UnipalmPIPEX server (post doesn't reflect views of UnipalmPIPEX) Lines: 15 Message-ID: <4g4mt7$h5b@soap.news.pipex.net> NNTP-Posting-Host: ak221.du.pipex.com X-Newsreader: Forte Free Agent v0.55 I have just had my first (and possibly last) 15 minutes playing with an ancient NMR spectroscope. I was only given a brief explaination of how it worked. Can someone explain to me how the next-door neighbour effect works? That baffled me completely. Thank you in advance William Payne P.S. Please bear in mind that I am only in yr. 12, and I am not a specialist in the field. -- William Payne ohm@dial.pipex.com From owner-structural-nmr@net.bio.net Mon Feb 19 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!warwick!lyra.csx.cam.ac.uk!news From: Tim Hubbard Newsgroups: bionet.structural-nmr Subject: Announcement: Call for prediction targets for CASP2 Date: 20 Feb 1996 18:52:08 GMT Organization: Centre for Protein Engineering Lines: 255 Message-ID: <4gd58o$9f4@lyra.csx.cam.ac.uk> NNTP-Posting-Host: ccpeshiva1-mac2.mrc-lmb.cam.ac.uk 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:bionet.structural-nmr Announcement: Call for prediction targets for CASP2 =================================================== This is a call to X-ray crystallographers and NMR spectroscopists. In 1994 the first protein structure prediction experiment was held to evaluate prediction methods through blind prediction. Details of about 33 protein sequences, which were expected to be solved before the end of 1994, were submitted by experimentalists and this allowed 135 blind predictions to be made by 35 different groups, and led to the most objective assessment of prediction methods so far. The results of the experiment are published in the November 1995 issue of Proteins: Structure, Function, and Genetics. This is the announcement of the second prediction experiment, which will run throughout 1996 and culminate in an evaluation meeting in December. As before, for the experiment to succeed, it is essential that we obtain the help of the experimental community. Therefore, we would like to invite Protein crystallographers and NMR spectroscopists who expect to solve a structure before 1st October 1996 to submit the sequence so that attempts can be made to predict it before it is publically announced. Each prediction will be given a deadline prior to the date on which the first information about the structure is to be made public. Targets of all sizes and types are required. Small structures (less than 100 residues) are needed to test some of the ab initio structure prediction methods. Proteins with folds related to those of known structures are needed to test fold identification methods. Proteins with sequences homologous to that of one or more known structures are needed to test comparative modeling methods. Protein-Protein and Protein-Ligand complexes are required to test docking methods. All that is requested is: - the sequence or a sequence accession number of the protein - an estimate of the likely date of public release (and updates if the work procedes faster or slower) - a commitment to make the coordinates available to the independent assessors not latter than 1st October should the structure be solved by then. Any coordinates provided will be treated with strict confidentiality as requested and used only to evalute the accuracy of predictions. For further information and on-line forms and documents see: http://iris4.carb.nist.gov/casp2/ http://www.mrc-cpe.cam.ac.uk/casp2/ A Target protein submission form is also attached to this message and can be mailed to casp2@mrc-lmb.cam.ac.uk Tim Hubbard Co-chair Centre for Protein Engineering, Cambridge, UK. Steve Bryant Co-chair NCBI, National Library of Medicine, USA. John Moult President CARB, University of Maryland, USA. Jan T. Pedersen CARB, University of Maryland, USA Krzysztof Fidelis Lawrence Livermore National Laboratory, USA. Richard Judson Sandia National Laboratory, USA. ------------------------------------------------------------------------ - CASP2: Second Meeting on the Critical Assessment of Techniques for Protein Structure Prediction Target submission form ====================== Instructions for completing this form ------------------------------------- (0) Please only use this form if you are unable to complete the WWW version at http://iris4.carb.nist.gov/casp2/ or http://www.mrc-cpe.cam.ac.uk/casp2/ (1) Save this page as a text file (2) Complete all sections (3) send by email to casp2@mrc-lmb.cam.ac.uk (4) if you have filled out the form correctly, you should receive an email acknowledgement (though not necessarily immediately) cut here ------------------------------------------------------------------------ - CASP2: Second Meeting on the Critical Assessment of Techniques for Protein Structure Prediction Target submission form ====================== This is the text version of the Prediction target submission form for the Second Critical Assessment Techniques for Protein Structure Prediction Experiment (CASP2). Introduction ============ Protein crystallographers and NMR spectroscopists are asked to provide details of structures they expect to have solved before 1st October 1996 using this form. Targets of all sizes and types are required. Small structures (less than 100 residues) are needed to test some of the ab initio structure prediction methods. Proteins with folds related to those of known structures are needed to test fold recognition methods. Proteins with sequences homologous to that of one or more known structures are needed to test comparative modelling methods. To be useful to the predictors, a period of at least a month is required before any details of the structure will be released. Please notify us immediately when the details are going to be made public, so that we can ask the predictors to stop work in a timely manner. This can be done by sending a mail to casp2@mrc-lmb.cam.ac.uk. In order for the predictions to be assessed in time for the meeting in December, we will need a set of co-ordinates by the beginning of October at the latest. If necessary, these can be for limited distribution until the meeting. A. Scientific information ========================= 1. [ ] Protein Name 2. [ ] Organism Name 3. [ ] Number of amino acids (does not need to be exact) Please provide accession number and database of the protein or the actual sequence (both if possible). 4. [ ] Accession number 5. Sequence Database [ ] Swiss-prot [ ] PIR [ ] Genbank [ ] EMBL [ ] Other [ ] 6. Amino acid sequence One letter code (ACEDFTK) is preferred, but three letter code (ala cys glu asp) can also be processed. 7. Are there homologous sequences of known structure to this protein? Yes [ ] No [ ] 8. Current state of the experimental work Please describe briefly where things are at, addressing as many of the following points as you wish to/are relevant/can. The more information, the easier it is for a modeler to decide whether to predict your structure. Protein supply? Crystals? Diffraction quality? Molecular replacement in progress? Molecular replacement solution in hand? Heavy atom derivative search in progress? Heavy atom derivatives in hand? 9. Do you already have an interpretable map? Yes [ ] No [ ] 10. [ ] Estimated date of chain tracing completion. In order to assess the predictions before the meeting, this date should be before 1st October 1996. 11. [ ] Estimated date of public release of structure 12. If you have any other useful information about this sequence family please enter it below B. Administrative information ============================= 13. [ ] Name 14. Mailing address: [ ] 15. [ ] Tel 16. [ ] Fax 17. [ ] Email 18. How did you hear about this prediction experiment? [ ] Nature Add [ ] Poster [ ] Newsgroup [ ] Email [ ] Other [ ] ------------------------------------------------------------------------ - From owner-structural-nmr@net.bio.net Mon Feb 19 22:00:00 1996 Path: biosci!KS.UIUC.EDU!feng From: feng@KS.UIUC.EDU (Zhou Feng) Newsgroups: bionet.structural-nmr Subject: Excuse me but this CHARMM documentation .. Date: 20 Feb 1996 09:02:14 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: <199602201659.AA069255577@london.ks.uiuc.edu> NNTP-Posting-Host: net.bio.net Excuse me but I can't repress my frustration while trying to get my CHARMM input file to work but to ask this question: Is there a better CHarmm documentation out there besides the very intelligent but also abstract .doc files? I can guess but there is simpler too much I can't figure out in the commands. Maybe some example input files would help. Feng From owner-structural-nmr@net.bio.net Mon Feb 19 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: th@mrc-cpe.cam.ac.uk (Tim Hubbard) Newsgroups: bionet.structural-nmr Subject: Announcement: Call for prediction targets for CASP2 Date: 20 Feb 1996 18:55:49 -0000 Lines: 238 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4gd5fl$lje@mserv1.dl.ac.uk> X-Sender: th@ind1.mrc-lmb.cam.ac.uk Original-To: bionews@dl.ac.uk, proteins@dl.ac.uk, xtal-log@dl.ac.uk, str-nmr@dl.ac.uk, pdb-l@pdb.pdb.bnl.gov Announcement: Call for prediction targets for CASP2 =================================================== This is a call to X-ray crystallographers and NMR spectroscopists. In 1994 the first protein structure prediction experiment was held to evaluate prediction methods through blind prediction. Details of about 33 protein sequences, which were expected to be solved before the end of 1994, were submitted by experimentalists and this allowed 135 blind predictions to be made by 35 different groups, and led to the most objective assessment of prediction methods so far. The results of the experiment are published in the November 1995 issue of Proteins: Structure, Function, and Genetics. This is the announcement of the second prediction experiment, which will run throughout 1996 and culminate in an evaluation meeting in December. As before, for the experiment to succeed, it is essential that we obtain the help of the experimental community. Therefore, we would like to invite Protein crystallographers and NMR spectroscopists who expect to solve a structure before 1st October 1996 to submit the sequence so that attempts can be made to predict it before it is publically announced. Each prediction will be given a deadline prior to the date on which the first information about the structure is to be made public. Targets of all sizes and types are required. Small structures (less than 100 residues) are needed to test some of the ab initio structure prediction methods. Proteins with folds related to those of known structures are needed to test fold identification methods. Proteins with sequences homologous to that of one or more known structures are needed to test comparative modeling methods. Protein-Protein and Protein-Ligand complexes are required to test docking methods. All that is requested is: - the sequence or a sequence accession number of the protein - an estimate of the likely date of public release (and updates if the work procedes faster or slower) - a commitment to make the coordinates available to the independent assessors not latter than 1st October should the structure be solved by then. Any coordinates provided will be treated with strict confidentiality as requested and used only to evalute the accuracy of predictions. For further information and on-line forms and documents see: http://iris4.carb.nist.gov/casp2/ http://www.mrc-cpe.cam.ac.uk/casp2/ A Target protein submission form is also attached to this message and can be mailed to casp2@mrc-lmb.cam.ac.uk Tim Hubbard Co-chair Centre for Protein Engineering, Cambridge, UK. Steve Bryant Co-chair NCBI, National Library of Medicine, USA. John Moult President CARB, University of Maryland, USA. Jan T. Pedersen CARB, University of Maryland, USA Krzysztof Fidelis Lawrence Livermore National Laboratory, USA. Richard Judson Sandia National Laboratory, USA. ------------------------------------------------------------------------- CASP2: Second Meeting on the Critical Assessment of Techniques for Protein Structure Prediction Target submission form ====================== Instructions for completing this form ------------------------------------- (0) Please only use this form if you are unable to complete the WWW version at http://iris4.carb.nist.gov/casp2/ or http://www.mrc-cpe.cam.ac.uk/casp2/ (1) Save this page as a text file (2) Complete all sections (3) send by email to casp2@mrc-lmb.cam.ac.uk (4) if you have filled out the form correctly, you should receive an email acknowledgement (though not necessarily immediately) cut here ------------------------------------------------------------------------- CASP2: Second Meeting on the Critical Assessment of Techniques for Protein Structure Prediction Target submission form ====================== This is the text version of the Prediction target submission form for the Second Critical Assessment Techniques for Protein Structure Prediction Experiment (CASP2). Introduction ============ Protein crystallographers and NMR spectroscopists are asked to provide details of structures they expect to have solved before 1st October 1996 using this form. Targets of all sizes and types are required. Small structures (less than 100 residues) are needed to test some of the ab initio structure prediction methods. Proteins with folds related to those of known structures are needed to test fold recognition methods. Proteins with sequences homologous to that of one or more known structures are needed to test comparative modelling methods. To be useful to the predictors, a period of at least a month is required before any details of the structure will be released. Please notify us immediately when the details are going to be made public, so that we can ask the predictors to stop work in a timely manner. This can be done by sending a mail to casp2@mrc-lmb.cam.ac.uk. In order for the predictions to be assessed in time for the meeting in December, we will need a set of co-ordinates by the beginning of October at the latest. If necessary, these can be for limited distribution until the meeting. A. Scientific information ========================= 1. [ ] Protein Name 2. [ ] Organism Name 3. [ ] Number of amino acids (does not need to be exact) Please provide accession number and database of the protein or the actual sequence (both if possible). 4. [ ] Accession number 5. Sequence Database [ ] Swiss-prot [ ] PIR [ ] Genbank [ ] EMBL [ ] Other [ ] 6. Amino acid sequence One letter code (ACEDFTK) is preferred, but three letter code (ala cys glu asp) can also be processed. 7. Are there homologous sequences of known structure to this protein? Yes [ ] No [ ] 8. Current state of the experimental work Please describe briefly where things are at, addressing as many of the following points as you wish to/are relevant/can. The more information, the easier it is for a modeler to decide whether to predict your structure. Protein supply? Crystals? Diffraction quality? Molecular replacement in progress? Molecular replacement solution in hand? Heavy atom derivative search in progress? Heavy atom derivatives in hand? 9. Do you already have an interpretable map? Yes [ ] No [ ] 10. [ ] Estimated date of chain tracing completion. In order to assess the predictions before the meeting, this date should be before 1st October 1996. 11. [ ] Estimated date of public release of structure 12. If you have any other useful information about this sequence family please enter it below B. Administrative information ============================= 13. [ ] Name 14. Mailing address: [ ] 15. [ ] Tel 16. [ ] Fax 17. [ ] Email 18. How did you hear about this prediction experiment? [ ] Nature Add [ ] Poster [ ] Newsgroup [ ] Email [ ] Other [ ] ------------------------------------------------------------------------- From owner-structural-nmr@net.bio.net Mon Feb 19 22:00:00 1996 Path: biosci!NMR.UTMB.EDU!david From: david@NMR.UTMB.EDU (David Gorenstein) Newsgroups: bionet.structural-nmr Subject: Final Announcement, STRUCTURAL BIOLOGY SYMPOSIUM, UTMB Date: 20 Feb 1996 14:24:19 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 383 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Final Announcement STRUCTURAL BIOLOGY SYMPOSIUM UNIVERSITY OF TEXAS MEDICAL BRANCH AT GALVESTON Sealy Center for Structural Biology and the Department of Human Biological Chemistry & Genetics MARCH 1-3, 1996 Dear Colleague: Final details for the Structural Biology Symposium at UTMB are enclosed. If you have not already registered, we would like to invite you and your colleagues to join us in our inaugural celebration of the UTMB Structural Biology Program and the Sealy Center for Structural Biology by participating in our Structural Biology Symposium scheduled for March 1-3, 1996. This meeting will bring together scientists who are interested in applying insights from structural biology and solution thermodynamics to solve biological and biomedical problems. The speakers at the symposium are distinguished researchers from a wide spectrum of scientific disciplines. If you are planning to attend the Symposium, please inform us of your coming as well as who may be accompanying you by no later than February 26th. Furthermore, if you intend to participate in the poster session, all abstracts must be received no later than February 26th as well. Regarding accomodations for the event, a block of rooms has been reserved for Symposium attendants at the beachfront Hotel Galvez. However, prior to your arrival in Galveston it is necessary that you fill out the hotel form provided below to guarantee a reserved room. Although there is no registration fee, $50 will be assessed for those who wish to optionally participate in the Friday reception, Saturday lunch and dinner banquet, and Sunday brunch. Please make all payments made out to UTMB-SCSB. In addition, checks will be the only form of payment accepted. Send all inquiries and responses to: Jacqueline Luxon; Administrative Secretary ADDRESS: Sealy Center for Structural Biology Dept. for Human Biological Chemistry and Genetics University of Texas Medical Branch Galveston, TX. 77555-1157 PHONE: (409)747-6800 FAX: (409)747-6850 EMAIL: jacky@nmr.utmb.edu Thank you, and we look forward to your participation in the Symposium. UTMB Symposium Organizing Committee: D. Wayne Bolen Werner Braun Wlodzimierz M. Bujalowski Edmund W. Czerwinski Robert Fox David G. Gorenstein James C. Lee Bruce A. Luxon Jan F. Post Stanley Watowich ---------------------------------------------------------------------- Symposium Information and Registration Information and the registration and hotel forms may also be found on the Sealy Center for Structural Biology server- URL http://www.scsb.utmb.edu:90/ You may also e-mail or print the registration and hotel forms below and send them to Jacqueline Luxon at the above address. ---------------------------------------------------------------------- CALL FOR ABSTRACTS, HOTEL AND REGISTRATION FORMS DEADLINE FOR THE SUBMISSION OF ABSTRACTS: FEBRUARY 26, 1996 --------------------------------------------------------------------- FINAL SCHEDULE _______________________________________________________________________________ FRIDAY, MARCH 1, 1996 _______________________________________________________________________________ 3:00 P.M. - 4.00 P.M. Registration Levin Hall 4:00 P.M. Opening Remarks Levin Hall President Thomas James - UTMB 4:15 P.M. Plenary Lecture Levin Hall Frederic Richards - Yale "The Structure of Proteins - Change in Dogma with Time" 6:00 P.M. - 7:30 P.M. Reception Levin Hall ________________________________________________________________________________ SATURDAY, MARCH 2, 1996 ________________________________________________________________________________ 9:00 A.M. - 9:50 A.M. Angela Gronenborn - NIH Levin Hall "Structure of Protein-DNA COmplexes: Intercalation, DNA Bending and Transcriptional Control" 9:50 A.M. - 10:40 A.M. Don Wiley - Harvard Levin Hall "Structural Biology of Cellular Immunity" 10:40 A.M. - 11:10 A.M. Break & Posters Levin Hall 11:10 A.M. - 12:00 noon Robert L. Baldwin - Stanford Levin Hall "The Molten Globule Intermediate of an Apomyoglobin" 12:00 noon - 12:30 P.M. Werner Braun - UTMB Levin Hall "Self-Correcting Distance Geometry: A New Method for Protein Modeling and NMR Determination" 12:30 P.M. - 2:00 P.M. Lunch and visit to the NMR Center Dockside Blg. 2:00 P.M. - 2:50 P.M. Florante Quiocho - Baylor Levin Hall "Molecular Recognition by Proteins: From the Stringent to the very Loose" 2:50 P.M. - 3:40 P.M. Thomas James - University of Levin Hall California - San Francisco "Nucleic Acid Structure and Dynamics" 3:40 P.M. - 4:00 P.M. Break 4:00 P.M. - 4:50 P.M. Gary Ackers - Washington U. Levin Hall "The Intermediates of Hemoglobin Cooperativity Provide Striking New Insights into Allostery" 4:50 P.M. - 5:20 P.M. Robert Fox - UTMB Levin Hall "SH3 Domain Peptide Recognition" 5:20 P.M. - 6:30 P.M. Poster and Reception Levin Hall 7:30 P.M. Banquet Hotel Galvez ________________________________________________________________________________ SUNDAY, MARCH 3, 1996 ________________________________________________________________________________ 10:00 A.M. - 12:00 noon Discussion - Brunch Levin Hall "Future Directions of Structural Biology" ALL SPEAKERS WILL SERVE AS PANEL MEMBERS 12:00 noon - 1:00 P.M. Break NMR Techniques Workshop Levin Hall (In Cooperation with Varian Instruments) 1:00 P.M. - 2:00 P.M. George Gray - Varian Instruments Levin Hall "Recent Advances in NMR Technology for Biomolecular NMR" 2:00 P.M. - 2:30 P.M. Shanmin Zhang - UTMB Levin Hall "Suppression of Radiation Damping During Acquisition" 2:30 P.M. - 4:00 P.M. Additional short contributions Levin Hall 4:00 P.M. - 5:00 P.M. Applications on Varian/Oxford 600 Dockside Blg. and 750 Unity Plus and Varian/HARC 400 MHz Unity PLus systems with George Gray and NMR Center staff ---------------------------------------------------------------------- CLIMATE The weather in Galveston, a resort island off the Texas coast near Houston, in March is warm with average temperatures ranging from a low of 55 degrees to a high of 75 degrees. ---------------------------------------------------------------------- TRAVEL AND ACCOMMODATION Hotel space has been reserved at the Hotel Galvez, however, it is not possible to guarantee conference rates: Rate: $65/Single, $85/Double $95/Triple & Quad, $175/Deluxe Suites FOR RESERVATIONS CALL: 1-800-392-4285 ---------------------------------------------------------------------- POSTER INFORMATION Posters should be no larger than 4'x6'. Abstracts of 1 page listing title, authors and affiliation should be provided prior to the meeting. ---------------------------------------------------------------------- COSTS: There is no registration fee. However, payment of $50.00 total for optional receptions, lunches and dinners should be made to UTMB-SCSB by February 26th. Please, payment by checks only. ---------------------------------------------------------------------- TRAVEL TO GALVESTON AND PARKING INFORMATION >From Houston to the Hotel Galvez Take I-45 South, upon entering Galveston, I-45 ends and becomes Broadway. Stay on Broadway till 20th Street. Turn right on 20th and stay until it ends at the Seawall. The hotel will be at the corner of 20th and Seawall. >From Hotel Galvez to UTMB Campus Go down the Seawall till 6th Street, also called University Boulevard. Turn left on 6th and stay until you arrive on Campus. Gerland Grocery store will be on your right and the parking garage on your left. Note: This parking will be only for Friday. On Saturday and Sunday you will park in a lot behind Levin Hall, where the meeting will be held, and it will be free. >From Friday Parking to Levin Hall Exit parking garage on Market Street, stay on Market Street till Levin Hall, you will pass on your right, the Admin Annex, Child Health Center, Moody Medical Library, a small rose garden and then Levin Hall, so the 4th Building on your right will be Levin Hall. As soon as you pass the rose garden, there will be stairs going up to the second floor of Levin Hall where the meeting will be held. >From Hotel Galvez to Saturday Parking for Levin Hall Go down the Seawall and turn left on 11th Street. The parking entrance faces 11th Street and is located between Market Street and Mechanic Street. The back of Levin Hall faces the parking lot. From the parking lot cross the street, stay on the left side of Levin Hall and walk around the building until you find stairs going up to the 2nd floor where the symposium will be held. You must enter this side only. ---------------------------------------------------------------------- STRUCTURAL BIOLOGY SYMPOSIUM, UNIVERSITY OF TEXAS MEDICAL BRANCH AT GALVESTON MARCH 1-3, 1996 REGISTRATION FORM NAME:______________________________________________________________________ WORK ADDRESS:______________________________________________________________ INSTITUTION NAME:____________________________________________________________ INSTITUTION NAME:____________________________________________________________ CITY:__________________________________STATE:_____________ZIP CODE:__________ OFFICE PHONE:____________________FAX NUMBER:_________________________________ EMAIL ADDRESS:______________________________________________________________ CHECK THOSE WHICH APPLY: ______Enclosed is my check for $50.00. ______I will be participating in the Symposium on: FRIDAY_________ SATURDAY_______ SUNDAY_________ ______I will be participating in the poster session and have included a copy of my abstract. ---------------------------------------------------------------------- HOTEL REGISTRATION FORM NAME:______________________________________________________________________ WORK ADDRESS:______________________________________________________________ INSTITUTION NAME:____________________________________________________________ CITY:__________________________________STATE:_____________ZIP CODE:__________ OFFICE PHONE:____________________FAX NUMBER:_________________________________ EMAIL ADDRESS:______________________________________________________________ ARRIVAL DATE:_____________________DEPARTURE DATE:____________________________ FOR ARRIVALS LATER THAN 6:00 P.M., A CREDIT CARD NUMBER IS NEEDED CREDIT CARD (i.e. type)______________________________________________________ CREDIT CARD ACCT. #_______________________________________EXP. DATE__________ ACCOMMODATION DESIRED: ________SINGLE ACCOMMODATIONS $65.00/NIGHT ________DOUBLE ACCOMMODATIONS $85.00/NIGHT ________TRIPLE AND QUAD ACCOMODATIONS $95.00/NIGHT ________DELUXE SUITES $175.00/NIGHT ----------------------------------------------------------------------------- Please complete and return the conference registration form and/or hotel registration form, together with your payment, to: Jacqueline Luxon; Administrative Secretary ADDRESS: Sealy Center for Structural Biology Dept. for Human Biological Chemistry and Genetics University of Texas Medical Branch Galveston, TX. 77555-1157 PHONE: (409)747-6800 FAX: (409)747-6850 EMAIL: jacky@nmr.utmb.edu David Gorenstein Director, Sealy Center for Structural Biology Professor, Dept. of Human Biological Chemistry and Genetics University of Texas Medical Branch Galveston, TX 77555-1157 Office: (409) 747 6801 Main Office/Voice Mail: (409) 747 6800 Fax: (409) 747 6850 E-MAIL ADDRESS: david@nmr.utmb.edu http://www.nmr.utmb.edu/ David Gorenstein Director, Sealy Center for Structural Biology Professor, Dept. of Human Biological Chemistry and Genetics University of Texas Medical Branch Galveston, TX 77555-1157 Office: (409) 747 6801 Main Office/Voice Mail: (409) 747 6800 Fax: (409) 747 6850 E-MAIL ADDRESS: david@nmr.utmb.edu http://www.nmr.utmb.edu/ David Gorenstein Director, Sealy Center for Structural Biology Professor, Dept. of Human Biological Chemistry and Genetics University of Texas Medical Branch Galveston, TX 77555-1157 Office: (409) 747 6801 Main Office/Voice Mail: (409) 747 6800 Fax: (409) 747 6850 E-MAIL ADDRESS: david@nmr.utmb.edu http://www.nmr.utmb.edu/ David Gorenstein Director, Sealy Center for Structural Biology Professor, Dept. of Human Biological Chemistry and Genetics University of Texas Medical Branch Galveston, TX 77555-1157 Office: (409) 747 6801 Main Office/Voice Mail: (409) 747 6800 Fax: (409) 747 6850 E-MAIL ADDRESS: david@nmr.utmb.edu http://www.nmr.utmb.edu/ David Gorenstein Director, Sealy Center for Structural Biology Professor, Dept. of Human Biological Chemistry and Genetics University of Texas Medical Branch Galveston, TX 77555-1157 Office: (409) 747 6801 Main Office/Voice Mail: (409) 747 6800 Fax: (409) 747 6850 E-MAIL ADDRESS: david@nmr.utmb.edu http://www.nmr.utmb.edu/ From owner-structural-nmr@net.bio.net Tue Feb 20 22:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!newsfeed.internetmci.com!tank.news.pipex.net!pipex!lade.news.pipex.net!pipex!ggr.co.uk!ussun2n.glaxo.com!concert!bigblue.oit.unc.edu!hrm From: hrm@med.unc.edu (Helen R Mott) Newsgroups: bionet.structural-nmr Subject: Re: pKa value determination of Histidines Date: 20 Feb 1996 13:48:34 GMT Organization: UNC-CH School of Medicine Lines: 47 Distribution: world Message-ID: <4gcjfi$lk3@bigblue.oit.unc.edu> References: NNTP-Posting-Host: hasty.med.unc.edu Cc: In article , Johan Schultz wrote: >Dear Netters, > >I would like to know the pKa value of a histidine (actually there is only >one) in my 15N-labelled, not fully assigned protein. How do I determine >this pKa value easiest? I imagine that recording 1H-15N HSQC:s at a number >of different pH-values and determining the volume of the Histidine >imidazole ring "epsilon NH" peak would be a good method. If so, does >anyone know what a typical (or random coil) 15N chemical shift for this >nitrogen would be? > >All suggestions are highly appreciated! > >Thanks in advance > >Johan Schultz > Dear Johan, I have recently been investigating the His ring peaks, and I would suggest that you look at papers by Gooley et al Biochemistry (1993) 32 13098-13108 and Blomberg et al JACS (1977) 99 8149-8159. If you record an HSQC with the 1/4J delay set to 11 msecs, you will see the cross-peaks due to the 2 bond couplings in the HIs ring and the one bond couplings in the backbone NH will be suppressed. The chemical shift of the epsilon nitrogen when it is unprotonated should be about 249 ppm, and upon protonation it should shift to about 176 ppm, so it should be quite obvious when you have reached the pKa! Helen Mott ----------------------------------------------------------------- Dr Helen R. Mott Department of Biochemistry and Biophysics hrm@med.unc.edu University of North Carolina, CB #7260 Chapel Hill, NC 27599 Fax(919) 966 2852 Ph:(919) 966 6781 ----------------------------------------------------------------- -- ----------------------------------------------------------------- Dr Helen R. Mott Department of Biochemistry and Biophysics From owner-structural-nmr@net.bio.net Wed Feb 21 22:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.structural-nmr Subject: BIOSCI miniFAQ, ver. 14-DEC-95 Date: 22 Feb 1996 02:01:04 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 199 Sender: daemon@net.bio.net Distribution: world Message-ID: <199602221000.CAA18691@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 14-DEC-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. Contents: -------- 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index in addition to the master index for the entire set. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-structural-nmr@net.bio.net Thu Feb 22 22:00:00 1996 Path: biosci!WWITCH.UNL.EDU!rshoe From: rshoe@WWITCH.UNL.EDU (Richard Shoemaker) Newsgroups: bionet.structural-nmr Subject: My "old" Survey about jobs in Bio-NMR... Date: 23 Feb 1996 13:10:49 -0800 Organization: UNL-Chemistry Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: <312E48F6.4165@wwitch.unl.edu> References: <9602091913.AA17529@laplace.csb.yale.edu> NNTP-Posting-Host: net.bio.net Dear All: Some time back, I requested information about the general current/future outlook for jobs in the Biomolecular NMR field. Many requested that I summarize the results of my informal "survey", and I've done so....albeit, indirectly. A general summary/discussion of the above topic is currently available as an editorial on the Otsuka/Chemagnetics, Inc. Web-Page: URL: http://www.otsuka.com , select "Editorial Page" from the main homepage if you would like to read my assement/summary of the responses that I received in regard to my inquiry earlier this year. Best Regards, 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 Thu Feb 22 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!lade.news.pipex.net!pipex!ggr.co.uk!ussun2n.glaxo.com!usenet From: Tai-he Xia Newsgroups: bionet.structural-nmr Subject: Re: conversion of spectra from VNMR to FELIX Date: Fri, 23 Feb 1996 14:04:51 -0500 Organization: Glaxo Wellcome Lines: 24 Message-ID: <312E0FD3.41C6@glaxo.com> References: <01I1755BQD388ZJGH1@ubaclu.unibas.ch> NNTP-Posting-Host: ussg2m.glaxo.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) Ronald Wiltscheck wrote: > > Dear netter, > > does anyone of you know how to trnasfer already processed > VNMR-spectra ('/datdir/data' file) into a Felix *.mat format? The program converter which I wrote can be used to convert the processed vnmr data into fexix data format which can be read into the matrix by macro. If you are interested, I could send you the program plus the macro. Tai-he Xia > > I'm greatful for any kind of suggestions, > > ============================================================================= > Ronald Wiltscheck e-mail: wiltscheck@ubaclu.unibas.ch > University of Basel phone: ++41-61/267-2091 > Biozentrum/Structural Biology fax: ++41-61/267-2190 > CH-4053 Basel/Switzerland home: ++41-61/361-8605 > ============================================================================= From owner-structural-nmr@net.bio.net Sun Feb 25 22:00:00 1996 Path: biosci!GUITAR.ROCKEFELLER.EDU!roberto From: roberto@GUITAR.ROCKEFELLER.EDU (Roberto Sanchez) Newsgroups: bionet.structural-nmr Subject: ANNOUNCING EUROPEAN MIRROR SITE FOR MODELLER-3 Date: 25 Feb 1996 16:18:26 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 92 Sender: daemon@net.bio.net Distribution: world Message-ID: <199602260010.AAA06474@guitar.rockefeller.edu> NNTP-Posting-Host: net.bio.net A mirror site for the distribution of MODELLER (A Protein Structure Modeling Program) was established in europe at the International Centre for Genetic Engineering and Biotechnology (ICGEB) Trieste, Italy: ftp://ftp.icgeb.trieste.it/pub/modeller The announcement of MODELLER release 3 follows: MODELLER PROTEIN MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS MODELLER 3, December 31, 1995 Copyright(c) 1989-1995 Andrej Sali All Rights Reserved Written by Andrej Sali Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Andrej Sali, Box 270, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA. Tel: +1-212-327-7550. Fax: +1-212-327-7540. E-mail: sali@rockvax.rockefeller.edu. ** DESCRIPTION: MODELLER is most frequently used for homology or comparative modeling of protein three-dimensional structure: the user provides an alignment of a sequence to be modeled with known related structures and MODELLER will automatically calculate a full-atom model. More generally, MODELLER models protein 3D structure by satisfaction of spatial restraints (A. Sali & T.L. Blundell. J.Mol.Biol. 234, 779-815, 1993). In principle, the restraints can be derived from a number of different sources. These include homologous structures (comparative modeling), NMR experiments (NMR refinement), rules of secondary structure packing (combinatorial modeling), cross-linking experiments, fluorescence spectroscopy, image reconstruction in electron microscopy, site-directed mutagenesis, intuition, residue-residue and atom-atom potentials of mean force, etc. The output of MODELLER is a 3D structure of a protein that satisfies these restraints as well as possible. The optimization is carried out by the variable target function procedure employing methods of conjugate gradients and molecular dynamics with simulated annealing. MODELLER can also do several other tasks, including multiple comparison of protein sequences and/or structures, clustering, and searching of sequence databases. The program is described in a 120-page manual. MODELLER is written in Fortran and is meant to run on a UNIX system. ** DISTRIBUTION: MODELLER is available free of charge to academic non-profit institutions. First, please use the anonymous ftp account on guitar.rockefeller.edu (IP 129.85.13.198) or on the european mirror site at ftp.icgeb.trieste.it to copy at least the following files from the pub/modeller directory to your computer: the license form (PostScript file academic-license.ps), the distribution file that contains the data files necessary to run MODELLER (modeller3-data.tar.Z), and an executable for each machine type that you need (described in file INSTALLATION). Next, please sign and mail (or fax) the license form to Andrej Sali. You will then receive the key (MODELLER_KEY) that has to be assigned to the environment variable KEY_MODELLER3 in your login script (.cshrc). See file INSTALLATION for installation instructions. There is also a MODELLER home page on World Wide Web at URL http://guitar.rockefeller.edu that can be used to ftp the program and view the manual. A graphical interface to MODELLER is available as part of QUANTA and INSIGHT, interactive molecular modeling programs with many tools for protein modeling and structural analysis. QUANTA and INSIGHT facilitate preparation of input files for MODELLER as well as analysis of the results produced by MODELLER; in particular, the preparation of an alignment and evaluation of the models are made much easier. If you are interested in QUANTA or INSIGHT, please contact Ms. Brenda Pfeiffer, BIOSYM / Molecular Simulations Inc., 9685 Scranton Road, San Diego, CA 92121-3752, tel: +1-619-546-5319, fax: +1-619-458-0136, email: blp@biosym.com. ** CONTENTS: src\ sources or executables for MODELLER; modlib\ libraries and data files for the programs; scripts\ script files used to compile and use MODELLER; doc\ MODELLER documentation; Makefile Makefile for compiling/installing MODELLER modules; modeller3.README this file; INSTALLATION how to install MODELLER; Install compilation and installation script relying on Makefile; tests\ tests and examples; From owner-structural-nmr@net.bio.net Tue Feb 27 22:00:00 1996 Path: biosci!PICASSO.UCSF.EDU!schmitz From: schmitz@PICASSO.UCSF.EDU (Ulrich Schmitz) Newsgroups: bionet.structural-nmr Subject: (none) Date: 28 Feb 1996 10:36:36 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 36 Sender: daemon@net.bio.net Distribution: world Message-ID: <199602281833.KAA18623@picasso.ucsf.EDU> NNTP-Posting-Host: net.bio.net Postdoctoral Postion available University of California San Francisco in the lab of Uli Schmitz and Thomas L. James Starting in summer 96 a post-doctoral position is available at UCSF, Department of Pharmaceutical Chemistry in the lab of Uli Schmitz which is closely associated with the Thomas L. James group. We are currently engaged in the structure determination of double-labeled RNA fragments using multidimensional heteronuclear NMR methods. The NMR facility at UCSF is equipped with two GE 500MHz and one Varian UnityPlus 600MHz spectrometer. A network of Sparc workstations, SGI Indigos and Apple computers is available for data processing and analysis and the structure refinement work for which access to supercomputers is available as well. Besides a number of UCSF software packages (AMBER, MARDIGRAS, SPARKY, MIDADPLUS) we also have several commercial modeling and NMR processing software packages available. UCSF offers a rather unique, open and stimulating research environment . Interested candidates should send a cv to: Uli Schmitz, UCSF, Dept. Pharm. Chem, San Francisco, CA94143-0446 or send email to schmitz@picasso.ucsf.edu More information about the NMR facility and the ongoing work is available on the world wide web URL: http://picasso.ucsf.edu/~schmitz From owner-structural-nmr@net.bio.net Tue Feb 27 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!nntp.coast.net!news00.sunet.se!sunic!news99.sunet.se!news.rccn.net!titan.ci.ua.pt!zeus.ci.ua.pt!goodfell From: goodfell@ci.ua.pt (B.GOODFELLOW) Newsgroups: bionet.structural-nmr Subject: 13C chem shift of tris-base Date: 28 Feb 1996 14:19:14 GMT Organization: Universidade de Aveiro, Portugal Lines: 5 Message-ID: <4h1o92$bsn@titan.ci.ua.pt> NNTP-Posting-Host: zeus.ci.ua.pt X-Newsreader: TIN [version 1.2 PL2] Does anyone know off hand the 13C chem shift of tris - I need it to referencea HMQC spectrum. It was run in H2O at pH 7.2 303K. Cheers From owner-structural-nmr@net.bio.net Wed Feb 28 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!gatech!newsfeed.internetmci.com!tank.news.pipex.net!pipex!peer-news.britain.eu.net!uknet!bhamcs!news.ox.ac.uk!news From: Clemens Glaubitz Newsgroups: bionet.structural-nmr Subject: BRUKER MSL and FELIX Data Conversion Date: Thu, 29 Feb 1996 12:07:22 +0000 Organization: Oxford University Lines: 22 Message-ID: <313596FA.6897@bioch.ox.ac.uk> NNTP-Posting-Host: bioch.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; SunOS 5.4 sun4d) Hi, I wonder if someone knows a programm to convert Bruker MSL files (Kermit, Bruknet) into Felix. Any hints much appreciated, Clemens -- ======================================================================== Clemens Glaubitz Department of Biochemistry Oxford University South Parks Road Oxford OX1 3QU U.K. Voice 44+(0)1865++275270 FAX 44+(0)1865++275259 e-mail glaubitz@bioch.ox.ac.uk ======================================================================== From owner-structural-nmr@net.bio.net Wed Feb 28 22:00:00 1996 Path: biosci!SPICA.BIOCHEM.UALBERTA.CA!smg From: smg@SPICA.BIOCHEM.UALBERTA.CA (Stephane Gagne) Newsgroups: bionet.structural-nmr Subject: Re: 13C chem shift of tris-base Date: 28 Feb 1996 18:51:29 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 34 Sender: daemon@net.bio.net Distribution: world Message-ID: <199602282314.QAA14383@spica.biochem.ualberta.ca> References: <4h1o92$bsn@titan.ci.ua.pt> NNTP-Posting-Host: net.bio.net + + Does anyone know off hand the 13C chem shift of tris - I need it + to referencea HMQC spectrum. It was run in H2O at pH 7.2 303K. + Hi, I