From owner-structural-nmr@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!galaxy.ucr.edu!library.ucla.edu!agate!overload.lbl.gov!lll-winken.llnl.gov!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!pipex!sunsite.doc.ic.ac.uk!daresbury!trane.uninett.no!sunic!news.uni-c.dk!unidhp.uni-c.dk!carlmk From: carlmk@unidhp.uni-c.dk (Mogens Kjaer) Newsgroups: bionet.structural-nmr,sci.techniques.mag-resonance Subject: Re: Anyone who knows an ftp site to hold Pronto/3D ? Followup-To: bionet.structural-nmr,sci.techniques.mag-resonance Date: 2 Feb 1995 12:22:28 GMT Organization: News Server at UNI-C, Danish Computing Centre for Research and Education. Lines: 36 Message-ID: <3gqiq4$25d@news.uni-c.dk> References: <3go4r9$lpm@news.uni-c.dk> NNTP-Posting-Host: unidhp.uni-c.dk X-Newsreader: TIN [version 1.2 PL1] Xref: biosci bionet.structural-nmr:407 sci.techniques.mag-resonance:611 Krzysztof Wroblewski (chris@highresnmr.biophys.upenn.edu) wrote: : In article <3go4r9$lpm@news.uni-c.dk> carlmk@unidhp.uni-c.dk (Mogens Kjaer) writes: : >From: carlmk@unidhp.uni-c.dk (Mogens Kjaer) : >Subject: Anyone who knows an ftp site to hold Pronto/3D ? : >Date: 1 Feb 1995 14:11:53 GMT : >Summary: Does anyone know a place where I can put a version of Pronto/3D : >Keywords: ftp, anonymous, Pronto : There is NMR related anonymous ftp site: ftp@nmrsg.biophys.upenn.edu : Why don't you send it there? : Krzysztof Wroblewski I've put it there, in the /contrib/pronto directory. However, I was not able to inform the person in charge "ftpman@nmrsg.biophys.upenn.edu" of that site; the mail bounced. The program is in one big tar file, which should be split up in individual files, as people don't need to down- load everything, just the code for the platform they need. I've also downloaded it to info.dfh.dk, in /incoming/pronto, as the individual files, but I'm not sure if it stays in that directory or it will be moved... Mogens -- Mogens Kjaer Pronto Software - Development and Distribution Carlsberg Research Center Gamle Carlsberg Vej 10 DK-2500 Valby Denmark Phone: + 45 33 27 53 25 Fax: + 45 33 27 47 08 Email: carlmk@unidhp.uni-c.dk From owner-structural-nmr@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!BIOC01.UTHSCSA.EDU!raman From: raman@BIOC01.UTHSCSA.EDU (C.S.RAMAN) Newsgroups: bionet.structural-nmr Subject: Conference Announcement Date: 2 Feb 1995 14:08:46 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 67 Sender: daemon@net.bio.net Distribution: world Message-ID: <9502022208.AA01392@bioc01.uthscsa.edu> NNTP-Posting-Host: net.bio.net >>INTERNATIONAL CONFERENCE ON MOLECULAR STRUCTURAL BIOLOGY << Organized by the Austrian Chemical Society Vienna (Austria), September 17-20, 1995 TOPICS: 1) The Impact of Molecular Biology on Structural Biology 2) Biomolecular Structure Determination a) X-Ray Diffraction b) NMR Spectroscopy 3) Dynamics and Function of Biomolecules 4) Computational Methods 5) Protein Engineering and Design Speakers include: Tom Blundell(UK), Hans-J. Boehm(D), Charles Cantor(USA), Christopher Dobson(UK), Manfred Eigen(D), Alan Fersht(UK), Robert Huber(D), Oleg Jardetzky(USA), Martin Karplus(USA), Joseph Lakowicz(USA), Paul Roesch(D), Ilme Schlichting(D), Jeffrey Skolnick(USA), Malcom Walkinshaw(CH) Posters are invited on any of the conference topics Outstanding posters will be selected for 20 minute oral presentations Abstract deadline: MAY 31, 1995 Head of Scientific Committee: P.Schuster Preliminary Participation Fees: Regular Participant 4000 ATS GOeCH Member 3500 ATS Student 2000 ATS For further information and preregistration, contact: A.Kungl Gesellschaft Oesterreichischer Chemiker AG Biophysikalische Chemie Nibelungengasse 11 A-1010 Wien, Austria Tel.: (43) 1 587249 FAX.: (43) 1 587966 e-mail: msb95@helix.mdy.univie.ac.at -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ C.S.RAMAN _/ _/ Department of Biochemistry _/ _/ University of Texas Health Science Center _/ _/ 7703 Floyd Curl Drive _/ _/ San Antonio, TX 78284-7760 _/ _/ USA _/ _/ _/ _/ Tel: (210) 567-6623 _/ _/ Fax: (210) 567-6595 _/ _/ E-mail: raman@bioc01.uthscsa.edu _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ How can it be that mathematics, a product of human thought _/ _/ independent of experience, is so admirably adapted to the _/ _/ objects of reality? "-Albert Einstein" _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From owner-structural-nmr@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!BIOC01.UTHSCSA.EDU!raman From: raman@BIOC01.UTHSCSA.EDU (C.S.RAMAN) Newsgroups: bionet.structural-nmr Subject: Faculty Positions in Structural NMR Date: 2 Feb 1995 08:23:42 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 86 Sender: daemon@net.bio.net Distribution: world Message-ID: <9502021623.AA00962@bioc01.uthscsa.edu> NNTP-Posting-Host: net.bio.net Dear Colleague: I would greatly appreciate it if you could bring to the attention of appropriate candidates the attached information for NMR tenure-track faculty positions at the University of Texas Medical Branch at Galveston. With funding from an NIH building grant, support of the Lucille P. Markey Foundation and other endowed foundation for a Structural Biology Program at UTMB, we continue our effort to establish a major NMR Center. Positions Available: NMR Faculty Positions at the University of Texas Medical Branch Galveston, Texas NMR spectroscopists are invited to apply for junior-level, tenure-track faculty positions at the University of Texas Medical Branch at Galveston. The instrumentation includes new multinuclear Varian UNITYplus 750, 600 and wide-bore 400 MHz and other lower field instruments. (The 4-channel, 750 MHz instrument is scheduled for installation in early Spring 1995.) The Center is housed in its own renovated building on campus, with operating funds, equipment and building funded by several endowed foundations, UT and NIH. The UTMB Structural Biology Program, supported in part by a new Lucille P. Markey Foundation award, will be expanded to include four or more faculty in NMR spectroscopy, several in computational biochemistry and several in x-ray crystallography. The successful candidate must have outstanding potential for independent research and record in the field of NMR; will be expected to attract funding from national agencies and to fully participate in graduate education at the departmental level. Affiliation with the Sealy Center for Molecular Science or other relevant academic departments will be available. Applications should include a complete curriculum vitae, a summary of research interests and names and addresses of at least three references. Review of applications will continue until the positions are filled. Applications should be addressed to: Dr. James C. Lee Structural Biology Search Committee Department of Human Biological Chemistry and Genetics and The Sealy Center for Molecular Science University of Texas Medical Branch Galveston, Texas 77555-1055 UTMB is an equal opportunity M/F/V/H affirmative action employer. UTMB hires only individuals authorized to work in the United States. Thanks very much for your help. Sincerely yours, ------------------------------------------------- David Gorenstein Director, UTMB NMR Center 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 NOTE NEW E-MAIL ADDRESS: david@nmr.utmb.edu http://www.nmr.utmb.edu/ -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ C.S.RAMAN _/ _/ Department of Biochemistry _/ _/ University of Texas Health Science Center _/ _/ 7703 Floyd Curl Drive _/ _/ San Antonio, TX 78284-7760 _/ _/ USA _/ _/ _/ _/ Tel: (210) 567-6623 _/ _/ Fax: (210) 567-6595 _/ _/ E-mail: raman@bioc01.uthscsa.edu _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ How can it be that mathematics, a product of human thought _/ _/ independent of experience, is so admirably adapted to the _/ _/ objects of reality? "-Albert Einstein" _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From owner-structural-nmr@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!uunet!newsfeed.ACO.net!info.univie.ac.at!helix!hs From: hs@helix.mdy.univie.ac.at (Hellfried Schreiber) Newsgroups: bionet.structural-nmr Subject: Conference Announcement Date: 2 Feb 1995 14:43:31 GMT Organization: Inst. for Theoretical Chemistry / Univ. of Vienna Lines: 64 Sender: hs@helix (Hellfried Schreiber) Distribution: world Message-ID: <3gqr2j$nrs@infosrv.edvz.univie.ac.at> NNTP-Posting-Host: helix.mdy.univie.ac.at >> INTERNATIONAL CONFERENCE ON MOLECULAR STRUCTURAL BIOLOGY << Organized by the Austrian Chemical Society Vienna (Austria), September 17-20, 1995 TOPICS: 1) The Impact of Molecular Biology on Structural Biology 2) Biomolecular Structure Determination a) X-Ray Diffraction b) NMR Spectroscopy 3) Dynamics and Function of Biomolecules 4) Computational Methods 5) Protein Engineering and Design Speakers include: Tom Blundell(UK), Hans-J. Boehm(D), Charles Cantor(USA), Christopher Dobson(UK), Manfred Eigen(D), Alan Fersht(UK), Robert Huber(D), Oleg Jardetzky(USA), Martin Karplus(USA), Joseph Lakowicz(USA), Paul Roesch(D), Ilme Schlichting(D), Jeffrey Skolnick(USA), Malcom Walkinshaw(CH) Posters are invited on any of the conference topics Outstanding posters will be selected for 20 minute oral presentations Abstract deadline: MAY 31, 1995 Head of Scientific Committee: P.Schuster Preliminary Participation Fees: Regular Participant 4000 ATS GOeCH Member 3500 ATS Student 2000 ATS For further information and preregistration, contact: A.Kungl Gesellschaft Oesterreichischer Chemiker AG Biophysikalische Chemie Nibelungengasse 11 A-1010 Wien, Austria Tel.: (43) 1 587249 FAX.: (43) 1 587966 e-mail: msb95@helix.mdy.univie.ac.at -- +-----------------------------------------------------------------------------+ | | | Hellfried Schreiber, Ph.D. | | | +---------------------------------------+-------------------------------------+ | | | | Institute for Theoretical Chemistry | | | Theoretical Biochemistry Group | Mail: hs@helix.mdy.univie.ac.at | | Waehrigerstrasse 17 | Voice: +43 1 40480 - 618 | | A-1090 Wien, Austria, Europe | FAX: +43 1 40285625 | | | | +-----------------------------------------------------------------------------+ From owner-structural-nmr@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!daresbury!trane.uninett.no!sunic!umdac!news From: peterl@umdix.umdc.umu.se (Peter Lundberg) Newsgroups: bionet.structural-nmr,sci.techniques.mag-resonance Subject: Re: Anyone who knows an ftp site to hold Pronto/3D ? Date: 2 Feb 1995 17:05:31 GMT Organization: Phys Chem, University of Umea, Sweden Lines: 62 Sender: -Not-Authenticated-[2976] Message-ID: <3gr3cr$1l0@kitten.umdc.umu.se> References: <3go4r9$lpm@news.uni-c.dk> <3gqiq4$25d@news.uni-c.dk> NNTP-Posting-Host: plgmac.chem.umu.se X-Posted-From: InterNews 1.0.1@plgmac.chem.umu.se Xdisclaimer: No attempt was made to authenticate the sender's name. Xref: biosci bionet.structural-nmr:408 sci.techniques.mag-resonance:612 In article <3gqiq4$25d@news.uni-c.dk> carlmk@unidhp.uni-c.dk (Mogens Kjaer) writes: > : >Summary: Does anyone know a place where I can put a version of Pronto/3D > : >Keywords: ftp, anonymous, Pronto > > : There is NMR related anonymous ftp site: ftp@nmrsg.biophys.upenn.edu > : Why don't you send it there? > Dear Mogens, How about the NMRFAM in Wisconsin (gopher.nmrfam,wisc.edu)? You could also try the EBI-ftp-site in UK (ftp.ebi.ac.uk). They have a lot of useful bio-related programs and should be interested? Here is the 'readme' info for your convenience: =========================== "Welcome to the EBI Molecular Biology Archives ! A large collection of databases, software and other information products for molecular biology can be found in /pub. Please take the time to read the README files provided in most directories of this FTP server. All README files are also collected and available in /pub/help. The directory /pub/contrib is for packages that are contibuted to the EBI for distribution. Authors who have tar or zip files of a program that works on different hardware platforms can use this directory. The directory /pub/databases contains a large number of various important data collections in molecular biology. The directory /pub/software contains free software for UNIX, VMS, Macintosh and DOS platforms. The directory /pub/doc contains various 'RFC' documents. Please feel free to contact us in case you have problems or if you have any suggestions how we can improve this service. Note: The EBI archives can also be accessed by Gopher at gopher.ebi.ac.uk, port 70, or by World-Wide Web at www.ebi.ac.uk" ====================== 73, Peter (from a dark corner of the EU empire) O==O ================================== O==O O==O Peter Lundberg O==O O==O Email: peterl@umdix.umdc.umu.se O==O O==O ============761.91141============= O==O From owner-structural-nmr@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!galaxy.ucr.edu!library.ucla.edu!agate!overload.lbl.gov!lll-winken.llnl.gov!uwm.edu!math.ohio-state.edu!howland.reston.ans.net!gatech!bloom-beacon.mit.edu!eru.mt.luth.se!news.luth.se!sunic!news.uni-c.dk!unidhp.uni-c.dk!carlmk From: carlmk@unidhp.uni-c.dk (Mogens Kjaer) Newsgroups: bionet.structural-nmr,sci.techniques.mag-resonance Subject: Pronto/3D available Date: 3 Feb 1995 07:41:34 GMT Organization: News Server at UNI-C, Danish Computing Centre for Research and Education. Lines: 37 Message-ID: <3gsmne$85m@news.uni-c.dk> NNTP-Posting-Host: unidhp.uni-c.dk Summary: List of FTP sites with Pronto/3D Keywords: pronto,ftp,license X-Newsreader: TIN [version 1.2 PL1] Xref: biosci bionet.structural-nmr:411 sci.techniques.mag-resonance:615 Hello, I've managed to upload the pronto program at the following sites: ================================================================= banyo.nmrfam.wisc.edu (144.92.18.12), /incoming/pronto - this site may change name to ftp.nmrfam.wisc.edu... nmr.utmb.edu, /pub/pronto nmrsg.biophys.upenn.edu, /contrib/pronto info.dfh.dk, /incoming/pronto Note, on some sites the program is located in the /incoming directory, so it might be moved/deleted if it turns out that the people there won't hold it there anyway. How to get a license: ===================== Fill out the lines in the file LICENSE, and email it to me. I'll send you the license code, also by email. No money needed. Mogens -- Mogens Kjaer Pronto Software - Development and Distribution Carlsberg Research Center Gamle Carlsberg Vej 10 DK-2500 Valby Denmark Phone: + 45 33 27 53 25 Fax: + 45 33 27 47 08 Email: carlmk@unidhp.uni-c.dk From owner-structural-nmr@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!atlas.rc.m-kasei.co.jp!yao From: yao@atlas.rc.m-kasei.co.jp (Toru YAO) Newsgroups: bionet.structural-nmr Subject: unscribe Date: 2 Feb 1995 19:11:03 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <9502030310.AA19016@atlas.rc.m-kasei.co.jp> NNTP-Posting-Host: net.bio.net unscribe str-nmr From owner-structural-nmr@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!NMR1.IOC.AC.RU!strel From: strel@NMR1.IOC.AC.RU ("Strelenko Yuri A.") Newsgroups: bionet.structural-nmr Subject: CALM - 8 (1/2) spins NMR spectra calculator/iterator .... Date: 3 Feb 1995 00:31:33 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 83 Sender: daemon@net.bio.net Distribution: world Message-ID: <54335.strel@nmr1.ioc.ac.ru> Reply-To: NNTP-Posting-Host: net.bio.net CALM CALM CALM CALM CALM CALM CALM CALM CALM CALM CALM CALM CALM CALM CALM Dear colleagues, I have a pleasure to inform you that now you can find via anonymous FTP on the Bruker Users Mail (BUM) server the iterative program CALM: Bloch.cchem.berkeley.edu (IP 128.32.144.132) in the directory: /pub/nmr/ms-dos/calm.zip: calm.exe calminst.exe calmview.exe manual.txt test.par test.spc test.sta u3.exe /pub/nmr/ms-dos/coder7.zip: coder7.exe coder7.hlp coder7.sta /pub/nmr/ms-dos/readme.asc (this message) /pub/nmr/ms-dos/select (should be FTPed and KERMITed as binary) This program calculates NMR spectra up to 8 spins (1/2) on the IBM compatible PC starting from AT286 with DOS 3.2 or higher. Should you have the experimental spectrum it is possible to do assignment and iterative analysis. In the same directory the program CODER7 can be used to prepare on PC the experimental spectrum in the internal calm's format from DISNMR, UXNMR and WinNMR formats and vice versa (moreover, from any format to any one). The program SELECT for Aspect 3000 should be called from DISNMR via PASC SELECT. It creates calm's format experimental spectrum file from the fixed region of the current spectrum in the current JOB. This file should be sent to PC by KERMIT or FASTRAN as FOREIGN (without -1 sector). The CALM is a copy protected program, so you must to install it using "install.exe" on your PC. All programs mentioned above were created some years ago by the RESONANCE Co. (Moscow, Russia) for needs of NMRists in N.D.Zelinsky Institute of Organic Chemistry. Now I have the permision from authors to distribute free this program for NMRist comunities. We were going to upgrate this programs for MS Windows, increase number of spins, include dipole-dipole and quadrupole constants but not found financial support for this project in Russia this time. The CALM authors are: Khlopkov V.N. (Resonance Co.) Kireev E. V. (Resonance Co.) Shakhatuni A.G. (Institute of Organic Chemistry, Armenian Academy of Science, Erevan, Armenia, e-mail: alexsh@gitak.armenia.su) The CODER7 author is: Krasavin A.O. (student of the Higher Chemical College, Russian Academy of Sciences, Moscow, e-mail: kras@nmr1.ioc.ac.ru) The SELECT author is: Khlopkov V.N. (Resonance Co.) Any questions concerning for the CALM and related programs should be sent to Strelenko Yu.A. via e-mail: strel@nmr1.ioc.ac.ru CALM CALM CALM CALM CALM CALM CALM CALM CALM CALM CALM CALM CALM CALM CALM With best wishes and kind regards, Yuri Strelenko. ********************************************************************* | Dr. Yuri A. Strelenko | | | N.D.Zelinsky Institute | Fax (7-095) 135 5328 | | of Organic Chemistry, | Tel (7-095) 135 9094 | | Leninsky prospect 47, | e-mail strel@nmr1.ioc.ac.ru | | 117913 Moscow B-334, | | | Russia | | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ From owner-structural-nmr@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: Andre Padilla Newsgroups: bionet.structural-nmr Subject: CINDY_NMR_program Date: 3 Feb 1995 09:07:25 -0000 Lines: 30 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3gsrod$rk@mserv1.dl.ac.uk> Original-To: str-nmr@dl.ac.uk _/_/_/ _/ _/_/ _/ _/_/_/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/_/ _/ _/ _/ _/_/ _/ _/ _/ _/_/_/ _/ _/ _/_/ _/_/_/ _/ Program for analysis of NMR spectra The file CINDY.tar.Z is a demonstration version of the program CINDY. It includes help and tutorial files, but has some limits ! CINDY works only on SGI. CINDY is a program used for assignment of nuclear magnetic resonance spectra of macromolecules. This version is distributed freely. The program is available from anomymous ftp at : groupe-rmn@tome.cbs.univ-montp1.fr _______________________________________________________________________________ Andre' Padilla Centre de Biochimie Structurale andre@cbs.univ-montp1.fr Faculte de Pharmacie tel : (33) 67 04 34 33 34060 Montpellier cedex fax : (33) 67 52 96 23 FRANCE From owner-structural-nmr@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!BIOC01.UTHSCSA.EDU!raman From: raman@BIOC01.UTHSCSA.EDU (C.S.RAMAN) Newsgroups: bionet.structural-nmr Subject: Postdoctoral Position in Biomolecular NMR Date: 3 Feb 1995 15:36:58 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 53 Sender: daemon@net.bio.net Distribution: world Message-ID: <9502032336.AA02448@bioc01.uthscsa.edu> NNTP-Posting-Host: net.bio.net A newly established laboratory in Sydney, Australia seeks a postdoctoral associate to pursue studies on biomolecular recognition, especially the structure, dynamics and interactions of nucleic acids. The position is initially available for three years, renewed annually, with a suggested salary in the range $A 37,345-40,087 p.a. Candidates should have a solid background in hands-on NMR, preferably with experience in multidimensional biomolecular experiments, although appropriately-qualified chemists with an interest in moving into biomolecular work will be considered. Strong computational skills are a bonus. The associate will work with other members of a small group with active projects in C-13 relaxation analysis of nucleic acid motions, discovery of new RNA structures/activities using SELEX methods and analysis of protein/nucleic acid-ligand interactions. Further projects are under development. Spectrometer and computational facilities are very good. The lab has major use of a Bruker DMX-600 equipped with x,y,z gradients, and secondary use of a Bruker DMX-500 equipped with a z gradient. The two Biochemistry NMR labs share a small workstation cluster which includes an SGI R8000 Indigo2, an Indigo2 Extreme, an Indy and two older Personal Irises. These systems currently run a range of Biosym, Molecular Simulations Inc. and academic software. Please direct enquiries to Dr. Garry C. King: School of Biochemistry and Molecular Genetics The University of New South Wales Sydney 2052 Australia Ph: 61-2-385-2021 Fax: 61-2-313-6271 Email: garry@bioc.unsw.edu.au -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ C.S.RAMAN _/ _/ Department of Biochemistry _/ _/ University of Texas Health Science Center _/ _/ 7703 Floyd Curl Drive _/ _/ San Antonio, TX 78284-7760 _/ _/ USA _/ _/ _/ _/ Tel: (210) 567-6623 _/ _/ Fax: (210) 567-6595 _/ _/ E-mail: raman@bioc01.uthscsa.edu _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ How can it be that mathematics, a product of human thought _/ _/ independent of experience, is so admirably adapted to the _/ _/ objects of reality? "-Albert Einstein" _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From owner-structural-nmr@net.bio.net Fri Feb 03 22:00:00 1995 Path: biosci!PUCC.PRINCETON.EDU!PMCDONNE%ALLOY.BITNET From: PMCDONNE%ALLOY.BITNET@PUCC.PRINCETON.EDU Newsgroups: bionet.structural-nmr Subject: 300MHz nmr Date: 3 Feb 1995 12:27:28 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: <199502032027.MAA18987@net.bio.net> Dear netters, Does any one know of a company that sells refurbished NMRs? We are interested in getting a 300 MHz instrument that would perform 1H and 13C. Thanks, Patty McDonnell pmcdonnell@alloy.bitnet RWJ Pharmaceutical Research Institute From owner-structural-nmr@net.bio.net Fri Feb 03 22:00:00 1995 Path: biosci!bath.ac.uk!N.C.Chan From: N.C.Chan@bath.ac.uk (N C Chan) Newsgroups: bionet.structural-nmr Subject: subscribe Date: 3 Feb 1995 04:02:58 -0800 Organization: University of Bath Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <9502031200.aa11727@ss1.bath.ac.uk> subscribe From owner-structural-nmr@net.bio.net Fri Feb 03 22:00:00 1995 Path: biosci!NMR1.IOC.AC.RU!strel From: strel@NMR1.IOC.AC.RU ("Strelenko Yuri A.") Newsgroups: bionet.structural-nmr Subject: DISNMR - 94 .... Date: 3 Feb 1995 05:03:50 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 41 Sender: daemon@net.bio.net Distribution: world Message-ID: <69060.strel@nmr1.ioc.ac.ru> Reply-To: Dear colleagues, Bruker Analytische Messtechnik GmbH have the honour of informing you that the newest version of DISNMR programs are available on the Bruker's FTP-server: ftp.bruker.de (IP 149.236.1.1) in the directories: pub/nmr/disnmr/disn94 pub/nmr/disnmr/disb94 pub/nmr/disnmr/disr94 All files from diskettes were combined into libraries by the program LIB.2000/LIB.3004 and can be extracted by the same program. For user convenience every library file is supplied by the text file with the same name and extension .EXE. This EXE file should be started on the Aspect 2000/3000 to extract files from the library: *EXE DISN94.EXE (for example). Both library file and appropriated .EXE file are combined into a single archive file with the same name and .zip extension. So, this .zip file should be 'got' as binary by FTP, 'pkunziped' and sent to the Aspect by KERMIT or FASTRAN - the library file in binary format and the EXE file as ASCII. Note, that the program LIB.2000/LIB.3004 must be on the Aspect 2000/3000 disk. You can get it from the same directory via FTP as binary. All files were prepared in N.D.Zelinsky Institute of Organic Chemistry (Moscow, Russia) according to agreement with Bruker Analytische Messtechnik GmbH. Any questions should be sent to Dr. Yuri A. Strelenko via e-mail: strel@nmr1.ioc.ac.ru ********************************************************************* | Dr. Yuri A. Strelenko | | | N.D.Zelinsky Institute | Fax (7-095) 135 5328 | | of Organic Chemistry, | Tel (7-095) 135 9094 | | Leninsky prospect 47, | e-mail strel@nmr1.ioc.ac.ru | | 117913 Moscow B-334, | | | Russia | | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ From owner-structural-nmr@net.bio.net Sat Feb 04 22:00:00 1995 Newsgroups: bionet.structural-nmr Path: biosci!bcm!cs.utexas.edu!swrinde!pipex!uunet!sangam!iitb!powai!rama From: rama@powai.cc.iitb.ernet.in (ramakrishna) Subject: test mail Message-ID: Date: Sun, 5 Feb 1995 18:09:38 GMT Organization: Computer Centre, Indian Institute of Technology, Bombay X-Newsreader: TIN [version 1.2 PL2] Lines: 4 this is a test mail. someone kindly acknowlegde this mail. it assures me that i can access this group and participate in this group. From owner-structural-nmr@net.bio.net Sat Feb 04 22:00:00 1995 Newsgroups: bionet.structural-nmr From: Paul@pdchem.demon.co.uk (Paul Davis) Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!peernews.demon.co.uk!pdchem.demon.co.uk!Paul Subject: Naive protein question Organization: Myorganisation Reply-To: Paul@pdchem.demon.co.uk X-Newsreader: Demon Internet Simple News v1.29 Lines: 14 X-Posting-Host: pdchem.demon.co.uk Date: Sun, 5 Feb 1995 00:04:44 +0000 Message-ID: <791942684snz@pdchem.demon.co.uk> Sender: usenet@demon.co.uk Hello, I would like to know what is the current capabilty of protein nmr for complete structure determination, and for gaining useful contraints for use in model-building. For example, how many residues can be accommodated, and how dilute can the solution be? I have become rather out of touch with these things, and would be interested to gain a little insight into what can be accomplished at the forefront of the technology. Thank you for your time, -Paul -------------------------------------------------------------------- Paul Davis paul@pdchem.demon.co.uk From owner-structural-nmr@net.bio.net Sun Feb 05 22:00:00 1995 Path: biosci!rutgers!uwm.edu!caen!newsxfer.itd.umich.edu!agate!nntp-ucb.barrnet.net!nntp-hub.barrnet.net!barrnet.net!syntex.com!usenet From: Mike@arvax.syntex.com Newsgroups: bionet.structural-nmr Subject: Re: 300MHz nmr Date: Mon, 06 Feb 95 08:24:52 PDT Organization: SYNTEX (U.S.A.) Inc. Lines: 8 Message-ID: <3h5im5$9sq@yoda.Syntex.Com> References: <199502032027.MAA18987@net.bio.net> NNTP-Posting-Host: mlmpc.syntex.com Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Newsreader: NEWTNews & Chameleon -- TCP/IP for MS Windows from NetManage In article <199502032027.MAA18987@net.bio.net>, writes You might try: MR Resources 158R Main St Gardner, MA 01440 (508) 632=7000 From owner-structural-nmr@net.bio.net Sun Feb 05 22:00:00 1995 Path: biosci!UGA.CC.UGA.EDU!JLEE From: JLEE@UGA.CC.UGA.EDU (John Lee) Newsgroups: bionet.structural-nmr Subject: naive protein question Date: 5 Feb 1995 08:05:00 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <950205.110646.EST.JLEE@UGA.CC.UGA.EDU> In response to the query by Paul Davis, the group may be interested in a discussion I had yesterday with Robert Huber (I kid you not!). His opinion is that the present limit for a meaningful protein structure is 15 kD. He says that the NMR result does not have sufficient accuracy for a meaningful result on structure that one can interpret in terms of a biochemical function. NMR does have power in terms of changes that may occur in solution and of information on protein dynamics and that is where everyone should be directing their attention. I'm ready for the flames! John Lee Department of Biochemistry University of Georgia Athens GA 30602-7229 USA Phone 706-542-3298 FAX 706-542-1738 From owner-structural-nmr@net.bio.net Sun Feb 05 22:00:00 1995 Newsgroups: bionet.structural-nmr Path: biosci!adam.cc.sunysb.edu!news.sprintlink.net!howland.reston.ans.net!news.cac.psu.edu!news.pop.psu.edu!hudson.lm.com!godot.cc.duq.edu!newsfeed.pitt.edu!uunet!sangam!iitb!powai!rama From: rama@powai.cc.iitb.ernet.in (ramakrishna) Subject: thanks for the response Message-ID: Date: Mon, 6 Feb 1995 16:49:22 GMT Organization: Computer Centre, Indian Institute of Technology, Bombay X-Newsreader: TIN [version 1.2 PL2] Lines: 3 dear netters, thanks for the response for my test mail. From owner-structural-nmr@net.bio.net Sun Feb 05 22:00:00 1995 Newsgroups: bionet.structural-nmr Path: biosci!ns1.faseb.org!darwin.sura.net!nih-csl!loglady.ninds.nih.gov!johnk From: johnk@spasm.niddk.nih.gov (John Kuszewski) Subject: Re: naive protein question Message-ID: <1995Feb6.194252.853@alw.nih.gov> Sender: postman@alw.nih.gov (AMDS Postmaster) Reply-To: johnk@spasm.niddk.nih.gov (John Kuszewski) Organization: National Insts. of Health References: <950205.110646.EST.JLEE@UGA.CC.UGA.EDU> Date: Mon, 6 Feb 1995 19:42:52 GMT Lines: 53 In article <950205.110646.EST.JLEE@UGA.CC.UGA.EDU>, JLEE@UGA.CC.UGA.EDU (John Lee) writes: |> In response to the query by Paul Davis, the group may be interested in a |> discussion I had yesterday with Robert Huber (I kid you not!). His |> opinion is that the present limit for a meaningful protein structure is |> 15 kD. He says that the NMR result does not have sufficient accuracy for |> a meaningful result on structure that one can interpret in terms of a |> biochemical function. |> NMR does have power in terms of changes that may occur in solution and |> of information on protein dynamics and that is where everyone should be |> directing their attention. |> I'm ready for the flames! |> First, in response to the original questions, NMR structural work is usually done with ~0.5 ml of ~1 mM solutions. The current limit is ~18-25 kD (depending on how nicely the sample behaves and so on, and what you're willing to call a "structure"). But I'm not sure what you mean about the limit of NMR structures' accuracy as the size gets above 15 kD. In most cases, the RMSD between NMR structures and crystal structures is about as big as among crystal structures of the same protein solved by different groups (for example, interleukin 1 beta). A good argument can be (and has been) made that "high resolution" NMR structures are about equal to 2 Angstrom crystal structures. I certainly don't see why the accuracy of a structure should drop as the MW goes above 15 kD. Because of overlap and relaxation, it might be difficult to get many NOEs (and therefore high precision), that should have nothing to do with the accuracy of the structural constraints. And certainly in terms of "being able to interpret structures in terms of biochemical function," if you've been reading bionet.molbio.proteins lately, you'll see that molecular biologists can often be satisfied with extremely low resolution models. If I'm missing something, I'd love to learn what it is. -- _____________ | ___/_ | |/ / -- /\ // /-- || || / /|| || || / / || || ||/ / || John Kuszewski || |/ /| || johnk@spasm.niddk.nih.gov || / /|| || \/ / / || \/ that's MISTER protein G to you! |/__/| | /_________| From owner-structural-nmr@net.bio.net Sun Feb 05 22:00:00 1995 Path: biosci!news.cs.umb.edu!hsdndev!purdue!mozo.cc.purdue.edu!cv4.chem.purdue.edu!lev From: "Lev A. Gorenstein" Newsgroups: bionet.structural-nmr Subject: Re: naive protein question Date: Mon, 6 Feb 1995 09:56:03 -0500 Organization: Purdue University Lines: 14 Message-ID: References: <950205.110646.EST.JLEE@UGA.CC.UGA.EDU> NNTP-Posting-Host: cv4.chem.purdue.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In-Reply-To: <950205.110646.EST.JLEE@UGA.CC.UGA.EDU> In response to the query by Paul Davis, nice references: Gerhard Wagner, Journal of Biomolecular NMR, 3(1993), pp.375-385. "Prospects for NMR of Large Proteins" ______________________________________________________________________________ Lev A. Gorenstein Dept. of Chemistry, Purdue University *~~~~ ____ |~~~~~~~~~~~~~| W.Lafayette, IN 47907, USA Y_,___|[]| | Go Boilers! | (317)494-9150; Fax (317)494-0239 {|_|_|_|PU|_,_|_____________| lev@chem.purdue.edu //oo---OO=OO OOO OOO ------------------------------------------------------------------------------ From owner-structural-nmr@net.bio.net Mon Feb 06 22:00:00 1995 Newsgroups: bionet.structural-nmr Path: biosci!galaxy.ucr.edu!ratatosk.yggdrasil.com!news.duke.edu!godot.cc.duq.edu!hudson.lm.com!news.pop.psu.edu!news.cac.psu.edu!howland.reston.ans.net!lamarck.sura.net!darwin.sura.net!nih-csl!loglady.ninds.nih.gov!johnk From: johnk@spasm.niddk.nih.gov (John Kuszewski) Subject: Re: naive protein question Message-ID: <1995Feb6.194252.853@alw.nih.gov> Sender: postman@alw.nih.gov (AMDS Postmaster) Reply-To: johnk@spasm.niddk.nih.gov (John Kuszewski) Organization: National Insts. of Health References: <950205.110646.EST.JLEE@UGA.CC.UGA.EDU> Date: Mon, 6 Feb 1995 19:42:52 GMT Lines: 53 In article <950205.110646.EST.JLEE@UGA.CC.UGA.EDU>, JLEE@UGA.CC.UGA.EDU (John Lee) writes: |> In response to the query by Paul Davis, the group may be interested in a |> discussion I had yesterday with Robert Huber (I kid you not!). His |> opinion is that the present limit for a meaningful protein structure is |> 15 kD. He says that the NMR result does not have sufficient accuracy for |> a meaningful result on structure that one can interpret in terms of a |> biochemical function. |> NMR does have power in terms of changes that may occur in solution and |> of information on protein dynamics and that is where everyone should be |> directing their attention. |> I'm ready for the flames! |> First, in response to the original questions, NMR structural work is usually done with ~0.5 ml of ~1 mM solutions. The current limit is ~18-25 kD (depending on how nicely the sample behaves and so on, and what you're willing to call a "structure"). But I'm not sure what you mean about the limit of NMR structures' accuracy as the size gets above 15 kD. In most cases, the RMSD between NMR structures and crystal structures is about as big as among crystal structures of the same protein solved by different groups (for example, interleukin 1 beta). A good argument can be (and has been) made that "high resolution" NMR structures are about equal to 2 Angstrom crystal structures. I certainly don't see why the accuracy of a structure should drop as the MW goes above 15 kD. Because of overlap and relaxation, it might be difficult to get many NOEs (and therefore high precision), that should have nothing to do with the accuracy of the structural constraints. And certainly in terms of "being able to interpret structures in terms of biochemical function," if you've been reading bionet.molbio.proteins lately, you'll see that molecular biologists can often be satisfied with extremely low resolution models. If I'm missing something, I'd love to learn what it is. -- _____________ | ___/_ | |/ / -- /\ // /-- || || / /|| || || / / || || ||/ / || John Kuszewski || |/ /| || johnk@spasm.niddk.nih.gov || / /|| || \/ / / || \/ that's MISTER protein G to you! |/__/| | /_________| From owner-structural-nmr@net.bio.net Mon Feb 06 22:00:00 1995 Path: biosci!MED.UNC.EDU!sheng From: sheng@MED.UNC.EDU (Sheng Zhong) Newsgroups: bionet.structural-nmr Subject: www address for any reference you want Date: 6 Feb 1995 21:13:00 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <9502070512.AA17976@hasty.med.unc.edu> NNTP-Posting-Host: net.bio.net Dear netters, I posted a request for NMR book list few weeks ago. I have got some list which are not complete. However, I've found nice www address that will allow one to find almost any book (or other reference) he want. The address is, http://sunsite.unc.edu/reference/ I am sorry to say that I don't have the time to complete NMR book list from those Libraires now, but I think this reference source will help us a lot in the future. Good luck, Dr Sheng Zhong Dept of Biochem & Biophys UNC at Chapel Hill sheng@med.unc.edu From owner-structural-nmr@net.bio.net Mon Feb 06 22:00:00 1995 Newsgroups: bionet.structural-nmr Path: biosci!galaxy.ucr.edu!ratatosk.yggdrasil.com!news.duke.edu!godot.cc.duq.edu!newsfeed.pitt.edu!uunet!sangam!iitb!powai!rama From: rama@powai.cc.iitb.ernet.in (ramakrishna) Subject: thanks for the response Message-ID: Date: Mon, 6 Feb 1995 16:49:22 GMT Organization: Computer Centre, Indian Institute of Technology, Bombay X-Newsreader: TIN [version 1.2 PL2] Lines: 3 dear netters, thanks for the response for my test mail. From owner-structural-nmr@net.bio.net Mon Feb 06 22:00:00 1995 Path: biosci!galaxy.ucr.edu!ratatosk.yggdrasil.com!news.duke.edu!godot.cc.duq.edu!hudson.lm.com!news.pop.psu.edu!news.cac.psu.edu!howland.reston.ans.net!news.starnet.net!wupost!newspump.wustl.edu!fas-news.harvard.edu!hsdndev!purdue!mozo.cc.purdue.edu!cv4.chem.purdue.edu!lev From: "Lev A. Gorenstein" Newsgroups: bionet.structural-nmr Subject: Re: naive protein question Date: Mon, 6 Feb 1995 09:56:03 -0500 Organization: Purdue University Lines: 14 Message-ID: References: <950205.110646.EST.JLEE@UGA.CC.UGA.EDU> NNTP-Posting-Host: cv4.chem.purdue.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In-Reply-To: <950205.110646.EST.JLEE@UGA.CC.UGA.EDU> In response to the query by Paul Davis, nice references: Gerhard Wagner, Journal of Biomolecular NMR, 3(1993), pp.375-385. "Prospects for NMR of Large Proteins" ______________________________________________________________________________ Lev A. Gorenstein Dept. of Chemistry, Purdue University *~~~~ ____ |~~~~~~~~~~~~~| W.Lafayette, IN 47907, USA Y_,___|[]| | Go Boilers! | (317)494-9150; Fax (317)494-0239 {|_|_|_|PU|_,_|_____________| lev@chem.purdue.edu //oo---OO=OO OOO OOO ------------------------------------------------------------------------------ From owner-structural-nmr@net.bio.net Mon Feb 06 22:00:00 1995 Path: biosci!galaxy.ucr.edu!library.ucla.edu!agate!newsxfer.itd.umich.edu!gatech!bloom-beacon.mit.edu!eru.mt.luth.se!news.luth.se!sunic!news.uni-c.dk!unidhp.uni-c.dk!carlmk From: carlmk@unidhp.uni-c.dk (Mogens Kjaer) Newsgroups: bionet.structural-nmr,sci.techniques.mag-resonance Subject: Pronto FAQ 950207 Date: 7 Feb 1995 13:19:10 GMT Organization: News Server at UNI-C, Danish Computing Centre for Research and Education. Lines: 519 Message-ID: <3h7s0e$597@news.uni-c.dk> NNTP-Posting-Host: unidhp.uni-c.dk Summary: FAQ for Pronto Keywords: FAQ, Pronto X-Newsreader: TIN [version 1.2 PL1] Xref: biosci bionet.structural-nmr:427 sci.techniques.mag-resonance:619 =============================================== ###### # # ##### #### # # ##### #### # # # # # # ## # # # # ###### # # # # # # # # # # # ##### # # # # # # # # # # # # # # ## # # # # # # #### # # # #### ####### # ##### # # # # # # # # # # ##### # # # # # ####### # # # # # # # # # # # #### # ##### ####### ### ##### ### ####### # # # # # # # # # # # # # # # # # # # # ###### ###### # # ##### # # # # # # # # # # # # # # # # # # # # # ##### ##### ### ####### ### # =============================================== Frequently asked questions about the Pronto program - and their answers: History: This is version 950207. The first release of this FAQ. There are no specific plans for where and how often this is released. Contents: 1. What is Pronto/3D? 1.1 What is Pronto/3D^2? 2. Where can I find Pronto/3D? 3. What kind of spectra can Pronto read? 3.1 Where should the spectra be located? 4. What is MNMR? 5. Misc. questions: 5.1 Help, my screen is full of windows! 5.2 How do I use the backups? 5.3 Why does Pronto use so much memory? 5.4 Why can't I zoom in the contour diagram using the mouse? 5.5 How do I analyze a series of NOESY spectra? 5.6 How do I read in the assignments I already have made? 5.7 Why doesn't the measure distance tool work? 5.8 How do I change colors and fonts? 5.9 Why doesn't the help system work? 6. Future plans? 7. Where can I get further information? Q1: What is Pronto/3D? Pronto: The PROtein Nmr TOol Pronto/3D is a computer program, running on UNIX workstations. The interface to the program uses X-Windows. All information obtained about the moleculed studied is maintained in a data base. The input to the program is a series of processed nD spectra (n>1). The output from the program is a list of constraints to be used in structure calculations. The program was primarily designed to handle spectra of peptides and proteins, but has also been used to assign carbohydrates and nucleic acids. The program has the following main features: a. Display of spectra. One or more spectra can be displayed in one or more windows simultaneously. Cross peaks are labeled. 2D and 3D spectra can be contoured in the same window. b. Locating cross peaks. This can be done automatically or inter- actively. c. Build up of spin systems. Starting from a single cross peak, e.g. a HN-HA peak in a COSY spectrum, the rest of the spin system is built using the cross peaks in the data base. 2D and 3D spectra can be used. Spin systems identified as a specific residue can be labeled so, or as belonging to a class of residues, e.g. an AMX spin system. d. Assign cross peaks. Identify the atoms to which a certain cross peak is linked. A PDB structure file can be consulted to measure atom distances. e. Sequential assignments. Spin systems are linked together using assigned or unassigned cross peaks. The primary sequence is consulted to match residue types. f. A set of check routines are used to find possible errors in the assignment process, i.e. multiple assigned cross peaks. g. Tools for integrating cross peaks and measurement of coupling constants. h. Report facilities for printing or plotting out information. A list of assigned NOE's and their intensity class can be produced, ready for an X-PLOR calculation. Currently, versions for Silicon Graphics and Sun SPARC workstations are distributed. Pronto was designed in a collaboration between Carlsberg Laboratory, CRI A/S, and Bruker Analytische Messtechnik, GmbH. After the design phase, Pronto Software - Development and Distribution was set up at Carlsberg Research Center to handle distribution and further development. This was made in close contact with people doing protein and carbohydrate NMR at Carlsberg Laboratory, using the Pronto program in the assignment phase. At January 1, 1995, the Pronto Software - Development and Distribution project was closed, and Pronto/3D, version 930401, is now available by anonymous ftp for all interested. Q1.1: What is Pronto/3D^2? Pronto/3D^2 is the latest version of Pronto. A few bugs in the 930401 version has been corrected, some tools for the analysis of triple resonance spectra have been added, and mainly, a tool for the display of structures. The structure display facility can show one or more structures simultaneously, as sticks, balls, cartoons, or ribbons. Lines showing NOE's between atoms can be shown. The structure display window can work on an X11 terminal, but better results are obtained on a Silicon Graphics workstation, running GL. Currently, Pronto/3D^2 has the status of being a commercial program, the price being 2000 US$ for academics and 3500 US$ for non-academics, but work is in progress to make it public domain. Q2. Where can I find Pronto/3D? Pronto/3D, version 930401, is available at the following FTP sites: Address: Directory: ftp.nmrfam.wisc.edu /pub/pronto nmr.utmb.edu /pub/pronto nmrsg.biophys.upenn.edu /contrib/pronto info.dfh.dk /incoming/pronto The program is stored in a gzip'ed tar file. The 930401I.tar.gz file contains the SGI version, and 930401S.tar.gz contain the Sun SPARC version. A PostScript file with the manual is stored in the manual subdirectory. Two files exist, one formatted for letter size paper and one for A4 sized paper. The manual is approx. 20 Mb when uncompressed, due to a number of screen dumps in the file. The manual is 117 pages. Q3. What kind of spectra can Pronto read? Pronto can read spectra processed by the following software: a. MNMR This is the library of programs used at the Carlsberg Laboratory for processing of NMR spectra. See later in this FAQ. b. Felix Felix files, compressed or uncompressed .mat files are read. c. Varian files. d. NMR2 files. NMR2 files are not in submatrix format. Contouring of non-submatrix spectra uses a lot of memory. e. Spectra processed by UXNMR or Xspec from Bruker or Spectrospin. - I think that there are still some problems when some of the parameter files are in binary, and some in ASCII... Q3.1 Where should the spectra be located? Pronto determines the type of the spectrum from the directory in which it is found. Each spectrum location is identified by the following parameters, set up in the spectrum catalog in Pronto: Max. 15 characters Max. 15 characters Max. 15 characters Specify an integer Specify an integer Note, not all of the parameters are used for all file formats. The character based parameters may contain the "/" character, specifying an extra subdirectory level. a. MNMR: //nmr//data/ b. Felix: //felix//data/ c. Varian: ///exp/datdir/phasefile d. NMR2: //nmri//data/ e. UXNMR et al.: 2D: //data//nmr///pdata//2rr 3D: //data//nmr///pdata//3rrr Note, also the files: acqus, acqu2s, acqu3s, proc, procs, proc2, proc2s, proc3, proc3s are necessary (the files containing "3" only for 3D spectra). Example: To read the MNMR file /usr/people/nmr/mk/data/COSY.2x2 specify the following parameters: disk: usr/people user: mk name: COSY.2x2 The expno and procno numbers are not used. If the directory layout does not match yours, try setting up some symbolic links. Remember the 15 character limit on the disk, user, and name fields. Q4. What is MNMR? MNMR (Multidimensional NMR) is a set of programs for the processing of nD spectra. n is greater than one, and (currently) less than or equal to ten. MNMR contains programs for: FFT (reading various types of FID files): The program does one dimension at a time, applying the window function, linear prediction phase correction, etc. Determine constants for phase correction Display of 3D spectra Making contour plots Baseline corrections Calculation of relaxation parameters Calculation of projections A set of routines to read and write spectrum files are provided. Use them for your own programs! MNMR is distributed as source code only! You'll need a C and a FORTRAN compiler in order to use the system. You probably would have to spend some time to modify the Makefiles to make it compile on your system. The system compiles on Silicon Graphics, Sun SPARC, IBM RS/6000, and HP workstations. You might need to obtain some fft libraries from various other ftp sites. Currently, MNMR has not been put on an anonymous ftp server. Send me a mail, and I'll send you the tar archive as a uuencoded, gzip'ed file. The size of this file is 1.4 Mb. Q5. Misc. questions: Q5.1 Help, my screen is full of windows! The first impression people get when they watch a demonstration of the program, or watching someone actually using the program is: Why all those windows? However, when you actually use the program, this is really not a problem. There are some things to remember: a. Close the windows not in use. b. Use a smaller font if the windows are too big. c. Start Pronto/3D with the flag "-2d" or "-3d" if you are only analysing 2D or 3D spectra: Some of the windows will be smaller in this case. d. Open the window survey window to see a list of windows currently open. e. Opening a lot of windows with small fonts makes it more difficult for you boss to see what you are doing... :-) The Pronto/3D^2 program stores a list of windows that were open when you exit, and reopens them at the same place the next time. Q5.2 How do I use the backups? This might sound simple, but we have had cases where people have lost several weeks of work because they used the backup system in a wrong manner. When Pronto/3D is running, it works on a copy of the data base, located in the directory pointed out by the environment variable PRONTO_WORK. If the machine crashes during this, the copy of the data base in PRONTO_WORK is left in an unknown state, and can't/shouldn't be used further. When you exit Pronto/3D, you can save a copy of the PRONTO_WORK data base in another directory. Do this! If you start Pronto/3D with the command: "Pronto" or "Pronto -2D", it will continue to work on the data base in PRONTO_WORK, if Pronto/3D was exited correctly the last time. You can also start with the command "Pronto ", and the contents of PRONTO_WORK will be overwritten with a copy of the data base stored under . Pressing "Backup" in the Pronto/3D program does the following: The access to the data base is closed, and the contents of PRONTO_WORK is stored under the name: backup. After a system crash, the contents of backup can be reloaded by starting the program by: "Pronto backup". The backup will be reloaded into PRONTO_WORK: Now comes the important thing: If you do this, you are adviced to exit Pronto/3D immediately, and store the data base under a new name. Never make it a habbit to start Pronto/3D with "Pronto backup" unless you really need to reload the backup. The scene when people have lost data was as follows: The user presses backup in Pronto/3D. The machine crashes during this. Now, it is important to remember that in this case, the contents of PRONTO_WORK will be OK, and the contents of the backup directory will miss some data. So, if the program is started with "Pronto backup", the good data base in PRONTO_WORK will be overwritten with the partial data base in backup! So: Press backup often! Store under a name when you exit Pronto/3D Clean up old data bases in the PRONTO_DATA directory Think before starting "Pronto backup" Q5.3 Why does Pronto use so much memory? During the contouring process, the last set of contours are stored as vectors in Pronto/3D. This area is released, when new contours are plotted. However, the memory is not released from the running process. The release storage is reused, but can sometimes get so fragmented that new storage is necessary to hold new contours. If you often contour large areas, you might need to exit and enter Pronto a couple of times during the day. The contouring in Pronto/3D has been specifically designed to make it fast to contour small (e.g. 0.1x0.1 ppm) areas quickly. Use the mcnt program in MNMR (also distributed with Pronto/3D) to contour whole spectra. Q5.4 Why can't I zoom in the contour diagram using the mouse? This is normally not needed. In most cases, the contouring regions are set by importing ppm values from the other windows in Pronto/3D. The ppm values are taken from the cross peak list, the spin system list, the spin system buildup tool, or from the cross peak assignment tool. You can move up, down, left, or right and zoom in and out by using the arrows and other buttons in the contouring setup window. During manual cross peak identification, these buttons are used to contour the spectrum in 1x1 ppm areas to locate the cross peaks. Q5.5 How do I analyze a series of NOESY spectra? Start by assigning the cross peaks in ONE of the spectra. Use the one in a series with the most intense peaks. Use the "copy" button in the spectrum catalog window to copy all information (including cross peaks and assignments) to a new spectrum name, and insert the information about the new spectrum. Now you can reintegrate the new spectrum, using the same cross peak positions and integration limits as used for the first spectrum. Q5.6 How do I read in the assignments I already have made? Pronto/3D does not contain any direct way of importing information like cross peaks or spin system assignments. An indirect way exists: When Pronto/3D data bases are converted from one version of the program to a newer version, a temporary, ASCII representation of the data base is used. This is created by the $PRONTO_DIR/$PRONTO_VER/prog/expIO program. This is inserted in the new data base using the corresponding impIO program. In theory, one could code the assignments in this undocumented ASCII format and insert (impIO appends to the data base) it into the database. However, you must be careful as little check is done by the impIO program for inconsistencies, etc. The way of doing it manually is as follows: To insert a spin system in Pronto/3D, fill in the ppm values of all the atoms in the spin system in the contouring setup window and display the spin system in small windows. If the ppm list is correct, you should see the relevant cross peaks in the center of each subwindow. Now it is easy to click in the new peaks and build the spin system using the spin system assignment tool. Q5.7 Why doesn't the measure distance tool work? This is a very old bug in the program, still only partially solved. It normally only shows up when we demonstrate the program for people, or when some of the programmers are looking the other way. In order for the distance to be measured, the following should be done: A PDB file should be specified, "Dist On" should be set for exactly two dimensions, and an atom should be selected in each of the two, selected dimensions. If the bug appear, the program still doesn't show any distances. Closing and reopening the window might help... Also, I think the problem is related to starting Pronto/3D with the "-2D" or "-3D" switch. Q5.8 How do I change colors and fonts? Most colors are controlled by the Pronto resource file. This is by default the file: $PRONTO_DIR/$PRONTO_VER/Resources/pronto_res You can make your own copy of this file and set the environment variable PRONTO_RES to point to the directory containing the file. The fonts used for the display of Pronto windows can be set in your own .Xdefaults file: prontoIO*font: -misc-fixed-medium-r-normal--20-*-*-*-c-*-iso8859-1 saveloadIO*font: -misc-fixed-medium-r-normal--15-*-*-*-c-*-iso8859-1 Change "IO" after pronto to "SO" for the SPARC version. The resource file generally contain a section for each window or tool in Pronto/3D. Most of the definitions in this file is the text displayed in the buttons in Pronto/3D. Some user relevant definitions: *Cur_wnd_color: Background color of current window *Add_wnd_color: Background color of additional window *##_lines: Number of browser lines in the ## window *cnt_cache: Number of sets of contours cached *cnt_color0: Colors for contouring *cntp_cnt.labelFont: Font used when cross peaks a labelled with cross & text *cntp_cnt.axisColor: Color number used to draw the axes Definitions only relevant to Pronto/3D^2: *stp_plot.labelFont: Font used to label atoms drawn by X11 *stp_plot.fontSize: Size of font, in points *stp_plot.fmFont: Font used by GL *stp_plot.rGBMode: Use RGB mode? *stp_plot.doubleBuffer: Use double buffering? *stp_plot.zBuffer: Use Z-buffer? *stp_plot.depthCue: Do depth cueing? *stp_plot.zClip: Clip in z dimension? *stp_plot.dcZmin: Z minimum for clip *stp_plot.dcZmax: Z maximum for clip *struc_color0: Colors of atoms... *smooth_factor: Smoothing of the spline function. *swidth: Width of sheet. *sthick: Thickness of sheet. *rthick: Thickness of ribbon. *nsubdiv: No. of subdivisions of sheet plots. *halfBond: Plot half bond from atoms. Normally, a bond is only plotted if both of the atoms involved are selected. If this is set to true, you will see a "half" bond going out from each selected atom. *nwormdiv: No. of subdivisions for worm display. Q5.9 Why doesn't the help system work? This is first implemented in the Pronto/3D^2 version. Don't use the help button in version 930401; the program might crash! Q6. Future plans? Currently, we are working on an improvement on Pronto/3D^2 making it possible to write BASIC-like programs running in the data base environment. This is called Pronto Interactive Language System, PILS. This would make it possible to write small programs for numerous tasks: Analysing structures, e.g. plots of RMSD by residue or Ramachandran plots. Make a program that reads a file of assignments and insert them into the data base. Test algorithms for automatic assignments. There is no date for when this is ready for release. Q7. Where can I get further information? Send me a mail/fax/email: Mogens Kjaer Carlsberg Laboratory, Dept. of Chemistry Gamle Carlsberg Vej 10 DK-2500 Valby Denmark Phone: +45 33 27 53 25 Fax: +45 33 27 47 08 Email: carlmk@unidhp.uni-c.dk From owner-structural-nmr@net.bio.net Mon Feb 06 22:00:00 1995 Path: biosci!adam.cc.sunysb.edu!news.sprintlink.net!cs.utexas.edu!howland.reston.ans.net!news.cac.psu.edu!news.pop.psu.edu!hudson.lm.com!godot.cc.duq.edu!news.duke.edu!news-server.ncren.net!taco.cc.ncsu.edu!biosci!MED.UNC.EDU!sheng From: sheng@MED.UNC.EDU (Sheng Zhong) Newsgroups: bionet.structural-nmr Subject: www address for any reference you want Date: 6 Feb 1995 21:13:00 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <9502070512.AA17976@hasty.med.unc.edu> NNTP-Posting-Host: net.bio.net Dear netters, I posted a request for NMR book list few weeks ago. I have got some list which are not complete. However, I've found nice www address that will allow one to find almost any book (or other reference) he want. The address is, http://sunsite.unc.edu/reference/ I am sorry to say that I don't have the time to complete NMR book list from those Libraires now, but I think this reference source will help us a lot in the future. Good luck, Dr Sheng Zhong Dept of Biochem & Biophys UNC at Chapel Hill sheng@med.unc.edu From owner-structural-nmr@net.bio.net Wed Feb 08 22:00:00 1995 Path: biosci!COSY.UTMB.EDU!bruce From: bruce@COSY.UTMB.EDU ("Bruce A. Luxon") Newsgroups: bionet.structural-nmr Subject: PRONTO/3D on WWW and FTP Date: 9 Feb 1995 07:35:54 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 52 Sender: daemon@net.bio.net Distribution: world Message-ID: <9502090940.ZM26327@cosy.utmb.edu> NNTP-Posting-Host: net.bio.net Howdy NMR Netters - PRONTO/3D is now available to be downloaded from the University of Texas Medical Branch NMR Center WWW server at http://www.nmr.utmb.edu/ You can browse the documentation and download the SGI or SPARC binaries as you wish. There is also a complete manual in PostScript format. PRONTO/3D and its documentation is also available via FTP anonymous from nmr.utmb.edu/pub/pronto. PRONTO/3D is a newly available X11-based program used for the assignment of multi-dimensional nuclear magnetic resonance (NMR) spectra of macromolecules developed by the Carlsberg Research Center in Denmark in collaboration with several other groups. Please email Mogens Kjaer at carlmk@unidhp.uni-c.dk in Denmark for technical and other assistance beyond what's contained in the above WWW address. Bruce ***************** Disclaimer: The UTMB NMR Center is providing distribution of this free software as a service to the world-wide NMR Community in general. We accept no responsibility as to the suitability of this software for any use, implied or otherwise. We also accept no responsibility as to the protection of intellectual rights, copyrights, licensing rights or any other legal rights that may be infringed by our distribution of this software. All such responsibilities are the sole duty of the Carlsberg Research Center and their representatives. They assure us that no such infringement is possible and they have agreed to indemnify the UTMB NMR Center from any action arising from the distribution of this software. ***************** -- *=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-* * Bruce A. Luxon * * Assistant Professor U * Dept. of Human Biological Chemistry & Genetics T * University of Texas Medical Branch M * Galveston, TX 77555-1157 B * * * (409)747-6802; Fax (409)747-6850 * * bruce@nmr.utmb.edu http://www.nmr.utmb.edu/ * *=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-* From owner-structural-nmr@net.bio.net Thu Feb 09 22:00:00 1995 Path: biosci!CMU.EDU!karatassos+ From: karatassos+@CMU.EDU (Harry Karatassos) Newsgroups: bionet.structural-nmr Subject: NMR workshop offered at the PSC Date: 10 Feb 1995 14:02:20 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 103 Sender: daemon@net.bio.net Distribution: world Message-ID: <0jCy7v200jeN0lABY0@andrew.cmu.edu> STRUCTURE DETERMINATION FROM NMR Pittsburgh Supercomputing Center June 25-28, 1995 Pittsburgh Supercomputing Center (PSC) is offering biomedical researchers a "Structure Determination From NMR" Workshop. The objective is to introduce participants to the different techniques for the elucidation of solution structures of biological macromolecules from nuclear magnetic resonance data. The workshop is free to academic participants. The worskhop will consist of lectures and extensive hands-on sessions. The programs AMBER, Mardigras and MidasPlus will be discussed. Hands-on sessions will be emphasized. Participants will be able to work on the examples provided or on their own experimental data. No prior supercomputing experience is necessary. Workshop leaders are: Dr. David Case, The Scripps Research Institute; and Drs Thomas James, Julie Newdoll and Uli Schmitz, University of California, San Francisco. This workshop is funded by a grant from the Biomedical Research Technology Program, National Center for Research Resources, National Institutes of Health. Travel, meals and hotel accommodations for researchers affilated with U.S. academic institutions are supported by this grant. Enrollment is limited to 20. An application form is included. Deadline for applications is: April 28, 1995. Additional information about this workshop can be found in http://pscinfo.psc.edu/biomed/workshops95.html * * * * * * * * * * PITTSBURGH SUPERCOMPUTING CENTER BIOMEDICAL INITIATIVE STRUCTURE DETERMINATION USING NMR June 25-28, 1995 APPLICATION 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 vita. Graduate students must have a letter of recommendation from a faculty member. Please return all application materials by APRIL 28, 1995 to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960. *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 09 22:00:00 1995 Path: biosci!newshost.lanl.gov!ncar!gatech!howland.reston.ans.net!news.sprintlink.net!EU.net!Austria.EU.net!newsfeed.ACO.net!fstgds15.tu-graz.ac.at!balu.kfunigraz.ac.at!boch13!sengst From: sengst@email.kfunigraz.ac.at (Sengstschmid) Newsgroups: bionet.structural-nmr,sci.techniques.mag-resonance,sci.techniques.spectroscopy,z-netz.wissenschaft.chemie Subject: spectrasimulation needed Date: Wed, 8 Feb 1995 18:59:11 Organization: Org.Chem. Lines: 10 Message-ID: NNTP-Posting-Host: boch13.kfunigraz.ac.at X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Xref: biosci bionet.structural-nmr:433 sci.techniques.mag-resonance:637 sci.techniques.spectroscopy:1222 I'm in need of a computer program simulating NMR-spectra. It should be able to draw a spectra after defining the spin-system and giving the offsets and coupling constants. If anybody out there knows a ftp-site where I could get such a thing please mail to sengst@bkfug.kfunigraz.ac.at many thanks in advance helmut sengstschmid From owner-structural-nmr@net.bio.net Sat Feb 11 22:00:00 1995 Newsgroups: bionet.structural-nmr Path: biosci!newshost.lanl.gov!news.ttu.edu!seas.smu.edu!convex!insosf1.infonet.net!solaris.cc.vt.edu!uunet!zib-berlin.de!news.cs.uni-magdeburg.de!RRZ.Uni-Koeln.DE!news.dfn.de!scsing.switch.ch!rzusuntk.unizh.ch!cweber From: cweber@oci.unizh.ch (Christoph Weber) Subject: Re: naive protein question Message-ID: <1995Feb9.135228.20333@rzu-news.unizh.ch> Sender: newsadm@rzu-news.unizh.ch (CNEWS ADMINISTRATION) Organization: University of Zurich, Switzerland X-Newsreader: TIN [version 1.2 PL2] References: <950205.110646.EST.JLEE@UGA.CC.UGA.EDU> <1995Feb6.194252.853@alw.nih.gov> Date: Thu, 9 Feb 1995 13:52:28 GMT Lines: 50 John Kuszewski (johnk@spasm.niddk.nih.gov) wrote: : In article <950205.110646.EST.JLEE@UGA.CC.UGA.EDU>, JLEE@UGA.CC.UGA.EDU (John Lee) writes: : |> In response to the query by Paul Davis, the group may be interested in a : |> discussion I had yesterday with Robert Huber (I kid you not!). His : |> opinion is that the present limit for a meaningful protein structure is : |> 15 kD. He says that the NMR result does not have sufficient accuracy for : |> a meaningful result on structure that one can interpret in terms of a : |> biochemical function. : |> NMR does have power in terms of changes that may occur in solution and : |> of information on protein dynamics and that is where everyone should be : |> directing their attention. : |> I'm ready for the flames! : First, in response to the original questions, NMR structural work is : usually done with ~0.5 ml of ~1 mM solutions. The current limit is : ~18-25 kD (depending on how nicely the sample behaves and so on, : and what you're willing to call a "structure"). But note that *most* high resolution NMR structures have been determined at higher concentrations, like 2-4 mM. : But I'm not sure what you mean about the limit of NMR structures' : accuracy as the size gets above 15 kD. I would second R. Huber's opinion in that most good NMR structures are from relatively small proteins (compared to what people call the limit of today's technology). There's a gaping hole between the size of proteins that people work out structures for and the size of what they claim they can do. : In most cases, the RMSD : between NMR structures and crystal structures is about as big as : among crystal structures of the same protein solved by different : groups (for example, interleukin 1 beta). A good argument can : be (and has been) made that "high resolution" NMR structures : are about equal to 2 Angstrom crystal structures. I certainly agree with that. Greg Petsko has made something like the former statement when prompted about the accuracy of X-ray structures. [Rest deleted] Please note that I'm into structural NMR myself. I'm simply a bit cynical when it comes to what we all do and what we would *like* to do. Christoph -- Christoph Weber email: cweber@oci.unizh.ch OCI Uni Zurich phone: +41 1 257 4925 Winterthurerstr. 190 FAX: +41 1 361 9895 CH-8057 Zurich, Switzerland From owner-structural-nmr@net.bio.net Sun Feb 12 22:00:00 1995 Newsgroups: bionet.structural-nmr,sci.techniques.mag-resonance,sci.techniques.spectroscopy,z-netz.wissenschaft.chemie Path: biosci!galaxy.ucr.edu!library.ucla.edu!agate!overload.lbl.gov!lll-winken.llnl.gov!uwm.edu!math.ohio-state.edu!howland.reston.ans.net!Germany.EU.net!zib-berlin.de!news.belwue.de!news.uni-ulm.de!rz.uni-karlsruhe.de!stepsun.uni-kl.de!sun.rhrk.uni-kl.de!seimet From: seimet@rhrk.uni-kl.de (Uwe Seimet) Subject: Re: spectrasimulation needed Message-ID: <1995Feb11.195927.18816@rhrk.uni-kl.de> Organization: University of Kaiserslautern, Germany References: Date: Sat, 11 Feb 1995 19:59:27 GMT Lines: 42 Xref: biosci bionet.structural-nmr:436 sci.techniques.mag-resonance:652 sci.techniques.spectroscopy:1246 sengst@email.kfunigraz.ac.at (Sengstschmid) writes: >I'm in need of a computer program simulating NMR-spectra. It should be able >to draw a spectra after defining the spin-system and giving the offsets and >coupling constants. Have a look at XNMR: -- NAME xnmr - Processing and simulation of NMR spectra SYNOPSIS xnmr DESCRIPTION Xnmr is an X11/Motif based program capable of simulating exchange broadened NMR spectra of dynamic molecules. Xnmr further allows processing of experimental data obtained from Bruker family NMR spectrometers running UXNMR. Basic features of xnmr are o Multiple datasets in multiple windows o Realtime graphics o Lineshape analysis o Stacked plots o Scalable PostScript output in monochrome and color o Thermodynamic calculations -- XNMR sources are available by fsp or anonymous ftp from acp5.chemie.uni-kl.de. *************************************************************************** * Uwe Seimet | I really hate this damned machine, * * | I wish that they would sell it. * * Internet: seimet@chemie.uni-kl.de | It never does that what I mean * * Mausnet: Uwe Seimet @ KL | but only what I tell it. * *************************************************************************** From owner-structural-nmr@net.bio.net Mon Feb 13 22:00:00 1995 Path: biosci!CVX12.INET.DKFZ-HEIDELBERG.DE!dok730 From: dok730@CVX12.INET.DKFZ-HEIDELBERG.DE (Karl Jalkanen) Newsgroups: bionet.structural-nmr Subject: please subscribe and send info Date: 14 Feb 1995 03:05:10 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: <199502141105.MAA15429@cvx12.inet.dkfz-heidelberg.de> NNTP-Posting-Host: net.bio.net Can you please subscribe to structural nmr group and send me info. From owner-structural-nmr@net.bio.net Thu Feb 16 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: mad@tome.cbs.univ-montp1.fr (Marc-Andre Delsuc) Newsgroups: bionet.structural-nmr Subject: Gifa v4.0 Date: 17 Feb 1995 11:45:34 -0000 Lines: 90 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3i228u$a6a@mserv1.dl.ac.uk> Original-To: str-nmr@dl.ac.uk Dear NMR users, ========================================================== * * * GGGGGG IIIIII FFFFFF AAA * * G I F A A * * G GGG I FFFF AAAAA * * G G I F A A * * GGGGGG IIIIII F A A * * * * 1D, 2D and 3D NMR Program * * * * M.A.Delsuc * * CBS - Faculte de Pharmacie * * 34060 Montpellier FRANCE * * * * Version 4.0 beta * * * * * ========================================================== I am glad to announce that the Gifa program version 4.0 is being made freely available to NMR community, with access by anonymous FTP. Since I moved to Montpellier, I had little time to distribute the program my self, was I asked Oxford Molecular Limited to do it for me. During that same period, we started a complete rewrite of the user interface, that some French Gifa-user have been enjoying already for a couple of Month. I am now able to distribute it the the Net, with a free licence agreement to academical users. What ? ====== Gifa v4.0 is a complete NMR program. It is still in beta realease, but seems fairly stable. Here is a brief description extracted from the manual: The Gifa program is a multi-purpose NMR program. It is designed for the processing, the display and the analysis of 1D, 2D & 3D NMR data-sets. The program includes all the classical processing, displaying and plotting capabilities of an NMR program, as well as more advanced processing techniques such as Maximum Entropy processing or Linear prediction. There is no actual limit to the size of the data-set which can be processed. A complete macro language permits to builds sophisticated processing. The Graphic User Interface is fully designable and programmable by the user. The program currently runs on several UNIX platforms. The graphics can be displayed on X-Windows terminals. Plots are generated on postscript or HP-GL devices. This version V4.0 is not stabilised yet, this distribution is still a beta version. This version is distributed under a licence. There is no fees for academic laboratories, however the licence requires that you refer to Gifa in any published work which depend in some manner on the Gifa program. Where? ====== Gifa is available by anonymous FTP at : ftp://tome.cbs.univ-montp1.fr/pub/gifa_v4_beta/ It is Ok if people wish to have Gifa on their local FTP sever How? ==== When you get the the needed files (there are several), there is a Make utility that takes all the burden of unpacking, testing and installing the program. Licence ======= Gifa v4.0 is distributed under a licence agreement. The licence is free for academical laboratories. When starting the program, you will get an annoying message telling you that you don't have a valid licence. Just sign and fax me the included licence agreement and you will receive a small licence file which will make the message disappear. Those who have been using the alpha version, which did not have a licence file should contact me as well. I hope this will help. _______________________________________________________________________________ Marc-Andre' Delsuc Centre de Biochimie Structurale mad@cbs.univ-montp1.fr Faculte de Pharmacie tel : (33) 67 04 34 36 34060 Montpellier cedex fax : (33) 67 52 96 23 FRANCE From owner-structural-nmr@net.bio.net Thu Feb 16 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!ix.netcom.com!netnews From: Nalorac@ix.netcom.com (James Carolan) Newsgroups: bionet.structural-nmr Subject: NMR SYMPOSIUM Date: 17 Feb 1995 21:46:28 GMT Organization: Netcom Lines: 16 Distribution: world Message-ID: <3i35fk$for@ixnews3.ix.netcom.com> NNTP-Posting-Host: ix-wc1-24.ix.netcom.com ADVANCES IN NMR APPLICATIONS SYMPOSIUM FEATURING THE LATEST DEVELOPMENTS IN EXPERIMENTAL TECHNIQUES AT THE WESTIN HOTEL COPLEY PLACE BOSTON SUNDAY, MARCH 26, 3:30PM TO 5:30PM The agenda includes a presentation of recent results by leading NMR experimentalists concerning applications of pulsed field gradient and classical NMR techniques to both large and small molecular systems. The results obtained with 3, 5, 8, and 10mm probes will be of interest to all liquid state NMR spectroscopists. The Symposium will be held Sunday afternoon prior to the start of ENC. Request a detailed program or RSVP by contacting our ENC Coordinator, Victoria Davies via our temporary email address: nalorac@ix.netcom.com From owner-structural-nmr@net.bio.net Sun Feb 19 22:00:00 1995 Newsgroups: bionet.structural-nmr Path: biosci!galaxy.ucr.edu!ratatosk.yggdrasil.com!news.duke.edu!solaris.cc.vt.edu!news.alpha.net!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!pipex!sunic!news.lth.se!news.lu.se!heimdall!bryan From: bryan@fkem2.lth.se (Bryan Finn) Subject: FELIX to mac Message-ID: <1995Feb20.154444.11453@nomina.lu.se> Sender: news@nomina.lu.se (USENET News System) Nntp-Posting-Host: heimdall.fkem2.lth.se Reply-To: bryan@fkem2.lth.se Organization: Physical Chemistry 2, Lund University, Sweden Date: Mon, 20 Feb 1995 15:44:44 GMT Lines: 37 This is actually a sort-of-followup to the discussion that went on last summer regarding conversion of Felix postscript or HPGL figures to a format that could be work with on a macintosh. To summarize very briefly, several possibilities were suggested: 1. HPGLtoClipboard, a utility for converting HPGL to PICT format that can be used on the mac. Reported to be available via ftp from dggpi2.chem.purdue.edu or the NMR gopher servers. 2. Illustrator 5.5/Acrobat Distiller package (commercial) or aimaker (freeware) from toby.princeton.edu to convert to Illistrator format. 3. EPSfilter from gopher.archive.merit.net. I tried to find HPGLtoClipboard but it must have disappeared from the servers (at least those I could access). So, what I was wondering was if it was still available and if anyone had other suggestions for conversion of FELIX HPGL or PS pictures to usable format (besides of course asking Biosym to include other formats in their hardcopy options (hint hint)). Bryan ___________________________________________________________________ | | | Dr. Bryan Finn | | Department of Physical Chemistry 2 Tel: +46-46-108254 | | Chemical Center Fax: +46-46-104543 | | University of Lund | | POB 124 | | S-221 00 Lund Sweden e-mail: bryan@freja.fkem2.lth.se | |_________________________________________________________________| From owner-structural-nmr@net.bio.net Sun Feb 19 22:00:00 1995 Path: biosci!COSY.UTMB.EDU!bruce From: bruce@COSY.UTMB.EDU ("Bruce A. Luxon") Newsgroups: bionet.structural-nmr Subject: HPGL2Clipboard Date: 20 Feb 1995 11:35:42 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: <9502201340.ZM19876@cosy.utmb.edu> NNTP-Posting-Host: net.bio.net NMR Netters, HPGL2Clipboard is available from FTP anonymous at nmr.utmb.edu. Please be aware that it really only works with Mac 6.x. though it may surprise you. Good Luck, Bruce -- *=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-* * Bruce A. Luxon, Ph.D * * Assistant Professor * * UTMB NMR Center U * Dept. of Human Biological Chemistry & Genetics T * University of Texas Medical Branch M * Galveston, TX 77555-1157 B * * * (409)747-6802; Fax (409)747-6850 * * bruce@nmr.utmb.edu http://www.nmr.utmb.edu/ * *=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-* From owner-structural-nmr@net.bio.net Mon Feb 20 22:00:00 1995 Path: biosci!ci.uminho.pt!mreb From: mreb@ci.uminho.pt Newsgroups: bionet.structural-nmr Subject: Re[2]: FELIX to mac Date: 21 Feb 1995 07:23:53 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 24 Sender: daemon@net.bio.net Distribution: world Message-ID: <9501217934.AA793412669@gwccmail.ci.uminho.pt> NNTP-Posting-Host: net.bio.net bryan@freja.fkem2.lth.se (Brian Finn) wrote: > if anyone had other suggestions for conversion of FELIX HPGL or PS pictures > to usable format To solve my problems of converting nmr files from our Varian saved in HPGL format to a Mac PICT format we are using without any problems the program PlotViewt from Stevens Creek Software Fax: 01-408-725-0424. --Mario Rebelo *************************************************************************** Mario R.J. Rebelo Snail mail Dep. of Chemistry, Univ. Minho Gualtar, 4700 Braga, Portugal Phone: 0351 53 604370/72 Fax: 0351 53 604370 E-mail mreb@ci.uminho.pt or um300@ci.uminho.pt **************************************************************************** From owner-structural-nmr@net.bio.net Mon Feb 20 22:00:00 1995 Path: biosci!STAN.XX.SWIN.OZ.AU!rmair From: rmair@STAN.XX.SWIN.OZ.AU (Ross Mair) Newsgroups: bionet.structural-nmr Subject: Re: FELIX to mac Date: 21 Feb 1995 01:45:42 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <9502210222.AA10260@stan.xx.swin.OZ.AU> References: <1995Feb20.154444.11453@nomina.lu.se> NNTP-Posting-Host: net.bio.net bryan@freja.fkem2.lth.se (Brian Finn) wrote: > if anyone had other suggestions for conversion of FELIX HPGL or PS pictures > to usable format (besides of course asking Biosym to include other formats > in their hardcopy options (hint hint)). Ahh..... You could use a PC... :-) HPGL code from Felix goes straight into Windows word-processors. Ross --------------------------------------------------------------------------- Ross Mair Email: rmair@stan.xx.swin.oz.au NMR Storage Lab Snail: Mail 41, Swinburne University, Applied Chemistry Dept PO Box 218, Hawthorn, 3122. Swinburne University of Technology Fax: +61-3-8190834 Hawthorn, Victoria, Australia Voice: +61-3-2148843 --------------------------------------------------------------------------- From owner-structural-nmr@net.bio.net Mon Feb 20 22:00:00 1995 Newsgroups: bionet.structural-nmr Path: biosci!bcm!cs.utexas.edu!swrinde!pipex!uknet!festival!leeds.ac.uk!news From: garyt@resumix.portal.com (Gary Thompson) Subject: Re: FELIX to mac Message-ID: <1995Feb21.090513.14182@leeds.ac.uk> Reply-To: garyt@resumix.portal.com Organization: Resumix, Inc., Santa Clara, CA Date: Tue, 21 Feb 1995 09:05:12 +0000 (GMT) References: <1995Feb20.154444.11453@nomina.lu.se> Lines: 30 In article 11453@nomina.lu.se, bryan@fkem2.lth.se (Bryan Finn) writes: > This is actually a sort-of-followup to the discussion that went on last summer > regarding conversion of Felix postscript or HPGL figures to a format that could be > work with on a macintosh. > > To summarize very briefly, several possibilities were suggested: > > 1. HPGLtoClipboard, a utility for converting HPGL to PICT format that can be used on > the mac. Reported to be available via ftp from dggpi2.chem.purdue.edu or the NMR > gopher servers. > I have found it on info-mac in grf/util/HPGL as hpgl-to-pict-hc.hqx the local url in england was ftp://ftp.uu.net/systems/mac/info-mac/grf/util/hpgl-to-pict-hc.hqx > 3. EPSfilter from gopher.archive.merit.net. I have not found EPSFilter I hope this helps gary From owner-structural-nmr@net.bio.net Mon Feb 20 22:00:00 1995 Newsgroups: bionet.structural-nmr Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!pipex!uknet!festival!leeds.ac.uk!news From: garyt@resumix.portal.com (Gary Thompson) Subject: Re: FELIX to mac Message-ID: <1995Feb21.083349.5761@leeds.ac.uk> Reply-To: garyt@resumix.portal.com Organization: Resumix, Inc., Santa Clara, CA Date: Tue, 21 Feb 1995 08:33:48 +0000 (GMT) References: <1995Feb20.154444.11453@nomina.lu.se> Lines: 24 In article 11453@nomina.lu.se, bryan@fkem2.lth.se (Bryan Finn) writes: > This is actually a sort-of-followup to the discussion that went on last summer > regarding conversion of Felix postscript or HPGL figures to a format that could be > work with on a macintosh. > We have used a program called plotview, however it is a memory hog and is very slow. Also, I don't think it has been updated properly. the details are as follows: PlotView v3.2 1992 Stevens Creek Software 21346 Rumford Drive, Cupertino, CA 95014 (408) 725-0424 Gary From owner-structural-nmr@net.bio.net Mon Feb 20 22:00:00 1995 Newsgroups: bionet.structural-nmr Path: biosci!agate!news.Stanford.EDU!MED.Stanford.EDU!CAMIS!jxc From: jxc@CAMIS.Stanford.EDU (Jerzy Czaplicki) Subject: Educational NMR software - where to get it? Message-ID: Keywords: nmr Sender: news@medmail.stanford.edu Organization: Stanford University, California, USA X-Newsreader: NN version 6.5.0 #4 Date: Tue, 21 Feb 1995 11:00:11 GMT Lines: 13 Hello, Someone here mentioned SSS (Spin System Simulation) program available for MS Windows. Does anyone know if there is an ftp site that carries it? Archie doesn't know about it. Besides SSS, are there any other educational NMR programs that could be recommended for illustrating principles of NMR? Thank you in advance, Jerzy. From owner-structural-nmr@net.bio.net Mon Feb 20 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news2.near.net!das-news2.harvard.edu!oitnews.harvard.edu!hsdndev!purdue!mozo.cc.purdue.edu!cv4.chem.purdue.edu!lev From: "Lev A. Gorenstein" Newsgroups: bionet.structural-nmr Subject: Re: Educational NMR software - where to get it? Date: Tue, 21 Feb 1995 10:54:33 -0500 Organization: Purdue University Lines: 24 Message-ID: References: NNTP-Posting-Host: cv4.chem.purdue.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In-Reply-To: On Tue, 21 Feb 1995, Jerzy Czaplicki wrote: > Hello, > > Someone here mentioned SSS (Spin System Simulation) program available > for MS Windows. Does anyone know if there is an ftp site that carries it? > Archie doesn't know about it. Jerzy, I think I saw it at kekule.osc.edu somewhere in /pub/chemitry/software/..., though not sure. I have it and can send to you if you want. Lev. ______________________________________________________________________________ Lev A. Gorenstein Dept. of Chemistry, Purdue University *~~~~ ____ |~~~~~~~~~~~~~| W.Lafayette, IN 47907, USA Y_,___|[]| | Go Boilers! | (317)494-9150; Fax (317)494-0239 {|_|_|_|PU|_,_|_____________| lev@chem.purdue.edu //oo---OO=OO OOO OOO ------------------------------------------------------------------------------ From owner-structural-nmr@net.bio.net Tue Feb 21 22:00:00 1995 Path: biosci!CSA3.LBL.GOV!volkman%lcbvax.hepnet From: volkman%lcbvax.hepnet@CSA3.LBL.GOV Newsgroups: bionet.structural-nmr Subject: (none) Date: 22 Feb 1995 09:28:10 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 32 Sender: daemon@net.bio.net Distribution: world Message-ID: <950222092742.3560322b@Csa3.LBL.Gov> NNTP-Posting-Host: net.bio.net In reply to Bryan's query about conversion of images from felix (specifically, postscript): We have used the program Transverter Pro for all types of postscript to Adobe Illust. (or Pict or TIFF) format for additional annotation on the Mac platform. It is availible from TechPool Software 1436 Warrensville Center Rd Cleveland, OH 44121-2676 (216)-291-1922 Fax (216)-382-1915 We have found TPro to be extremely useful for making nice figures (full color and b/w) of images from Felix, as well as InsightII. It reads any standard printer-ready postscript file and converts it into one of the aforementioned image formats. I think it is availible for Macintosh and PC, though we have used only the Mac version. I am also uncertain of the price. Brian Volkman bfvolkman@lbl.gov Wemmer Group Dept. of Chemistry U. C. Berkeley From owner-structural-nmr@net.bio.net Tue Feb 21 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!uunet!hodes.com!netcomsv!woody!uwoody Newsgroups: bionet.structural-nmr Message-ID: <426@woody.acornnmr.com> References: <1995Feb20.154444.11453@nomina.lu.se><9502210222.AA10260@stan.xx.swin.OZ.AU> Reply-To: uwoody@woody.acornnmr.com (Acorn NMR Support) From: uwoody@woody.acornnmr.com (Acorn NMR Support) Date: Wed, 22 Feb 1995 18:22:59 GMT Subject: Re: FELIX to mac Lines: 31 Ross Mair (rmair@STAN.XX.SWIN.OZ.AU) writes: >bryan@freja.fkem2.lth.se (Brian Finn) wrote: > >> if anyone had other suggestions for conversion of FELIX HPGL or PS pictures >> to usable format (besides of course asking Biosym to include other formats >> in their hardcopy options (hint hint)). > >Ahh..... > >You could use a PC... :-) We use a program on the PC called HiJaak which can import all kinds of graphics formats and then export in many different formats, including .PICT or .TIFF which the Mac can understand. I don't know if HiJaak is available for the Mac, but you could ask: Inset Systems 71 Commerce Dr. Brookfield, CT 06804-3405 (203) 740-2400 (203) 775-5634 FAX ==================================================================== Virginia W. Miner Voice (510) 683-8595 Acorn NMR Inc. FAX (510) 683-6784 46560 Fremont Blvd., #418 Email gina@acornnmr.com Fremont, CA 94538-6491 From owner-structural-nmr@net.bio.net Tue Feb 21 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: Graham Barlow Newsgroups: bionet.structural-nmr Subject: Re: Educational NMR software - where to get it? Date: 22 Feb 1995 11:14:21 -0000 Lines: 34 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3if6ad$nrj@mserv1.dl.ac.uk> Reply-To: gkb1 X-Sender: Original-To: str-nmr@dl.ac.uk In reply to: > >On Tue, 21 Feb 1995, Jerzy Czaplicki wrote: > >> Someone here mentioned SSS (Spin System Simulation) program available >> for MS Windows. Does anyone know if there is an ftp site that carries it? >> Archie doesn't know about it. > >Jerzy, > >I think I saw it at kekule.osc.edu somewhere in >/pub/chemitry/software/..., though not sure. I have it and can send to >you if you want. > >Lev. It's definitely in ftp://bloch.cchem.berkeley.edu/pub/nmr/mswin/ I just looked. Graham +-----------------------===============================================+ | Dr. Graham Barlow | tower / VAX mail: gkb1 | | NMR Service Manager | e-mail: gkb1@york.ac.uk | | Dept. of Chemistry | Telephone: +44 (0)1904 432506 DDI | | University of York | Fax: +44 (0)1904 432516 | | Heslington, YORK, UK | WWW: http://www.york.ac.uk/depts/chem/nmr | +-----------------------+==Mime OK ====================================+ From owner-structural-nmr@net.bio.net Tue Feb 21 22:00:00 1995 Newsgroups: bionet.structural-nmr Path: biosci!bloom-beacon.mit.edu!eru.mt.luth.se!news.luth.se!sunic!news.lth.se!news.lu.se!heimdall!bryan From: bryan@freja.fkem2.lth.se (Bryan Finn) Subject: Re: FELIX to mac Message-ID: <1995Feb22.095444.10228@nomina.lu.se> Sender: news@nomina.lu.se (USENET News System) Nntp-Posting-Host: heimdall.fkem2.lth.se Reply-To: bryan@freja.fkem2.lth.se Organization: Physical Chemistry 2, Lund University, Sweden References: <1995Feb21.090513.14182@leeds.ac.uk> Date: Wed, 22 Feb 1995 09:54:44 GMT Lines: 41 In article 14182@leeds.ac.uk, garyt@resumix.portal.com (Gary Thompson) writes: > I have found it on info-mac in grf/util/HPGL > as hpgl-to-pict-hc.hqx > > the local url in england was > > ftp://ftp.uu.net/systems/mac/info-mac/grf/util/hpgl-to-pict-hc.hqx > > > 3. EPSfilter from gopher.archive.merit.net. > > I have not found EPSFilter > I was given a copy of HPGLtoCLipboard (Thanks Peter L!) but that promptly hung my machine up because it was written for Mac 6.x (as Bruce Luxon pointed out). However, I found EPSFilter2.1a1 at: gopher://nic.merit.edu:7055/11/mac/graphics/graphicsutil It actually works quite well for conversion of HPGL to Illustrator format. This can in turn be opened and converted in other programs such as Canvas 3.5. Bryan _________________________________________________________________ | | | Dr. Bryan Finn | | Department of Physical Chemistry 2 Tel: +46-46-108254 | | Chemical Center Fax: +46-46-104543 | | University of Lund | | POB 124 | | S-221 00 Lund Sweden e-mail: bryan@freja.fkem2.lth.se | |_________________________________________________________________| From owner-structural-nmr@net.bio.net Tue Feb 21 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!uunet!hodes.com!netcomsv!woody!uwoody Newsgroups: bionet.structural-nmr Message-ID: <425@woody.acornnmr.com> References: Reply-To: uwoody@woody.acornnmr.com (Acorn NMR Support) From: uwoody@woody.acornnmr.com (Acorn NMR Support) Date: Wed, 22 Feb 1995 18:11:04 GMT Subject: Re: Educational NMR software - where to get it? Lines: 37 >Jerzy Czaplicki (jxc@CAMIS.Stanford.EDU) writes: > Someone here mentioned SSS (Spin System Simulation) program available >for MS Windows. Does anyone know if there is an ftp site that carries it? We offer an NMR processing package for Windows, available as 1D and 1D/2D versions, which includes spin simulation for up to 10 spins with iteration to match an actual spectrum. A demo copy of the program is available via anonymous ftp. Once it is installed, use the on-line Help and search for "simulated spectra" to get instructions. A demo copy of NUTS can be obtained by FTP-ing to: ftp.netcom.com logging in as anonymous, and cd-ing to: pub/wo/woodyc This directory contains: nuts.demo.instructions /* instructions for downloading and installing demo */ nuts32.zip /* The NUTS32 demo program */ win32s_1.zip /* First disk of Win32s DLLs (required to install NUTS) */ win32s_2.zip /* Second disk of Win32s DLLs (required to install NUTS) */ nuts.man /* ASCII text of NUTS manual */ nuts.whatsnew /* text file describing new features */ pk204g.exe /* PKZIP shareware; for unzipping files */ nuts.support /* prices, support policy, etc */ sprbar.zip /* shareware that lets you create custom toolbars */ sam.zip.demo */ SAM demo program ("Shimming Ain't Magic" for shim simulation) sam.demo.instructions */ text file describing program operation ==================================================================== Virginia W. Miner Voice (510) 683-8595 Acorn NMR Inc. FAX (510) 683-6784 46560 Fremont Blvd., #418 Email gina@acornnmr.com Fremont, CA 94538-6491 From owner-structural-nmr@net.bio.net Wed Feb 22 22:00:00 1995 Path: biosci!ABRAGAM.LJCRF.EDU!krish From: krish@ABRAGAM.LJCRF.EDU (V.V. Krishnan) Newsgroups: bionet.structural-nmr Subject: (none) Date: 23 Feb 1995 15:04:58 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <9502232303.AA07731@abragam.ljcrf.edu> NNTP-Posting-Host: net.bio.net subscribe str-nmr krish@ljcrf.edu (V.V.Krishnan) From owner-structural-nmr@net.bio.net Wed Feb 22 22:00:00 1995 Path: biosci!modul.bioch.nsk.su!denisov From: denisov@modul.bioch.nsk.su (Alexey Denisov) Newsgroups: bionet.structural-nmr Subject: (none) Date: 23 Feb 1995 04:48:15 -0800 Organization: Institute of Bioorganic Chemistry SD AS RUSSIA Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear colleagues, I search the literature information on topic "Protein-DNA or oligopeptide-oligonucleotide interactions by structural NMR" for future work. Do you know recent reviews or principal papers since 1988th year? I am in need of references. Thank you in advance. With regards, Dr. Aleksej Yu. Denisov, Novosibirsk Institute of Bioorganic Chemistry of RAS, Novosibirsk 630090, Russia fax: (3832)-353-459 e-mail: denisov@modul.bioch.nsk.su From owner-structural-nmr@net.bio.net Thu Feb 23 22:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!pipex!sunic!news.funet.fi!ousrvr.oulu.fi!eha From: eha@phoenix.oulu.fi (Esa Haapaniemi) Newsgroups: bionet.structural-nmr Subject: Re: Educational NMR software - where to get it? Date: 24 Feb 1995 07:25:54 GMT Organization: University of Oulu, Finland Lines: 26 Message-ID: <3ik1m2$mdm@ousrvr.oulu.fi> References: <425@woody.acornnmr.com> NNTP-Posting-Host: phoenix.oulu.fi Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: TIN [version 1.2 PL2] : > Someone here mentioned SSS (Spin System Simulation) program available : >for MS Windows. Does anyone know if there is an ftp site that carries it? : We offer an NMR processing package for Windows, available as 1D and 1D/2D versions, : which includes spin simulation for up to 10 spins with iteration to match an : actual spectrum. A demo copy of the program is available via anonymous ftp. SSS is just a spin simulator that shows magnetization vectors and how do they change in single or douple spin cases (homo and heteronuclear) with different pulse seguences and delays. It's fun but not that useful. And for actual spectrum simulation/iteration I'd suggest PERCH (PEakreseaRCH) program (only 1 D at present) but it can handle at least 12 nonequivalent spins, make Total Lineshape Fitting and alike. Demo of it is available at ftp.funet.fi under pub/sci/ ?? (I don't remember that now). New version should be out within a month though. And that runs on PC's both DOS and windows. I'll have a look at the program you mentioned and perhaps comment on it later. Esa Haapaniemi University of Oulu Department of Chemistry Finland From owner-structural-nmr@net.bio.net Thu Feb 23 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!pipex!sunic!trane.uninett.no!daresbury!not-for-mail From: thep@risc1.lrm.fi.cnr.it (Pornthep Sompornpisut) Newsgroups: bionet.structural-nmr Subject: Chianti Workshop on Magnetic Resonance Date: 24 Feb 1995 15:23:54 -0000 Lines: 85 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3iktma$nhs@mserv1.dl.ac.uk> Original-To: str-nmr@dl.ac.uk ******************************************************************************** 6th CHIANTI WORKSHOP ON MAGNETIC RESONANCE: NUCLEAR AND ELECTRON RELAXATION ******************************************************************************** SAN MINIATO (PISA), ITALY, MAY 27 - JUNE 2, 1995 CHAIRPERSONS: I. BERTINI (Univ. Florence), Conference Chairman K. MOEBIUS (Free Univ. Berlin), Program Chairman ORGANIZERS: R. BASOSI (Univ. Siena), C. LUCHINAT (Univ. Bologna), C.A. VERACINI (Univ. Pisa) The present Workshop, in the spirit of the series of the Chianti Workshops, aims at bringing together scientists involved in theoretical and experimental aspects of nuclear and electron spin relaxation to study the structure and dynamics of molecules. The main topics to be discussed by NMR and EPR scientists will deal with: structure determination of biomolecules, spin polarization phenomena and processes, relaxation in paramagnetic systems, quasi-ordered phases, spin imaging, new methodologies. The program will consist of invited lectures and poster presentations. At the moment the following scientists have accepted an invitation to present a lecture: L. Banci (Florence), G. Bodenhausen (Tallahassee), R.D. Britt (Davis), R. Bruschweiler (Zurich), M. Brustolon (Padova), D.A. Case (La Jolla), V. Chizhik (St. Petersburg), K.P. Dinse (Darmstadt), R.Y. Dong (Brandon), J.W. Emsley (Southampton), C. Forte (Pisa), J.H. Freed (Ithaca), E. Gaggelli (Siena), G. Giacometti (Padova), D. Goldfarb (Rehovot), C. Griesinger (Frankfurt/M.), R.G. Griffin (Cambridge, MA), E.J.J. Groenen (Leiden), B. Halle (Lund), A.J. Hoff (Leiden), B.M. Hoffman (Evanston), P. Hore (Oxford), W.L. Hubbell (Los Angeles), M. Huber (Berlin), J. Huttermann (Homburg), J.S. Hyde (Milwaukee), R. Ishima (Tsukuba), T.L. James (San Francisco), G. Kothe (Freiburg), J. Kowalewski (Stockholm), Ya.S. Lebedev (Moscow), H. Levanon (Jerusalem), W. Lubitz (Berlin), G.R. Luckhurst (Southampton), Z. Luz (Rehovot), M.W. Makinen (Chicago), K.A. McLauchlan (Oxford), A.E. Merbach (Lausanne), G. Navon (Tel Aviv), A. Pines (Berkeley), T.F. Prisner (Berlin), K.M. Salikhov (Kazan), S. Schlick (Detroit), R. Sharp (Ann Arbor), H.W. Spiess (Mainz), D. Stehlik (Berlin), U.E. Steiner (Konstanz), S. Styring (Stockholm), W.H. Thomann (Annandale), R.R. Vold (San Diego), L. Weiner (Rehovot), L. Werbelow (Marseille), P.O. Westlund (Umea). Participants intending to present posters on work related to the topics of the Workshop are asked to submit an abstract (max. 1 page A4 format typed single-spaced) of the proposed communication not later than April 15, 1995. Since the total number of participants is limited, acceptance will be on a "first come first served" basis. There is a registration fee of 250,000 Italian Lira for active participants and 120,000 Italian Lira for accompanying persons. The cost of the accommodation, based on sharing a twin-bedded room, plus all meals (including Chianti wine!) will be 700,000 Italian Lira per person. For further information, please contact: Prof. Riccardo Basosi, Dept. of Chemistry, Univ. of Siena, Pian dei Mantellini, 44, 53100 Siena, Italy,TEL. 39/577 298040,FAX 39/577 280405 Prof. Claudio Luchinat,c/o Dept. of Chemistry,Univ. of Florence Via G.Capponi, 7, 50121 Florence, Italy, TEL. 39/55 2757563, FAX 39/55 2757555 Prof. Carlo A.Veracini, Dept. of Chemistry, Univ. of Pisa Via Risorgimento, 35, 56100 Pisa, Italy, TEL. 39/50 918266, FAX 39/50 918260 or the Program Chairman: Prof. Klaus Moebius, Dept. of Physics, Free Univ. of Berlin, Arnimallee 14 D-14195 Berlin, Germany, TEL. 49/30 8382770, FAX 49/30 8386046 ############################################################################# For the REGISTRATION FORM please contact Giacomo Parigi giacomo@risc1.lrm.fi.cnr.it ############################################################################# From owner-structural-nmr@net.bio.net Thu Feb 23 22:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: " (Ton Rullmann)" Newsgroups: bionet.structural-nmr Subject: NMR in Structural Biology - EMBO Course Date: 24 Feb 1995 11:19:56 -0000 Lines: 65 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3ikfcs$ca8@mserv1.dl.ac.uk> Original-To: " (str-nmr)" EMBO Practical Course Multidimensional NMR in Structural Biology Torino, Italy, 27 August - 1 September, 1995 Co-sponsored by the European Initiative for Training in NMR Organizers: R. Kaptein C. Griesinger H. Oschkinat Speakers and instructors: R. Boelens (Utrecht) S. Glaser (Frankfurt) C. Griesinger (Frankfurt) S. Grzesiek (NIH Bethesda) C.W. Hilbers (Nijmegen) R. Kaptein (Utrecht) J.H. Keeler (Cambridge) L. Mitschang (EMBL Heidelberg) M. Nilges (EMBL Heidelberg) H. Oschkinat (EMBL Heidelberg) A. Palmer (Columbia Un, New York) G.W. Vuister (Utrecht) The course will cover NMR theory and methodology for the study of the structure and dynamics of biomolecules in solution. There will be lectures, practical sessions, poster sessions and round table discussions. Topics to be discussed include: - NMR theory (product operator formalism) - Description of pulse sequences including phase cycling and pulsed field gradients - Multidimensional and multinuclear NMR - Methods for spectral assignment - Relaxation theory and dynamics - Structure calculations (distance geometry, restrained molecular dynamics, etc) - Isotope labeling - Applications to proteins and nucleic acids Participation is limited to 60 students (Ph.D students or post-doc's), who should have a good basic knowledge of biomolecular NMR. Participants must pay a registration fee of DM 200. Board and lodging is covered by EMBO. Participants from industrial companies are required to pay an additional fee to EMBO. Applications should include a curriculum vitae, a short description of current research and a letter of recommendation, and should be sent to: Prof. R. Kaptein Bijvoet Center for Biomolecular Research University of Utrecht Padualaan 8, NL-3584 CH Utrecht The Netherlands Tel. 30-533787, FAX 30-537623 Deadline for applications: 16 May, 1995 -- | Ton Rullmann NMR Spectroscopy | | Bijvoet Center for Biomolecular Research | Tel. : int+31.30.533641 | | Utrecht University, Padualaan 8, | Fax : int+31.30.537623 | | 3584 CH Utrecht, The Netherlands | Email: rull@nmr.chem.ruu.nl | From owner-structural-nmr@net.bio.net Fri Feb 24 22:00:00 1995 Path: biosci!rutgers!csn!ub!newserve!schulte From: schulte@bingsuns.cc.binghamton.edu () Newsgroups: bionet.structural-nmr Subject: ZZNET Date: 25 Feb 1995 03:08:36 GMT Organization: Binghamton University, Binghamton, NY Lines: 19 Message-ID: <3im6vk$1i9@bingnet1.cc.binghamton.edu> NNTP-Posting-Host: 128.226.1.2 X-Newsreader: TIN [version 1.2 PL2] I am presently trying to set up a parallel data transfer between a Bruker ASPECT 3000 and an IBM PC using the "ZZNET" software. Does anyone have experience with ZZNET (configuring the Metrabyte PIO card, hardware/software modifications, base address and interrupt# , start address of the ZZNET program on the ASPECT 3000)? Any information regarding ZZNET is appreciated. Please post to this group or send me an e-mail. Thanks! Juergen Schulte SUNY Binghamton Chemistry Department Binghamton, NY 13902-6016 schulte@bingsuns.cc.binghamton.edu From owner-structural-nmr@net.bio.net Mon Feb 27 22:00:00 1995 Path: biosci!LAPLACE.CSB.YALE.EDU!abonvin From: abonvin@LAPLACE.CSB.YALE.EDU ("Alexandre Bonvin") Newsgroups: bionet.structural-nmr Subject: protein-DNA NMR studies Date: 28 Feb 1995 07:38:56 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 77 Sender: daemon@net.bio.net Distribution: world Message-ID: <9502281538.AA15994@laplace.csb.yale.edu> NNTP-Posting-Host: net.bio.net In answer to Aleksej request: > > Dear colleagues, > > I search the literature information on topic > "Protein-DNA or oligopeptide-oligonucleotide > interactions by structural NMR" for future work. > Do you know recent reviews or principal papers > since 1988th year? I am in need of references. > > Thank you in advance. > With regards, > > Dr. Aleksej Yu. Denisov, > Novosibirsk Institute of > Bioorganic Chemistry of RAS, > Novosibirsk 630090, Russia > fax: (3832)-353-459 > e-mail: denisov@modul.bioch.nsk.su > Here are a few: "Rullmann J.A.C., Boelens R., Lamerichs R.M.J.N., Vuister G.W., Kaptein R.","1990","NMR studies of proteins and protein-DNA interactions. Modelling of Molecular Structures and Properties. Proceedings of an International Meeting, Nancy, France, 11-15 September 1989","Studies in Physical and Theoretical Chemistry 71, Elsevier Science Publishers B.V., Amsterdam",,"661 - 678" "Boelens R., Scheek R.M., van Boom J.H., Kaptein R.","1987","Complex of lac Repressor Headpiece with a 14 Base-pair lac Operator Fragment Studied by Two-Dimensional Nuclear Magnetic Resonance","J Mol Biol","193","213 - 216" "Lamerichs R.M.J.N., Boelens R., van der Marel G.A., van Boom J.H., Kaptein R., Buck F., Fera B., RŸterjans H.","1989","1H NMR Study of a Complex between lac Repressor Headpiece and a 22 Base Pair Symmetric lac Operator","Biochemistry","28","2985 - 2991" "Freemont Paul S., Lane Andrew N., Sanderson Mark R.","1991","REVIEW ARTICLE: Structural aspects of protein-DNA recognition","Biochemistry","278","1 - 23" "Remerowski M.L., Kellenback E., Boelens R., van der Marel G.A., van Boom J.H., Maler A., Yamamoto K.R., Kaptein R.","1991","1H NMR Studies of DNA Recognition by the Glucocorticoid Receptor: Complex of the DNA Binding Domain with a Half-Site Response Element","Biochemistry","30","11620-11624" "ThŽriault Yves, Logan Timothy M., Meadows Robert, Yu Liping, Olejniczak Edward T., Holzman Thomas F., Simmer Robert L., Fesik Stephen W.","1993","Solution structure of the cyclosporin A/cyclophilin complex by NMR","Nature","361","88-91" "Omichinski James G., Clore Marius G., Schaad Olivier, Felsenfeld Gary, Trainor Cecelia, Appella Ettore, Stahl Stephen J., Groneborn Angela M.","1993","NMR structure of a specific DNA complex of Zn-containing DNA binding domain of GATA-1","Science","261","438-446" "Schwabe John W.R., Chapman Lynda, Finch John T., Rhodes Daniela, Neuhaus David","1993","DNA recognition by the oestrogen receptor: from solution to the crystal","Structure","1","187-204" "Clore Marius G., Gronenborn Angela M.","1994","Structures of larger proteins, protein-ligand and protein-DNA complexes by multidimensional heteronuclear NMR.","Protein Science","3","372-390" =============================================================================== | Alexandre Bonvin PhD | Phone: (203) 432-5066 | | Mol. Biophys. & Biochemistry | Fax: (203) 432-6946 | | Yale University, PO Box 208114 | Email: abonvin@laplace.csb.yale.edu | | New Haven CT 06511, USA | | =============================================================================== From owner-structural-nmr@net.bio.net Mon Feb 27 22:00:00 1995 Path: biosci!tips.rc.ac.ru!Rebrov From: Rebrov@tips.rc.ac.ru ("Alexandr Rebrov") Newsgroups: bionet.structural-nmr Subject: Subscribe Date: 28 Feb 1995 06:58:56 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <2f5332bc.tips@tips.rc.ac.ru> NNTP-Posting-Host: net.bio.net Subscribe -- ________________ Alexandr Rebrov NMR Center of Russian Academy of Sciences, A.V.Topchiev Institute of Petrochemical Synthesis Leninskii prosp. 29, 117912 Moscow, Russia FAX: +007 (095) 230-22-24 Tel: +007 (095) 955-41-57 E-mail rebrov@tips.rc.ac.ru From owner-structural-nmr@net.bio.net Tue Feb 28 22:00:00 1995 Path: biosci!ANDREW.CMU.EDU!ar1z+ From: ar1z+@ANDREW.CMU.EDU ("Alexander J. Ropelewski") Newsgroups: bionet.structural-nmr Subject: Structure Determination from NMR workshop Annoucement Date: 1 Mar 1995 10:09:27 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 100 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net STRUCTURE DETERMINATION FROM NMR Pittsburgh Supercomputing Center June 25-28, 1995 Pittsburgh Supercomputing Center (PSC) is offering biomedical researchers a "Structure Determination From NMR" Workshop. The objective is to introduce participants to the different techniques for the elucidation of solution structures of biological macromolecules from nuclear magnetic resonance data. The workshop is free to academic participants. The worskhop will consist of lectures and extensive hands-on sessions. The programs AMBER, Mardigras and MidasPlus will be discussed. Hands-on sessions will be emphasized. Participants will be able to work on the examples provided or on their own experimental data. No prior supercomputing experience is necessary. Workshop leaders are: Dr. David Case, The Scripps Research Institute; and Drs Thomas James, Julie Newdoll and Uli Schmitz, University of California, San Francisco. This workshop is funded by a grant from the Biomedical Research Technology Program, National Center for Research Resources, National Institutes of Health. Travel, meals and hotel accommodations for researchers affilated with U.S. academic institutions are supported by this grant. Enrollment is limited to 20. An application form is included. Deadline for applications is: April 28, 1995. Additional information about this workshop can be found in http://pscinfo.psc.edu/biomed/workshops95.html * * * * * * * * * * PITTSBURGH SUPERCOMPUTING CENTER BIOMEDICAL INITIATIVE STRUCTURE DETERMINATION FROM NMR June 25-28, 1995 APPLICATION 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 vita. Graduate students must have a letter of recommendation from a faculty member. Please return all application materials by APRIL 28, 1995 to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960. *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 Tue Feb 28 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!ix.netcom.com!netnews From: Nalorac@ix.netcom.com (James Carolan) Newsgroups: bionet.structural-nmr Subject: Advances in NMR Applications Symposium-Agenda Date: 1 Mar 1995 16:12:20 GMT Organization: Netcom Lines: 40 Distribution: world Message-ID: <3j26d4$lh7@ixnews2.ix.netcom.com> NNTP-Posting-Host: ix-wc2-20.ix.netcom.com ADVANCES IN NMR APPLICATIONS SYMPOSIUM - AGENDA You are invited to attend a special NMR Symposium prior to the 36th ENC. ADVANCES IN NMR APPLICATIONS SYMPOSIUM FEATURING THE LATEST DEVELOPMENTS IN EXPERIMENTAL TECHNIQUES AT THE WESTIN HOTEL COPLEY PLACE BOSTON SUNDAY, MARCH 26, 3:30 p.m. to 6:00 p.m. AGENDA INCLUDES: Redefining the Limits of Micro Detection Gary E. Martin & R.C. Crouch, Burroughs Wellcome Co. Practical Aspects of Gradient-Enhanced Heteronuclear Correlation Experiments with Small Molecules R.C. Crouch, Ann O. Davis, & Gary E. Martin, Burroughs Wellcome Co. Triple Resonance Isotope Edited Spectroscopy: A New Method for Metabolite Identification W.C. Hutton, J.K. Gard, J.R. Garbow, & J.J. Likos Monsanto Corporate Research Susceptibility Plugs- Theoretical Considerations Toby Zens & Jim Moore, Nalorac Microcells or Susceptibility Plugs at 5 & 8mm Ad Bax, Frank Ray, & Stephan Grzesiek, N.I.H. Spin-Locks, 2H decoupling, and Other Protein Spin Gymnastics at 8mm R. Andrew Byrd, Amanda S. Altieri, & Donna M. Baldisseri, NCI - FRDC Very High Temperature NMR of Polymers Thomas A. Early & Elizabeth A. Williams, General Electric Co. New Results From An H/C/X Triple Resonance Gradient Probe Peter Rinaldi, University of Ohio, Akron