From owner-structural-nmr@net.bio.net Mon Aug 01 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!bioc.cam.ac.uk!arcr1 From: arcr1@bioc.cam.ac.uk (Andy Raine) Newsgroups: bionet.structural-nmr Subject: Re: Degenerate NOES Date: 2 Aug 1994 11:06:35 GMT Organization: Somewhere in the University of Cambridge Lines: 15 Distribution: world Message-ID: <31l9br$5uv@lyra.csx.cam.ac.uk> References: <31l7d8$56s@lyra.csx.cam.ac.uk> NNTP-Posting-Host: nirvana.bioc.cam.ac.uk Ben, Why not use the sort and uniq utilities (you are using a Unix machine aren't you?) to sort the file and pull out unique occurences of lines. Andrew -------------------------------------------------------------------------------- Dr. Andrew Raine +44 223 333744 Department of Biochemistry or 333499 University of Cambridge Tennis Court Road Cambridge CB2 1QW United Kingdom -------------------------------------------------------------------------------- From owner-structural-nmr@net.bio.net Mon Aug 01 23:00:00 1994 Path: biosci!ncifcrf.gov!rabyrd From: rabyrd@ncifcrf.gov (R. Andrew Byrd) Newsgroups: bionet.structural-nmr Subject: Position Available Date: 2 Aug 1994 08:02:40 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 42 Sender: daemon@net.bio.net Distribution: world Message-ID: <9408021459.AA23881@nmrsgi2.ncifcrf.gov> NNTP-Posting-Host: net.bio.net NMR Electronics Engineer Position There is an immediate opening for an electronics engineer dedicated to NMR instrumentation at the Frederick Cancer Research and Development Center, Frederick, MD. This position involves both the general maintenance, repair, and upkeep of five (5) spectrometers and the involvement in development projects for adding new or enhanced capabilities to the spectrometers. The spectrometers include Unity-plus 600 and Unity-plus 500 systems equipped with four RF channels and pulsed field gradients [located in the lab of R. Andrew Byrd, Macromolecular NMR Section, ABL-Basic Research Program] and XL-200, VXR-500 and NT-300WB (currently being upgraded) systems in the lab of Drs. Bruce Hilton and Gwen Chmurny [Chemical Synthesis and Analysis Laboratory, PRI-Dyn Corp., FCRDC]. The desired candidate will have a sound fundamental knowledge of electronics, both analog RF and digital, and experience with NMR equipment. A minum of 2 years experience in instumentation electronics is required. Salary is comensurate with qualitfications. Interested candidates should contact either of the following parties: R. Andrew Byrd Macromolecular NMR Section ABL-Basic Research Program email: rabyrd@nmrsgi2.ncifcrf.gov Bruce Hilton Chemical Synthesis and Analysis Lab. PRI-Dyn Corp. FCRDC email: hilton@ncifcrf.gov ---------------------------------------------------------------------------- ------------------ Dr. R. Andrew Byrd Macromolecular NMR/MSL/ABL TEL: 301-846-1407 FAX: 301-846-6195 From owner-structural-nmr@net.bio.net Mon Aug 01 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!swrinde!pipex!lyra.csx.cam.ac.uk!bioc.cam.ac.uk!arcr1 From: arcr1@bioc.cam.ac.uk (Andy Raine) Newsgroups: bionet.structural-nmr Subject: Re: Degenerate NOES Date: 2 Aug 1994 16:26:11 GMT Organization: Somewhere in the University of Cambridge Lines: 38 Distribution: world Message-ID: <31ls33$cus@lyra.csx.cam.ac.uk> References: <31l7d8$56s@lyra.csx.cam.ac.uk> <31l9br$5uv@lyra.csx.cam.ac.uk> <31lb38$6ij@lyra.csx.cam.ac.uk> NNTP-Posting-Host: sheol.bioc.cam.ac.uk In article <31lb38$6ij@lyra.csx.cam.ac.uk>, bjd12@cus.cam.ac.uk (Ben Davis) writes: > Andy Raine (arcr1@bioc.cam.ac.uk) wrote: > : Ben, > > : Why not use the sort and uniq utilities (you are using a Unix machine aren't you?) to sort the file and pull out unique occurences of lines. > > > -- > Sorry, I should have made myself clearer. The problem is that the lines are > not unique - I want to pull out lines in which, say, fields 2 and 5 are the > same as fields 5 and 2 on a previous line. Identical lines I can cope with, > using uniq and sort; this is trickier (or at least I can't see an easier way > of doing it). > > Ben > ______________________________________________________________________________ > > Ben Davis, > MRC Protein Function and Design, > Cambridge, UK > ______________________________________________________________________________ > > "They can make me do it, but they can't make me do it with dignity." In that case, how about using awk to reorder the entries, and then use sort and uniq as before. Andrew -------------------------------------------------------------------------------- Dr. Andrew Raine +44 223 333744 Department of Biochemistry or 333499 University of Cambridge Tennis Court Road Cambridge CB2 1QW United Kingdom -------------------------------------------------------------------------------- From owner-structural-nmr@net.bio.net Mon Aug 01 23:00:00 1994 Path: biosci!rutgers!csn!ub!galileo.cc.rochester.edu!newstand.syr.edu!wtwinter From: wtwinter@newstand.syr.edu (William T. Winter) Newsgroups: bionet.structural-nmr Subject: meetings?? Date: 2 Aug 1994 04:59:43 GMT Organization: Syracuse University, Syracuse NY, USA Lines: 8 Message-ID: <31kjrv$vp@newstand.syr.edu> NNTP-Posting-Host: gamera.syr.edu X-Newsreader: TIN [version 1.2 PL2] - anyone have the mailing address ofr registration materials for the summer school on nmr of biological macromolecules to be held in Erice, Sicily in May 1995? =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Dr. William T. Winter Phone: (315)470-6876 315 Baker Lab FAX: (315)470-6856 SUNY-ESF Internet: wtwinter@mailbox.syr.edu Syracuse, NY 13210-2786 From owner-structural-nmr@net.bio.net Mon Aug 01 23:00:00 1994 Path: biosci!agate!spool.mu.edu!howland.reston.ans.net!gatech!newsxfer.itd.umich.edu!uunet!pipex!lyra.csx.cam.ac.uk!bjd12 From: bjd12@cus.cam.ac.uk (Ben Davis) Newsgroups: bionet.structural-nmr Subject: Degenerate NOES Date: 2 Aug 1994 10:33:12 GMT Organization: University of Cambridge, England Lines: 19 Message-ID: <31l7d8$56s@lyra.csx.cam.ac.uk> NNTP-Posting-Host: grus.cus.cam.ac.uk X-Newsreader: TIN [version 1.2 PL2] Hi, Has anyone got a programme or shell script to search through text file and pull out duplicate NOEs ? Its a pain to have to do it by hand before feeding it to xplor ... thanks, Ben -- ______________________________________________________________________________ Ben Davis, MRC Protein Function and Design, Cambridge, UK ______________________________________________________________________________ "They can make me do it, but they can't make me do it with dignity." From owner-structural-nmr@net.bio.net Mon Aug 01 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!bjd12 From: bjd12@cus.cam.ac.uk (Ben Davis) Newsgroups: bionet.structural-nmr Subject: Re: Degenerate NOES Date: 2 Aug 1994 11:36:08 GMT Organization: University of Cambridge, England Lines: 33 Distribution: world Message-ID: <31lb38$6ij@lyra.csx.cam.ac.uk> References: <31l7d8$56s@lyra.csx.cam.ac.uk> <31l9br$5uv@lyra.csx.cam.ac.uk> NNTP-Posting-Host: grus.cus.cam.ac.uk X-Newsreader: TIN [version 1.2 PL2] Andy Raine (arcr1@bioc.cam.ac.uk) wrote: : Ben, : Why not use the sort and uniq utilities (you are using a Unix machine aren't you?) to sort the file and pull out unique occurences of lines. : Andrew : -------------------------------------------------------------------------------- : Dr. Andrew Raine +44 223 333744 : Department of Biochemistry or 333499 : University of Cambridge : Tennis Court Road : Cambridge : CB2 1QW : United Kingdom : -------------------------------------------------------------------------------- -- Sorry, I should have made myself clearer. The problem is that the lines are not unique - I want to pull out lines in which, say, fields 2 and 5 are the same as fields 5 and 2 on a previous line. Identical lines I can cope with, using uniq and sort; this is trickier (or at least I can't see an easier way of doing it). Ben ______________________________________________________________________________ Ben Davis, MRC Protein Function and Design, Cambridge, UK ______________________________________________________________________________ "They can make me do it, but they can't make me do it with dignity." From owner-structural-nmr@net.bio.net Wed Aug 03 23:00:00 1994 Path: biosci!GIBBS.OIT.UNC.EDU!vaisman From: vaisman@GIBBS.OIT.UNC.EDU (Iosif Vaisman) Newsgroups: bionet.structural-nmr Subject: Molecular Modeling Conference 1994 Date: 3 Aug 1994 18:34:09 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 109 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Molecular Modeling Conference 1994 Fundamentals and Applications for the Pharmaceutical Industry 2-4 October 1994 Brunswick Hilton and Towers, East Brunswick, New Jersey Molecular Modeling Conference 1994 is organized by Advanstar Communications, the publishers of Pharmaceutical Technology, BioPharm, LC-GC, and Spectroscopy magazines. Conference Moderators: Alexander MacKerell, Assistant Professor, Department of Pharmaceutical Sciences, University of Maryland at Baltimore Alexander Tropsha, Assistant Professor, Director, Laboratory for Molecular Modeling, University of North Carolina at Chapel Hill Herschel J.R. Weintraub, Assistant Director, Medicinal Chemistry, R.W. Johnson Pharmaceutical Research Institute Sunday, 2 October 1994 Afternoon Session: Optional Introductory Workshop - Molecular Modeling Basics Instructors: Warren J. Hehre, Wavefunction, Inc., and University of California, Irvine Alexander Tropsha (Session Organizer), University of North Carolina, Chapel Hill Herschel J.R. Weintraub, R.W. Johnson Pharmaceutical Research Institute Monday, 3 October 1994 Plenary Lecture: Molecular Modeling - For Better, For Worse. For Richer, For Poorer. Peter Goodford, University of Oxford, UK On the Effect of Long-range Interactions on Protein Structure, Specificity, & Ligand Binding Free Energies Arnie Hagler, Biosym Technologies, Inc. Modeling Selectivity in Organic Reactions Warren J. Hehre, Wavefunction, Inc. and University of California, Irvine General Representation and Solution of the QSAR Problem Based Upon Tensor Analysis A. J. Hopfinger, University of Illinois at Chicago Rapid Prediction of Binding Energies Using Continuum Methods Barry Honig, Columbia University Pharmacophore Determination: The Critical Decision in Ligand-Based Design Richard D. Cramer, Tripos, Inc. Overview of 3D-Searching: A Powerful Technique for Computer-Assisted Molecular Design Robert S. Pearlman, University of Texas, Austin Tuesday, 4 October 1994 X-ray Crystallographic Analysis of Macromolecular Structures Wayne A. Hendrickson, Columbia University Free Energy Modeling Monte Pettitt, University of Houston Multidimensional Heteronuclear NMR of Proteins Angela M. Gronenborn, NIDDK, National Institutes of Health Models of G Protein-Linked Receptors: How Do We Get Them and What Can We Do With Them? Charles Hutchins, Abbott Laboratories Comparative Homology Modeling: What Is It Good For and How Well Does It Work? Jonathan Greer, Abbott Laboratories De Novo Predications of Quaternary Protein Structure: Applications to Coiled Coils Jeffrey Skolnick, Scripps Research Institute Computer Assisted Ligand Design I.D. Kuntz, University of California, San Francisco Retrospective and Prospective Successes of Molecular Modeling in the Pharmaceutical Industry Peter Gund, Molecular Simulations Inc. Registration Information To register or to receive a copy of the conference program brochure, please call the Molecular Modeling Conference Registrar at (800) 343-3423 or (503) 343-1200. Fees for Molecular Modeling Conference include all course materials, a copy of the conference proceedings, admission to the Technology Demonstration Room, the Optional Introductory Workshop, and refreshment breaks. Fees Early (postmarked by 19 August 1994): $545.00 Regular (postmarked after 19 August 1994): $645.00 On-Site: $695.00 For more information, contact: Molecular Modeling Conference 1994 859 Willamette Street Eugene, OR 97401-6806 Phone: (800) 343-3423 or (503) 343-1200 Fax: (503) 343-7024 From owner-structural-nmr@net.bio.net Wed Aug 03 23:00:00 1994 Path: biosci!REN.ONYX-PHARM.COM!bkarlak From: bkarlak@REN.ONYX-PHARM.COM (Brian Karlak) Newsgroups: bionet.structural-nmr Subject: protein structures . . . Date: 4 Aug 1994 13:42:42 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <9408042047.AA16544@ren.onyx-pharm.com> NNTP-Posting-Host: net.bio.net Does anyone know of a public domain Net site for NMR-derived protein structures? Are these stored in the Brookhaven database? Thanks, Brian Karlak Onyx Pharmaceuticals "For I am a cat, and since when has a cat given anyone a straight answer?" From owner-structural-nmr@net.bio.net Wed Aug 03 23:00:00 1994 Path: biosci!agate!headwall.Stanford.EDU!morrow.stanford.edu!camis.Stanford.EDU!holbrook From: holbrook@camis.Stanford.EDU (Robin Holbrook) Newsgroups: bionet.structural-nmr,bionet.cellbiol,bionet.xtallography Subject: NMR Summer Course in Italy Date: 4 Aug 1994 19:15:54 GMT Organization: Center for Advanced Medical Informatics at Stanford Lines: 13 Distribution: world Message-ID: <31repa$2kr@morrow.stanford.edu> NNTP-Posting-Host: camis.stanford.edu Xref: biosci bionet.structural-nmr:185 bionet.cellbiol:783 bionet.xtallography:1053 May 22-30, 1995 International School of Biological Magnetic Resonance, 2nd Course: "Dynamics and the Problem of Recognition in Biological Macromolecules" - Ettore Majorana Centre for Scientific Culture, Erice, Sicily, Italy For information and/or registration contact either: holbrook@camis.stanford.edu (Robin Holbrook, Course Administrator) or the Directors: Dr. Oleg Jardetzky (Email: jardetzky@camis.stanford.edu Fax: 415/723-2253) or Dr. Jean-Francois Lefevre (Email: lefevre@bali.u-strasbg.fr Fax: +33/88 65 53 43) From owner-structural-nmr@net.bio.net Wed Aug 03 23:00:00 1994 Path: biosci!sb.com!maclachlan_l%frgen.dnet From: maclachlan_l%frgen.dnet@sb.com Newsgroups: bionet.structural-nmr Subject: Position vacant. Date: 4 Aug 1994 08:11:50 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 48 Sender: daemon@net.bio.net Distribution: world Message-ID: <9408041503.AA03157@phinet.smithkline.com> NNTP-Posting-Host: net.bio.net POSITION VACANT. A temporary vacancy will be arising in the Biological NMR Section in Analytical Science, SmithKline Beecham Pharmaceuticals, due to a period of maternity leave. The position will become vacant in October/November 1994 and is expected to last until March or April 1995. Responsibilities of the job include maintaining a Bruker AMX-500 spectrometer, based at SB's Harlow site, in good running order, pursuing research on biomacromolecular structural topics, and assisting other users of the instrument. We are seeking someone with wide experience of NMR experimentation, preferably in the field of macromolecular structure determination, who is familiar with Bruker AMX series spectrometers. Knowledge of pulse sequence and experiment design and programming would be desirable. Please make informal enquiries to Dr. Lesley MacLachlan, Dr. David Reid or Dr. Julia Hubbard at the addresses below. Lesley K MacLachlan Phone: (0438)-782007 Analytical Science Fax: (0438)-782570 SmithKline Beecham Pharmaceuticals E-mail: maclachlan_l%frgen.dnet@sb.com The Frythe Welwyn Hertfordshire AL6 9AR United Kingdom. David G Reid Phone: (0438)-782345 Analytical Science Fax: (0438)-782570 SmithKline Beecham Pharmaceuticals E-mail: reid_d%frgen.dnet@sb.com The Frythe Welwyn Hertfordshire AL6 9AR United Kingdom. Julia A Hubbard Phone: (0279)-622398 Analytical Science Fax: (0279)-622386 SmithKline Beecham Pharmaceuticals E-mail: hubbardja%frgen.dnet@sb.com Coldharbour Road The Pinnacles Harlow Essex CM19 5AD United Kingdom. ------------------------------------------------------------------------------- Lesley K MacLachlan SmithKline Beecham Pharmaceuticals Phone: (0438)-782007 E-mail: maclachlan_l%frgen.dnet@sb.com -------------------------------------------------------------------------------- From owner-structural-nmr@net.bio.net Wed Aug 03 23:00:00 1994 Newsgroups: bionet.structural-nmr Path: biosci!CS.Arizona.EDU!uunet!pipex!lyra.csx.cam.ac.uk!warwick!doc.ic.ac.uk!nessie!mbdtihe From: mbdtihe@nessie.mcc.ac.uk (Tim Horne) Subject: Wavetek freq. synthesiser Message-ID: <1994Aug4.141341.22004@nessie.mcc.ac.uk> Organization: Manchester Computing Centre Date: Thu, 4 Aug 1994 14:13:41 GMT Lines: 14 We have a Wavetek freq. synthesiser, model. 5131-01-51026, but no documentation at all. Does anyone out there have any documentation or information that would enable us to use it successfully? Tim Horne Dept of Chemistry, University of Manchester, Manchester M13 9PL UK Email tim.horne@man.ac.uk Fax +44 61 275 4598 Phone +44 61 275 4581 From owner-structural-nmr@net.bio.net Thu Aug 04 23:00:00 1994 Path: biosci!newshost.lanl.gov!transposon.lanl.gov!pxc From: pxc@transposon.lanl.gov (Paolo Catasti) Newsgroups: bionet.structural-nmr Subject: Hydrogen bonds in peptides Date: 5 Aug 1994 17:34:27 GMT Organization: Los Alamos National Laboratory, T-10 Lines: 12 Distribution: bionet Message-ID: <31tt73$9od@newshost.lanl.gov> NNTP-Posting-Host: transposon.lanl.gov Hello, I'm basically interested in checking the presence of hydrogen bonds in a peptide i'm studying. I'm trying to do that monitoring the temperature dependence of chemical shifts of labile protons. Does anybody have any reference to suggest me for such a problem? Thanks, Paolo Catasti From owner-structural-nmr@net.bio.net Thu Aug 04 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!sunic!trane.uninett.no!daresbury!not-for-mail From: " (Ton Rullmann)" Newsgroups: bionet.structural-nmr Subject: Re: protein structures . . . Date: 5 Aug 1994 10:03:56 +0100 Lines: 33 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <31sv9s$234@mserv1.dl.ac.uk> Original-To: str-nmr@dl.ac.uk > > > Does anyone know of a public domain Net site for NMR-derived protein > structures? Are these stored in the Brookhaven database? > > Thanks, > Brian Karlak > Onyx Pharmaceuticals > > "For I am a cat, and since when has a cat given anyone a straight answer?" > > > Yes, they are (if the authors deposited them, and when they have got through the registration procedure - which may take time). At the PDB gopher server (gopher://pdb.pdb.bnl.gov) you can search on keywords, e.g. the entry name, author name, or a string like "NMR". I believe, however, that this search also finds entries having that particular string somewhere in the text of the header - so you might get a few wrong hits (but not many crystallographic entries will contain the string NMR). You can also go to the NIH server, which has an interesting display option, and a different (??) search method: http://www.nih.gov/htbin/pdb. Hope this helps, Ton Rullmann. -- | 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 Sat Aug 06 23:00:00 1994 Newsgroups: bionet.general,bionet.xtallography,bionet.structural-nmr Path: biosci!daresbury!trane.uninett.no!eunet.no!nuug!EU.net!uunet!munnari.oz.au!mel.dit.csiro.au!dmp.csiro.au!lachlan From: lachlan@dmp.csiro.au (Lachlan Cranswick) Subject: Announcing Scientist Friendly MS-Windows Internet Kit Message-ID: <1994Aug7.031011.24841@dmp.csiro.au> Organization: CSIRO Division of Mineral Products, Melbourne, AUSTRALIA Date: Sun, 7 Aug 1994 03:10:11 GMT Lines: 548 Xref: biosci bionet.general:10607 bionet.xtallography:1064 bionet.structural-nmr:189 ANNOUNCING SCIENTIST FRIENDLY MS WINDOWS INTERNET KIT ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ (One stop Winsock Shop) QUICK INSTALL :- ---- Obtaining the files. anonymous ftp to :- sol.dmp.csiro.au:/pub/internet/all/internet.exe (192.68.132.2) sol.dmp.csiro.au:/pub/internet/floppy/internt1.exe sol.dmp.csiro.au:/pub/internet/floppy/internt2.exe US mirror (expires in October) :- ftp://ftp.alumni.caltech.edu/pub/dank/internet-kit/internet.exe (ftp.alumni.caltech.edu:/pub/dank/internet-kit) --- Installing the files :- (the -d option is very important as this creates subdirectories and puts files in their correct place). internet c:\ -d or internt1 c:\ -d internt2 c:\ -d ----- 1. INTRODUCTION 2. GETTING THE SOFTWARE VIA ANONYMOUS FTP 3. ASSUMED KNOWLEDGE FOR INSTALLATION 4. WHAT SOFTWARE IS IN THIS KIT 5. BEFORE STARTING 6. NETWORK HARDWARE AND PC/SOFTWARE REQUIREMENTS 7. TO INSTALL OR NOT TO INSTALL THE TRUMPET WINSOCK? 8. LOADING ALL THE SOFTWARE ONTO YOUR PC 9. INSTALLING TRUMPET WINSOCK THE WINSOCK INSTALLATION BEGINS 10. INSTALLING THE INTERNET SOFTWARE ADDING THE WINDOWS PROGRAM ICONS HGOPHER WS_FTP TRMPTEL Wintrumpet Newsreader WinQVT 11. FINISHED! ========================================= INTRODUCTION This might help people who are trying to find MS-Windows internet software without having to browse several different sites and go through several different installation procedures. This is version 1.00 of this one-stop-shop so please be on the lookout for any errors. Also, suggestions of new software and/or viewers for MOSAIC and GOPHER and how to install them would be appreciated. ------- GETTING THE SOFTWARE VIA ANONYMOUS FTP This Scientist friendly MS Windows internet kit available by anonymous ftp from :- sol.dmp.csiro.au:/pub/ms-win-internet-kit/all/internet.exe (2181885) (192.68.132.2) (All the files in one pkzip self extracting exe file). US mirror (expires in October) :- ftp://ftp.alumni.caltech.edu/pub/dank/internet-kit/internet.exe (ftp.alumni.caltech.edu:/pub/dank/internet-kit) or sol.dmp.csiro.au:/pub/ms-win-internet-kit/floppy/internt1.exe (1200132) sol.dmp.csiro.au:/pub/ms-win-internet-kit/floppy/internt2.exe (994559) (Files to fit onto 1.2 Meg (and thus 1.44 Meg) floppy disks). All the software packages given in this kit is either public domain software or shareware. Some of this software is deliberately not the most recent versions. But it has been found to work reliably and be fairly easy for a "casual" MS-Windows user to install. Please email if there are any errors in the installation. ----- User friendly internet software is also available for Mac users at :- sol.dmp.csiro.au:/pub/mac And (friendly?) UNIX software also at :- sol.dmp.csiro.au:/pub/unix ----------------------------- ASSUMED KNOWLEDGE FOR INSTALLAION Some basic knowledge of the internet is required as well as editing with Windows Notepad. It also assumes you know how to use anonymous ftp to get the files. If not - consult you local PC/internet guru who should be able to help you. -------------------------------------------------- WHAT SOFTWARE IS IN THIS KIT This kit includes :- Trumpet winsock - shareware TCP-IP software (one of the best!) WINQVT - mainly telnet (but has other services - i.e., POP mail, NEWS, FTP) (you can print telnet screens to printer with ALT F2) NCSA Mosaic WWW client - old 16 bit version with picture viewer pre-installed. (easy to load). A new fast 32 bit version is available but requires Win32s to be installed prior to use for Win 3.1 and 3.11. HGOPHER - gopher client software WINTRUMPET - presently the best user-friendly Usenet newsreader around (Also has decent POP Mail) (my opinion only). WS_FTP - Very user friendly FTP program (point and click). TRMPTEL - Simple no-frills VT100 telnet program. -------- BEFORE STARTING (you must consult your system manager). You need to know :- Your network's "Domain Name" Your logon name - for telnet. Your Email address. The IP address and name of your PC The IP address and name of your Name Server. The IP address and name of your Gateway. The IP address and name of your News Server (Your system manager will have to edit the news server's nntp_access file to allow your PC to get news from the news server) The IP address and name of your Mail (SMTP/POP) Server. --- NETWORK HARDWARE AND INSTALLATION REQUIREMENTS This assumes that your PC has a correctly installed ethernet card and a link into the internet. SLIP is also possible via a PC serial port but your internet vendor would have to give you installation instructions. If you do not have Winsock already running, it assumes packet drivers are already installed and correctly configured. While it can be changed with user modification, this installation also assumes that :- MS-Windows is installed in the c:\windows directory. That you have at least 6 Meg free hard-disk on the C:\ drive. ---- TO INSTALL OR NOT TO INSTALL THE TRUMPET WINSOCK? A very brief (and possibly inaccurate) explanation of WINSOCK. The winsock protocol (Winsockets) is the "standard" TCP-IP protocol for MS-Windows to allow running of internet and network software that is Winsock complient. If you already have winsock(tcp-ip) installed on your system, ignore the following winsock installation procedures. If you are using another network protocol such as Windows for Workgroups NDIS drivers, PCNFS, etc, consult your system manager on how to get Winsock on your system. (i.e., ignore the following winsock installation procedures). For Windows for Workgroups 3.11 - a Microsoft 32 bit beta (bit flakey) winsock is available from :- sol.dmp.csiro.au:/pub/ms-winsock/MTCPB3.EXE (192.68.132.2) (self extracting exe file). (i.e., ignore the following winsock installation procedures). Note that some network software supports winsock by default. This includes Frontier Technology's Super TCP for Windows. (i.e., ignore the following winsock installation procedures). If you have Windows NT - buy the TCP-IP pack from Microsoft which gives you winsock by default. (i.e., ignore the following winsock installation procedures). If you have no network protocol installed or just have packet drivers installed - try applying the winsock installation procedures which follow. ------- LOADING ALL THE SOFTWARE ONTO YOUR PC. Assuming you have already ftp'd the software over :- Go into the directory or drive the file is located and type (this creates subdirectories) :- (the -d option is very important as this creates subdirectories and puts files in their correct place). internet c:\ -d For floppy disk files. internt1 c:\ -d internt2 c:\ -d This will load files into your c:\windows directory. mosaic.ini hgopher.ini internet.grp vt220.fon wnnetdll.sym wnqvtnet.sym Into your c:\windows\system directory vt100.fon wnnetdll.sym wnqvtnet.sym And will also create the following directory structure with files installed in their correct place :- c:\tmp c:\temp c:\internet c:\internet\annotate c:\internet\autoexec c:\internet\ethernet c:\internet\ethernet\ne2000 c:\internet\ethernet\ne2000\pktdrv c:\internet\ethernet\smc c:\internet\ethernet\smc\diagnose c:\internet\ethernet\smc\ezsetup c:\internet\ethernet\smc\pkt_drv c:\internet\gopher c:\internet\mail c:\internet\mosaic c:\internet\mosaic\lview c:\internet\mosaic\wham c:\internet\mosaic\wplany c:\internet\news c:\internet\qvtnet c:\internet\vt100 c:\internet\windows c:\internet\windows\system c:\internet\winsock c:\internet\wintrump c:\internet\ws_ftp ------------------ INSTALLING TRUMPET WINSOCK This is for a PC with network/ethernet card correctly installed and configured with packet drivers installed with packet vector pointing to 0x60. If you do not know what these are, consult your PC networking guru. If you do not have a packet driver for your ethernet card - a large list of packet drivers are at :- sol.dmp.csiro.au:/pub/ms-winsock/pkt_drv Packet drivers and sample autoexec.bat modifications are given with the internet kit for two common network cards - ne2000 and WD/SMC Elite plus. DO NOT DO ANY OF THIS IF YOU HAVE ANOTHER NETWORK PROTOCOL INSTALLED - THIS WILL CAUSE SERIOUS TROUBLE. AGAIN - BEFORE STARTING (you must consult your system manager). You need to know :- Your network's "Domain Name" Your logon name - for telnet. Your Email address. The IP address and name of your PC The IP address and name of your Name Server. The IP address and name of your Gateway. The IP address and name of your News Server (Your system manager will have to edit the nntp_access file to allow your PC to get news from the news server) The IP address and name of your Mail Server. ---------------- THE WINSOCK INSTALLATION BEGINS. IGNORE THIS IF YOU HAVE ANY OTHER NETWORK SOFTWARE RUNNING). Assuming that you have your packet driver correctly installed. --- Use the Windows notepad to edit c:\autoexec.bat Directly after the packet driver line add:- c:\internet\winsock\winpkt 0x60 Save the file and exit. --- EDIT (using notepad) C:\INTERNET\WINSOCK\TRUMPWSK.INI Where indicated :- Add your PC's IP address, gateway IP address, dns (domain name server) IP address, and the domain name. Save and exit the file. ---- Copy the c:\internet\windows\protocol file to c:\windows Copy the c:\internet\windows\services file to c:\windows Copy the c:\internet\windows\hosts file to c:\windows ---- Use Notepad to edit the c:\windows\hosts file. Add the IP and Name of your PC. Add the IP and Name of the DNS (domain name server) Add the IP and Name of the Gateway Save and exit the file. --- Go into the STARTUP FOLDER. Add a new ICON by File, New - and Browse to the c:\internet\winsock\ directory and select the tcpman.exe file. Click on the Run Minimized button and press OK. Now exit Windows and re-boot your computer. When you run Windows again - you will have Winsock/TCP-IP running and can use a variety of internet software - CONGRATULATIONS!!!! ========================= ========================= INSTALLING THE INTERNET SOFTWARE. ---- ADDING THE WINDOWS PROGRAM ICONS In Windows. Add a new folder (Program Group) with the name "Internet Kit" and Group File of - internet.grp. You will now have a new folder called "Internet Kit" with all the icons correctly installed. Do not run any of them yet as they still have to be configured. ------- HGOPHER Gopher will run quite OK. If you wish to change the homepage, go into Options, Gopher Setup and enter the home page you wish to see on startup. ------- WS_FTP This will work Instantly. The only host there is to anonymously log into sol.dmp.csiro.au. Add other hosts as you desire. ------- TRMPTEL (telnet program) This will work without configuration. Just type in the host you wish to log into. If you wish to log into a host all the time, use File Properties to add the host in the Command Line. ------- MOSAIC WWW (World Wide Web) Client. The LVIEW gif, jpg, etc picture viewer is already correctly installed. Use notepad to edit the c:\windows\mosaic.ini file. Add your email address on the second line. Mosaic will now work properly with your real email address should you use this option You can now go wild on the WWW. There are other options you can modify - but this will start you off quite happily. ------- Wintrumpet Newsreader. When you run WinTrumpet, you will be prompted for information such as your :- News Host Name Mail Host Name Your Email Address Full Name Organisation (Your signature file is at c:\internet\sig.txt, use notepad to edit this file). The rest is optional and depends if you want to use WinTrumpet as your POP mail program). You will then be prompted for newsgroups to add. Select a couple immediately to test out your NNTP connection (i.e., sci.chem.electrochem). ------- WINQVT. Use notepad to edit the c:\internet\qvtnet\qvtnet.ini file. Search for ??? and replace as required. It occurs in this order :- PC host name. PC IP Address. Router/Gateway Domain Name Name Server (Domain Name Server) The rest is optional depending of whether you want to Use QVTNET also as a mail program, ftp client and/or server, newsreader and talk to a line printer. ------ FINISHED In theory, you have now completed the installation. Good luck! :-) ------- Standard disclaimers apply - user is 100% responsible for any hassles, problems or loss of data. (It might not be lawyer proof but it will let me sleep nights!) :-) ------------------------- -- Lachlan Cranswick - CSIRO _--_|\ lachlan@dmp.CSIRO.AU Division of Mineral Products / \ tel +61 3 647 0367 PO Box 124, Port Melbourne \_.--._/ fax +61 3 646 3223 3207 AUSTRALIA v From owner-structural-nmr@net.bio.net Sun Aug 07 23:00:00 1994 Path: biosci!INDIANA.EDU!mpagel From: mpagel@INDIANA.EDU (Marty Pagel) Newsgroups: bionet.structural-nmr Subject: Re: Hydrogen bonds in peptides Date: 8 Aug 1994 06:53:59 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 40 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <31tt73$9od@newshost.lanl.gov> NNTP-Posting-Host: net.bio.net On 5 Aug 1994, Paolo Catasti wrote: > Hello, > > I'm basically interested in checking the presence of hydrogen bonds in a > peptide i'm studying. I'm trying to do that monitoring the temperature > dependence of chemical shifts of labile protons. > > Does anybody have any reference to suggest me for such a problem? > > Thanks, > > Paolo Catasti > > > Hi Paolo, This effect was reported in: Dyson, HJ, Rance, M, Houghten, RA, Lerner, RA, & Wright, PE (1988). Folding of immunogenic peptide fragments of proteins in water solution. 1. Sequence requirements for the formation of a reverse turn. J Mol Biol, v. 201, pp. 161-200. However, I've heard that this may not be a reproducible dependence for all peptides in various solvents. Unfortunately, the absence of a correlation can mean that it is difficult to publish, so references about a non-correlation may be difficult to find. For instance, the following briefly mentions that no correlation was found (although TFE is an unusual solvent): Storrs, RW, Truckses, D. & Wemmer, DE (1992) Helix propagation in trifluoroethanol in solutions. Biopolymers, v. 32, pp. 1695-1702. Marty Pagel Chemistry Department mpagel@indiana.edu Indiana University (812)-855-6492 Bloomington, IN 47405-4001 (812)-855-8300 (fax) From owner-structural-nmr@net.bio.net Sun Aug 07 23:00:00 1994 Newsgroups: bionet.structural-nmr,bionet.molbio.proteins,bionet.molec-model Path: biosci!agate!msuinfo!harbinger.cc.monash.edu.au!bunyip.cc.uq.oz.au!munnari.oz.au!mel.dit.csiro.au!dmp.csiro.au!lachlan From: lachlan@dmp.csiro.au (Lachlan Cranswick) Subject: SCA - "CRYSTAL XIX" - Ballarat Australia - April 1995 Message-ID: <1994Aug8.084900.15720@dmp.csiro.au> Organization: CSIRO Division of Mineral Products, Melbourne, AUSTRALIA Date: Mon, 8 Aug 1994 08:49:00 GMT Lines: 157 Xref: biosci bionet.structural-nmr:192 bionet.molbio.proteins:2422 bionet.molec-model:65 CRYSTAL XIX First Announcement of the Nineteenth Meeting of the Society of Crystallographers in Australia 18 - 21 April, 1995 University of Ballarat, Victoria INTRODUCTION The Organising Committee invites all crystallographers to attend the Nineteenth Meeting of the Society of Crystallographers in Australia. The conference will be held at the University of Ballarat in country Victoria, from the evening of Tuesday the 18th of April ('Easter Tuesday') to lunchtime on Friday the 21st of April, 1995. THE VENUE Ballarat University is set on 110 hectares of natural bushland about 10 km south east of the city of Ballarat. Very pleasant on-campus accommodation is provided by the Mount Helen Residence, capable of accommodating 514 people in single bed/study rooms at about $23 per night (room only). Common room and games room, kitchen areas, laundries and outdoor barbecue facilities are available in the residential complex. Numerous motels and other forms of accommodation are available within a few km of the campus. The University has a full range of lecture and seminar facilities. It also has full AARNet access,and e-mail and Internet access can be easily arranged on request for all participants. Excellent recreational facilities are available including fully equipped gymnasia, jogging and walking tracks and an Arboretum. All meals are provided by the University's catering service and fully licensed bar facilities serve the various function rooms. TRANSPORT Ballarat University is one and a half hours drive from the centre of Melbourne. There are up to six shuttle bus services per day from Tullamarine airport to Ballarat. Cost, about $15 each way. Numbers permitting, these buses will detour to the University campus. The committee will help coordinate private car transport from Melbourne. Train and private bus services also run from the centre of Melbourne to Ballarat. TENTATIVE COSTS The Conference Committee has obtained a favourable arrangement with the University to keep costs to a minimum. The University has its own catering system for all meals at reasonable prices. Drinks are at normal bar prices. We anticipate that the all inclusive cost of accommodation plus meals from Tuesday evening to Friday lunch will be less than $250 per person. Tentative registration costs are $100 for normal registration and $50 for students. SCIENTIFIC PROGRAM The Conference Lecture will be presented by the 1987 Fellow, Dr. Michael Hart. In addition to the usual topic areas (protein crystallography, inorganic and mineral structures etc) we welcome contributions in areas such as Applications of synchrotron radiation Structure studies using less traditional methods such as XANES, EXAFS, MASNMR, DAFS Structure determinations using TEM/SAED and ND Crystallographic teaching New developments in crystallographic hardware/software 1995 is the centenary of the discovery of X-rays and the Australian Academy of Science is sponsoring a conference celebrating this event in the week following Crystal XIX. We envisage that a special lecture will be devoted to commemorating this event in the Australian context. Further details will be given in the second circular. SOCIAL PROGRAM This will include a mixer (with possibly a wine tasting) on the Tuesday evening and the conference dinner on the Thursday evening. The Conference Lecture will be presented on Wednesday evening, allowing a free afternoon on Wednesday for various activities which could include visits to Sovereign Hill, to the Pyrenees Wineries and a tour of Ballarat and its surrounds. We will be seeking delegates preferences at the time of registration. ABSTRACTS/REGISTRATION Registration forms and a call for abstracts will be sent out at the end of October and the deadline for the submission of both will be 1st February 1995. CONTACT PERSON Further information can be obtained by contacting Lachlan Cranswick at CSIRO Division of Mineral Products, PO Box 124, Port Melbourne, Victoria 3207. Phone (613) 647-0211, Fax (613) 646-3223, e-mail: lachlan@dmp.csiro.au ORGANISING COMMITTEE Lachlan Cranswick (see above) Ian Grey CSIRO Division of Mineral Products, Port Melbourne Phone (613)-647-0211, Fax (613)-646-3223 e-mail: iang@dmp.csiro.au Mike Lawrence Biomolecular Research Institute, Parkville Phone (613)-342-4200, Fax (613)-342-4301 e-mail: mike@rox.mel.dbe.csiro.au Andrew Stevenson CSIRO Division of Materials Science and Technology, Clayton Phone (613)-542-2917, Fax (613)-544-1128 e-mail: stevens@rivett.mst.csiro.au Jonathan White Melbourne University, Chemistry Department, Parkville Phone (613)-344-4621, Fax (613)-347-5180 e-mail: jonathan_white@muwayf.unimelb.edu.au We thank Nikki Scarlett and Neil Manning for their help with the preparation of the first circular. -- Lachlan Cranswick - CSIRO _--_|\ lachlan@dmp.CSIRO.AU Division of Mineral Products / \ tel +61 3 647 0367 PO Box 124, Port Melbourne \_.--._/ fax +61 3 646 3223 3207 AUSTRALIA v From owner-structural-nmr@net.bio.net Sun Aug 07 23:00:00 1994 Newsgroups: bionet.structural-nmr Path: biosci!agate!howland.reston.ans.net!gatech!newsxfer.itd.umich.edu!uunet!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@chemie.uni-kl.de (Uwe Seimet) Subject: Adding hard disk to Bruker AMX Message-ID: Sender: news@rhrk.uni-kl.de Organization: University of Kaiserslautern, Germany Date: Mon, 8 Aug 1994 10:07:18 GMT Lines: 9 Is there anybody who has added a second hard disk to Bruker NMR spectrometers of the AMX type? If yes, did it work? *************************************************************************** * 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 Aug 08 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!europa.eng.gtefsd.com!newsxfer.itd.umich.edu!jobone!news1.oakland.edu!news From: mje@pookie.pass.wayne.edu (Michael J. Edelman) Newsgroups: bionet.structural-nmr Subject: Need peak-counting software or algorithms Date: 9 Aug 1994 14:52:40 GMT Organization: Wayne State University Lines: 19 Message-ID: <32857o$fco@oak.oakland.edu> Reply-To: mje@pookie.pass.wayne.edu NNTP-Posting-Host: pookie.pass.wayne.edu I have a problem that's not directly NMR related, but I've been told that it's a common one in NMR. I have time series data taken at (for instance) 2ms intervals. The data is mostly pretty constant at some baseline level, with sporadic peaks that can occur in very closely spaced bursts. What the investigators I'm working with would like to do is to count the of peaks occuring in a given time period- say, a couple of seconds- and output that data. Up til now they've been outputting plots and manually counting peaks. Can anyone advise? --mike ----------------------------------------------------------------------- Michael Edelman KE8YY Wayne State University mje@pookie.pass.wayne.edu (Sun) Computing & Infomation Technology medelma@waynest1 (BITNET) Planning & Support Services usermje@mts.cc.wayne.edu (MTS) Detroit, MI 48202 1-313-577-0742 From owner-structural-nmr@net.bio.net Mon Aug 08 23:00:00 1994 Path: biosci!stargate.metronet.com!don.woessner From: don.woessner@stargate.metronet.com (Don Woessner) Newsgroups: bionet.structural-nmr Subject: Function of "group" Date: 9 Aug 1994 02:03:12 -0700 Organization: STARGATE BBS - (214) 578-7618 Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: <9408090400091007@stargate.metronet.com> NNTP-Posting-Host: net.bio.net Please mail me information about this E-mail address. What does it do, etc.? Thanks, Don Woessner (of the "Woessner Equations") From owner-structural-nmr@net.bio.net Tue Aug 09 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!newsserver.jvnc.net!netnews.upenn.edu!news.cc.swarthmore.edu!image-slave.swarthmore.edu!user From: ehom1@cc.swarthmore.edu (Erik Forbes Y. Hom) Newsgroups: bionet.structural-nmr Subject: inquiry: base-pair stability constants Followup-To: bionet.structural-nmr Date: 10 Aug 1994 14:55:15 GMT Organization: Swarthmore College Lines: 11 Message-ID: NNTP-Posting-Host: image-slave.swarthmore.edu Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Does anyone know if someone followed up in determining base-pair stability constants in an aqueous environment - I have a paper: Kyogoku, Y. , et al. (1969) Biochim Biophys Acta 179:10-17 that determined these constants but in a deuterochloroform solvent system - which I don't think is entirely biologically practical. If someone could give me some references of this sort, I would be exceedingly grateful. (Are there any nucleic acid specialists out there?). Thanks in advanced, erik From owner-structural-nmr@net.bio.net Tue Aug 09 23:00:00 1994 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: 3D-NOE/NOE back calculation Date: 10 Aug 1994 07:11:04 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net I am looking for available software for back calculation of 3D-NOE/NOE spectra. We are intending to use it primarily for nucleic acids. Thanks, Istvan ------------------------------- Istvan Pelczer, Ph.D. Res. Assist. Professor Chemistry Department, CST Bldg. Syracuse University Syracuse, NY 13244-4100 ph# 315 443 1023 fax# x-4070 ------------------------------- From owner-structural-nmr@net.bio.net Tue Aug 09 23:00:00 1994 Path: biosci!TIFRVAX.TIFR.RES.IN!CHARY From: CHARY@TIFRVAX.TIFR.RES.IN Newsgroups: bionet.structural-nmr Subject: Stability of Proteins Date: 10 Aug 1994 05:42:21 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HFR4VQHDLS004I8L@tifrvax.tifr.res.in> NNTP-Posting-Host: net.bio.net Dear netters, I wish to know the answers for the following questions: 1) What are the methods of protecting protein samples used for NMR experiments from denaturation ? 2) which is the easiest method of determining the ISO-ELECTRIC point of a protein ? With regards, Chary K. V. R ===================================================================== K. V. R. Chary Chemical Physics Group T. I. F. R Colaba Bombay ===================================================================== From owner-structural-nmr@net.bio.net Tue Aug 09 23:00:00 1994 Path: biosci!CS.Arizona.EDU!math.arizona.edu!news.Arizona.EDU!helium.gas.uug.arizona.edu!bear From: bear@helium.gas.uug.arizona.edu (Soaring Bear) Newsgroups: bionet.structural-nmr Subject: keratin structure collaboration Date: 10 Aug 1994 02:42:24 GMT Organization: University of Arizona, Unix Users Group Lines: 9 Message-ID: <329eqg$t65@news.CCIT.Arizona.EDU> NNTP-Posting-Host: helium.gas.uug.arizona.edu Would any NMR folks be interested in a collaboration investigating interaction of keratin & other compounds? bear -- * UU UU SOARING BEAR * * UU UU A Pharmaceutical Molecular Modeling * * UUUU AAA U.A. New Pharmacy 404, Tucson, AZ 85721 * * AA AA e-mail:bear@ellington.pharm.arizona.edu * From owner-structural-nmr@net.bio.net Tue Aug 09 23:00:00 1994 Path: biosci!LAPLACE.CSB.YALE.EDU!abonvin From: abonvin@LAPLACE.CSB.YALE.EDU ("Alexandre Bonvin") Newsgroups: bionet.structural-nmr Subject: Re: 3D-NOE/NOE back calculation Date: 10 Aug 1994 08:45:08 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 52 Sender: daemon@net.bio.net Distribution: world Message-ID: <9408101545.AA29618@laplace.csb.yale.edu> NNTP-Posting-Host: net.bio.net Istvan Pelczer writes: >I am looking for available software for back calculation of 3D-NOE/NOE >spectra. We are intending to use it primarily for nucleic acids. >Thanks, Computing 3D NOE-NOE intensities is not much more complicated than for the 2D case. You only need to multiply the two 2D NOE matrices corresponding to the two mixing times of your 3D experiment. So with software for 2D NOE calculations and a simple extra program you can compute 3D intensities. I have done this using IRMA (Iterative Relaxation Matrix Approach) for generating the 2D matrices and an additional program to multiply these matrices and extract the 3D peaks above a defined threshold. During my PhD in Kaptein's group in Utrecht I also developped a set of routines for direct NOE refinement using 2D and 3D NOE data grouped under the name DINOSAUR . The 3D DINOSAUR version allow the calculation of 3D NOE-NOE intensities, but you need a 3D NOE-NOE peak list as input (while IRMA only requires a structure). This of course will only give you 3D NOE-NOE intensities. You will have to use some other program if you want to simulate the 3D spectrum. For inforamtion on IRMA and DINOSAUR contact Dr. Boelens (boelens@nmr.chem.ruu.nl). Hope this helps, Alexandre =============================================================================== | Alexandre Bonvin PhD | Phone: (203) 432-5066 | | Dept. Mol. Biophys. & Biochemistry | Fax: (203) 432-6946 | | Yale University, 266 Whitney Avenue | Email: abonvin@laplace.csb.yale.edu | | New Haven CT 06511, USA | | =============================================================================== From owner-structural-nmr@net.bio.net Tue Aug 09 23:00:00 1994 Path: biosci!MED.UNC.EDU!sheng From: sheng@MED.UNC.EDU (Sheng Zhong) Newsgroups: bionet.structural-nmr Subject: use felix2.3 pick 4D Date: 10 Aug 1994 10:32:18 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: <9408101732.AA05825@hasty.med.unc.edu> NNTP-Posting-Host: net.bio.net Hi NMRnetter: I have been trying to use Feilx2.3 to pick the whole 4D matrix without success for several days now. What I did is that I first used null plot to get the coordinate drawing and then let the felix pick the whole display region. I got a small portion of real peaks (30% ?) with lots of other picks god knows where are they come from. I am wondering if someone can tell me simple tricks to do the correct picking (Whole Matrix!) before I have to write a macro with lots of loops! Thanks in advance Regards Dr. Sheng Zhong Dept. of Biochem. and Biophys. UNC at Chapel Hill sheng@med.unc.edu From owner-structural-nmr@net.bio.net Wed Aug 10 23:00:00 1994 Path: biosci!NODDY.CM.UTEXAS.EDU!dave From: dave@NODDY.CM.UTEXAS.EDU (david w. hoffman) Newsgroups: bionet.structural-nmr Subject: (none) Date: 11 Aug 1994 10:56:54 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <9408111756.AA00422@noddy.cm.utexas.edu> NNTP-Posting-Host: net.bio.net Dear NMR-netters, I am looking for NMR data processing and display software for a Power Macintosh (6100/60) "power PC". I am biased toward relatively inexpensive stuff. Does anyone have any suggestions? Thanks. Dave Hoffman Dept of Chemistry and Biochemistry Univ. of Texas at Austin dave@noddy.cm.utexas.edu From owner-structural-nmr@net.bio.net Wed Aug 10 23:00:00 1994 Newsgroups: bionet.structural-nmr Path: biosci!agate!howland.reston.ans.net!EU.net!sunic!ki.se!csb.ki.se!ln From: ln@csb.ki.se (Lennart Nilsson) Subject: Re: inquiry: base-pair stability constants Sender: news@ki.se (News admin) Message-ID: Date: Thu, 11 Aug 1994 06:59:23 GMT Lines: 23 Reply-To: ln@csb.ki.se (Lennart Nilsson) References: Nntp-Posting-Host: pike.csb.ki.se Organization: CSB, KI X-Newsreader: mxrn 6.18-9 In article , ehom1@cc.swarthmore.edu (Erik Forbes Y. Hom) writes: |>Does anyone know if someone followed up in determining base-pair stability |>constants in an aqueous environment - I have a paper: Kyogoku, Y. , et al. |>(1969) Biochim Biophys Acta 179:10-17 that determined these constants but |>in a deuterochloroform solvent system - which I don't think is entirely |>biologically practical. If someone could give me some references of this |>sort, I would be exceedingly grateful. (Are there any nucleic acid |>specialists out there?). |> |>Thanks in advanced, |> |>erik |> Base-pairing is relatively weak in aqueous solution, where base stacking tends to dominate, so most base-pairing studies are performed in apolar solvents (chloroform, DMSO). A good reference, with a good bibliography, still is: Saenger, W., Principles of Nucleic Acid Structure. Springer-Verlag, 1984. Check also Raszka&Kaplan, PNAS 69, 2025, 1972 for a qualitative base-pairing study in aqueous solution. good luck! lennart From owner-structural-nmr@net.bio.net Wed Aug 10 23:00:00 1994 Path: biosci!rutgers!csn!yuma!purdue!mozo.cc.purdue.edu!sonata.cc.purdue.edu!(null pointer) From: (null pointer)@sonata.cc.purdue.edu () Newsgroups: bionet.structural-nmr Subject: Re: 3D-NOE/NOE back calculation Date: 10 Aug 1994 23:50:14 GMT Organization: Purdue University Lines: 47 Distribution: world Message-ID: <32bp3m$e17@mozo.cc.purdue.edu> References: NNTP-Posting-Host: sonata.cc.purdue.edu In article ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) writes: > >I am looking for available software for back calculation of 3D-NOE/NOE >spectra. We are intending to use it primarily for nucleic acids. >Thanks, > >Istvan > > >------------------------------- >Istvan Pelczer, Ph.D. >Res. Assist. Professor >Chemistry Department, CST Bldg. >Syracuse University >Syracuse, NY 13244-4100 >ph# 315 443 1023 fax# x-4070 >------------------------------- > > We are developing the 3D version of our NMR simulation and refinement program called MORASS (Multispin Overhauser Relaxation Analysis and Simulations) in the Gorenstein group at Purdue University (will move to UTMB in Texas). Currently, the 3D version can simulate 3D NOE-NOE volumes based on a starting model, and refine the structures based on the newly developed hybrid-hybrid method using exsiting 2D software (Papers will come out in August in JMR). The 2D version of the MORASS code is maintained by Dr. Bruce Luxon in our group and is available via anonymous ftp at dggpi2.chem.purdue.edu. For the 3D code, contact anyone of the following: Dr. David Gorenstein (david@chem.purdue.edu) Dr. Bruce Luxon (bruce@dggpi2.chem.purdue.edu) David Donne (donne@dggpi2.chem.purdue.edu) Qun Zhang (qun@dggpi2.chem.purdue.edu) ---------------------- David Donne Department of Chemistry Purdue University donne@dggpi2.chem.purdue.edu From owner-structural-nmr@net.bio.net Wed Aug 10 23:00:00 1994 Path: biosci!CSA4.LBL.GOV!alee%lcbvax.hepnet From: alee%lcbvax.hepnet@CSA4.LBL.GOV Newsgroups: bionet.structural-nmr Subject: Re: Felix 4D Date: 11 Aug 1994 11:53:42 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 52 Sender: daemon@net.bio.net Distribution: world Message-ID: <940811115221.45001b17@Csa4.LBL.Gov> NNTP-Posting-Host: net.bio.net In responds to Dr. Sheng Zhong's letter: >Hi NMRnetter: >I have been trying to use Feilx2.3 to pick the whole 4D matrix without >success for several days now. What I did is that I first used null plot to get >the coordinate drawing and then let the felix pick the whole display region. I >got a small portion of real peaks (30% ?) with lots of other picks god knows >where are they come from. I am wondering if someone can tell me simple >tricks to do the correct picking (Whole Matrix!) before I have to write a >macro with lots of loops! >Thanks in advance > >Regards > >Dr. Sheng Zhong >Dept. of Biochem. and Biophys. >UNC at Chapel Hill >sheng@med.unc.edu Dear Dr. Zhong, We have encountered the same problem you are having with Felix 2.3 and 4D matrices. I believe that the Felix peak picking algorithm is simply not sophisticated enough to pick 4D peaks in a reliable manner. You can use the null plot trick to have peaks picked automatically, but many peaks are missed and too many noise or artifact peaks ARE picked. In fact, most good peak picking algorithms used for NMR require some editing after execution. In order to get around this problem I have written a couple of Felix macros which allow display of 2D slices from 4D matrices (Felix can already to this, but it is painful to use) and picking of 4D peaks. The peak-picking is done manually, by specifying the center of the peak from two 2D slices. The result is a table (Felix entity) of the coordinates of each 4D peak in points and PPMs. We have found this to work well. It has been written for a 1H/13C HMQC-NOESY-HMQC data set, so the matrix size is hard-wired for the peak-picking, but this should be easy to change for your specific needs. The 2D slice viewing macro is more flexible in that it can handle different matrix sizes. Please e-mail me if you would like more details. Andrew Lee Department of Chemistry UC Berkeley alee@lcbvax.cchem.berkeley.edu From owner-structural-nmr@net.bio.net Thu Aug 11 23:00:00 1994 Path: biosci!rutgers!netnews.upenn.edu!news.cc.swarthmore.edu!psuvax1!news.pop.psu.edu!news.cac.psu.edu!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!bjd12 From: bjd12@cus.cam.ac.uk (Ben Davis) Newsgroups: bionet.structural-nmr Subject: XPLOR topology file Date: 12 Aug 1994 13:41:42 GMT Organization: University of Cambridge, England Lines: 20 Message-ID: <32fu6m$gpp@lyra.csx.cam.ac.uk> NNTP-Posting-Host: grus.cus.cam.ac.uk X-Newsreader: TIN [version 1.2 PL2] Hi, I've got a homoserine (product of CNBr cleavage on Met) in a peptide I want to run an XPLOR job on - has anyone got a topology file for homoserine so I can avoid doing it myself ? (save reinventing the wheel and all that). Thanks, Ben -- ______________________________________________________________________________ Ben Davis, MRC Protein Function and Design, Cambridge, UK ______________________________________________________________________________ "They can make me do it, but they can't make me do it with dignity." From owner-structural-nmr@net.bio.net Thu Aug 11 23:00:00 1994 Path: biosci!rutgers!netnews.upenn.edu!newsserver.jvnc.net!howland.reston.ans.net!torn!nott!nrcnet0.nrc.ca!BRI.NRC.CA!Yi.Zhu From: Yi.Zhu@BRI.NRC.CA (Yi Zhu) Newsgroups: bionet.structural-nmr Subject: Postdoctoral Positions Available Date: 12 Aug 1994 21:18:03 GMT Organization: Institut de recherche en biotechnologie, Montréal Lines: 32 Distribution: world Message-ID: <32goub$p2b@nrcnet0.nrc.ca> NNTP-Posting-Host: bobino.bri.nrc.ca Keywords: NMR, Protein Structure, Protein-Ligand Interaction, Molecular Design POST-DOCTORAL POSITIONS IN NMR STUDIES OF PROTEIN STRUCTURE AND INTERACTIONS The NMR laboratory of the Biotechnology Research Institute (BRI) have one or two postdoctoral/NSERC research fellow positions in the near future (by the end of 94), to work on the solution structure and interactions of proteins and to develop the transferred NOE method for determining the dynamic structures of protein-ligand complexes and for applications in molecular/peptide design. The candidate must have a Ph.D. degree in Chemistry or Biochemistry, have a good understanding of multi-dimensional NMR spectroscopy and principles of protein structure. Experience in protein purification will be an asset. NSERC research fellows will require postdoctoral experience, but we will consider new Ph.D.s if they are independent enough to lead research projects. These positions will be supported by the Natural Science and Engineering Research Council (NSERC) and the Medical Research Council of Canada (MRC). For more information, please contact: Dr. Feng Ni Biotechnology Research Institute 6100 Royalmount Ave. Montreal, Quebec, H4P 2R2 Canada phone: (514)-496-6729 fax: (514)-496-5143 e_mail: fengni@bobino.bri.nrc.ca From owner-structural-nmr@net.bio.net Mon Aug 15 23:00:00 1994 Path: biosci!NODDY.CM.UTEXAS.EDU!dave From: dave@NODDY.CM.UTEXAS.EDU (david w. hoffman) Newsgroups: bionet.structural-nmr Subject: (none) Date: 16 Aug 1994 08:39:20 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <9408161535.AA06161@noddy.cm.utexas.edu> NNTP-Posting-Host: net.bio.net Dear NMR-netters, I am looking for NMR data processing and display software for a Macintosh computer (any variety). I am biased toward relatively inexpensive stuff. Does anyone have any suggestions? Thanks. Dave Hoffman Dept of Chemistry and Biochemistry Univ. of Texas at Austin dave@noddy.cm.utexas.edu From owner-structural-nmr@net.bio.net Tue Aug 16 23:00:00 1994 Path: biosci!IRIS4.CARB.NIST.GOV!tunc From: tunc@IRIS4.CARB.NIST.GOV (John Moult) Newsgroups: bionet.structural-nmr Subject: Request for Structure Prediction targets Date: 17 Aug 1994 11:31:09 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 111 Sender: daemon@net.bio.net Distribution: world Message-ID: <9408171827.AA11643@iris4.carb.nist.gov> NNTP-Posting-Host: net.bio.net CALL FOR SEQUENCES OF STRUCTURES TO PREDICT To all protein NMR Spectroscopists: Many of you will have seen messages from me over the last several months, asking for details of structures you are about to solve. The purpose of those requests was to provide material for a blind test of strcuture prediction methods. As a result of these appeals we have collected 26 prediction targets, and so far have received 27 predictions on eight of those targets from 10 different groups. The prediction experiment will continue until the end of October, and the meeting to discuss the results will take place in Asilomar in December. The following groups have either already submitted some predictions, or have made a commitment to do so: Ruben Abaygan, NYU, USA Geoffrey Barton, Oxford University, UK Steve Benner, ETH, Zurich, Switzerland Tom Blundell, University of London, UK Steve Bryant, NLM, Bethesda, USA David Covell, NCI, Frederick, USA Andrew Coulson, University of Edinburgh, UK David Eisenberg, UCLA, USA Adam Godzik, Scripps, USA Tim Hubbard, MRC, Cambridge,UK Rod Hubbard, MSI, USA. Yo Matsuo, PERI, Japan David Mosenkis, Tripos, USA Chris Sander, EMBL, Germany Mansoor Saqi, Glaxo, UK Harold Scheraga, Cornell University, USA Manfred Sippl, University of Salzburg, Austria Janet Thornton, University of London, UK Gert Vriend, EMBL, Germany Irene Weber, Thomas Jefferson University, USA Peter Wolynes, University of Illinois, USA. Things gave gotten off to a very good start , but we need more prediction targets. We need details of structures of all sizes and types. Small structures (less than 100 residues ) are needed to test some of the ab initio structure prediction methods. Proteins with folds related to those of known structures are needed to test fold identification methods. Proteins with sequences homologous to that of one or more known structures are needed to test comparative modeling methods. So: if you have a structure that you are just solving, and that will remain confidential for a period of at least a month, please fill in the form below and return it to me. The only other thing we will need is a set of co-ordinates for at least limited use by the end of October. Our thanks to those of you who have responded already to our request. With the current targets and some new ones we should really find out what works and what does not in the structure prediction field. ----------------------------------------------------------------------------- John Moult Tel 301-738 6241 Chairman, Organizing Committee. Fax 301-738 6255 email:jmoult@iris4.carb.nist.gov CARB University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850, USA _____________________________________________________________________________ STRUCTURE FOR PREDICTION INFORMATION FORM Please fill out as much of the following as is relevant and email it back to jmoult@iris4.carb.nist.gov (i.e 'reply' to this message) Name and address of group working on the structure: ------------------------------------------------------------------------ Name and other identifiers of the protein, and source organism: ------------------------------------------------------------------------ Amino acid sequence and its source (I.e. database acquisition number and/or journal reference): ------------------------------------------------------------------------ Other references to work on the protein: ------------------------------------------------------------------------ Known homologies: ------------------------------------------------------------------------ Current state of the experimental work: Please briefly describe where things are at, addressing as many of the following points as you wish to/are relevant/can. The more information, the easier it is for a modeler to decide whether to predict your structure. ------------------------------------------------------------------------ protein supply? ------------------------------------------------------------------------ crystals? ------------------------------------------------------------------------ diffraction quality? ------------------------------------------------------------------------ molecular replacement in progress? ------------------------------------------------------------------------ molecular replacement solution in hand? ------------------------------------------------------------------------ heavy atom derivative search in progress? ------------------------------------------------------------------------ heavy atom derivatives in hand? ------------------------------------------------------------------------ interpretable map already? ------------------------------------------------------------------------ estimated date of chain trace completion: ------------------------------------------------------------------------ estimated date of public release of the structure (meeting, paper or pdb) ___________________________________________________________________ From owner-structural-nmr@net.bio.net Tue Aug 16 23:00:00 1994 Path: biosci!sb.com!maclachlan_l%frgen.dnet From: maclachlan_l%frgen.dnet@sb.com Newsgroups: bionet.structural-nmr Subject: 3D NOESY-HSQC/TOCSY-HSQC pulse sequences Date: 17 Aug 1994 09:04:17 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <9408171556.AA18465@phinet.smithkline.com> NNTP-Posting-Host: net.bio.net I'm currently doing some assignment work on a 15N labelled protein using 1H-15N 3D NOESY-HMQC and TOCSY-HMQC, but I am experiencing difficulties with overlap in the 15N dimension due to the peak shape in the HMQC dimension. I've got good results from a 2D HSQC, so has anyone got pulse sequences for 3D NOESY-HSQC and TOCSY-HSQC for a Bruker AMX500 (with tips for setting up) that they could send to me? Many thanks in anticipation, Yours, Lesley MacLachlan. ------------------------------------------------------------------------------- Lesley K MacLachlan SmithKline Beecham Pharmaceuticals Phone: (0438)-782007 E-mail: maclachlan_l%frgen.dnet@sb.com -------------------------------------------------------------------------------- From owner-structural-nmr@net.bio.net Sat Aug 20 23:00:00 1994 Path: biosci!ARIES.SCS.UIUC.EDU!jalkanen From: jalkanen@ARIES.SCS.UIUC.EDU (Karl Jalkanen) Newsgroups: bionet.structural-nmr Subject: Unsubscribe Date: 21 Aug 1994 15:38:53 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: <9408212238.AA09660@aries.scs.uiuc.edu> NNTP-Posting-Host: net.bio.net Can you please unsubscribe me from this group as I am leaving this location and confirm unsubscribing. Thanks much. Karl Jalkanen From owner-structural-nmr@net.bio.net Sat Aug 20 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!sunic!news.uni-c.dk!unidhp.uni-c.dk!carlmk From: carlmk@unidhp.uni-c.dk (Mogens Kjaer) Newsgroups: bionet.structural-nmr Subject: Mike's chemical shift software? Date: 21 Aug 1994 10:54:59 GMT Organization: News Server at UNI-C, Danish Computing Centre for Research and Education. Lines: 22 Message-ID: <337bq3$8kp@news.uni-c.dk> NNTP-Posting-Host: unidhp.uni-c.dk Summary: Anyone tried Mike Williamsons total.f software? Keywords: chemical shift X-Newsreader: TIN [version 1.2 PL1] Hi NMR-World! Is there anyone who have tried the chemical shift prediction software, that Mike Williamson presented at the ICMRBS last week? I've tried to download it from Sheffield and compile it, but it needs a file with random coil chemical shift values... Is this file available somewhere else, or do I have to retype the 179 entries myself? Mogens -- Mogens Kjaer Pronto Software - Development and Distribution Carlsberg Research Center Gamle Carlsberg Vej 10 DK-2500 Valby Denmark Phone: + 45 33 27 53 25 Fax: + 45 33 27 47 08 Email: carlmk@unidhp.uni-c.dk From owner-structural-nmr@net.bio.net Sun Aug 21 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!sunic!news.uni-c.dk!unidhp.uni-c.dk!carlmk From: carlmk@unidhp.uni-c.dk (Mogens Kjaer) Newsgroups: bionet.structural-nmr Subject: Re: Mike's chemical shift software? Date: 22 Aug 1994 06:21:02 GMT Organization: News Server at UNI-C, Danish Computing Centre for Research and Education. Lines: 43 Message-ID: <339g4e$de6@news.uni-c.dk> References: <337bq3$8kp@news.uni-c.dk> NNTP-Posting-Host: unidhp.uni-c.dk X-Newsreader: TIN [version 1.2 PL1] I (carlmk@unidhp.uni-c.dk) wrote: : Hi NMR-World! : Is there anyone who have tried the chemical shift prediction software, : that Mike Williamson presented at the ICMRBS last week? : I've tried to download it from Sheffield and compile it, but it needs : a file with random coil chemical shift values... Is this file available : somewhere else, or do I have to retype the 179 entries myself? : 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 OK - I got a mail from Mike Williamson: He'll upload the file missing, and a help file, on Monday. BTW, the ftp site is ftp.shef.ac.uk, directory /pub/sheffield/mbb 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 Sun Aug 21 23:00:00 1994 Path: biosci!WHITESWS.MC.DUKE.EDU!dave From: dave@WHITESWS.MC.DUKE.EDU (david w hoffman) Newsgroups: bionet.structural-nmr Subject: unsubscribe Date: 21 Aug 1994 17:33:10 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: <9408220032.AA21741@whitesws.mc.duke.edu> NNTP-Posting-Host: net.bio.net unsubscribe From owner-structural-nmr@net.bio.net Tue Aug 23 23:00:00 1994 Path: biosci!CONVEX.CSD.UWM.EDU!deng From: deng@CONVEX.CSD.UWM.EDU (Zhengwu Deng) Newsgroups: bionet.structural-nmr Subject: unsubscribe Date: 24 Aug 1994 16:59:52 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net unsubscribe From owner-structural-nmr@net.bio.net Tue Aug 23 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!bioc.cam.ac.uk!arcr1 From: arcr1@bioc.cam.ac.uk (Andy Raine) Newsgroups: bionet.structural-nmr Subject: Ed. Olejniczak's email address Date: 24 Aug 1994 16:18:30 GMT Organization: Somewhere in the University of Cambridge Lines: 17 Distribution: world Message-ID: <33frsm$b2@lyra.csx.cam.ac.uk> NNTP-Posting-Host: nirvana.bioc.cam.ac.uk The subject says it all really. Does anyone out there know Ed.'s email address Is he reading this? Thanks Andrew -------------------------------------------------------------------------------- Dr. Andrew Raine +44 223 333744 Department of Biochemistry or 333499 University of Cambridge Tennis Court Road Cambridge CB2 1QW United Kingdom -------------------------------------------------------------------------------- From owner-structural-nmr@net.bio.net Wed Aug 24 23:00:00 1994 Path: biosci!TELEMANN.PSE.UMASS.EDU!charlie From: charlie@TELEMANN.PSE.UMASS.EDU (leonard charles dickinson) Newsgroups: bionet.structural-nmr Subject: (none) Date: 25 Aug 1994 11:56:00 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: <9408251843.AA03595@telemann.pse.umass.edu> NNTP-Posting-Host: net.bio.net unsubscribe charlie@telemann.pse.umass.edu From owner-structural-nmr@net.bio.net Thu Aug 25 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!news.uoregon.edu!netnews.nwnet.net!news.u.washington.edu!kantola From: kantola@u.washington.edu (Angeline Kantola) Newsgroups: bionet.structural-nmr Subject: His tags Date: 26 Aug 1994 21:01:54 GMT Organization: University of Washington, Seattle Lines: 18 Message-ID: <33ll82$9em@news.u.washington.edu> NNTP-Posting-Host: carson.u.washington.edu Hey, Structure Folk, I'm trying to establish good NMR solution conditions for a protein with an N terminal hexaHis tag, for ease of purification. I'm grateful for that bonus, but have found it to be otherwise a pain--for instance, persistant HUGE water lines, likely due to residual nickel, and a maddening propensity to aggregate, which may or may not be metal-mediated. I'm working on chopping the offending sequence off and competing out the nickel with less troublesome metals. Does anyone have any experience with this behavior in proteins with polyHis tags? Any suggestions to share? Much obliged, Angie Kantola kantola@u.washington.edu From owner-structural-nmr@net.bio.net Thu Aug 25 23:00:00 1994 Path: biosci!BIOSYM.COM!biosym.com!chen From: biosym.com!chen@BIOSYM.COM (Wenqiao Chen) Newsgroups: bionet.structural-nmr Subject: (none) Date: 26 Aug 1994 09:32:36 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: <9408261614.AA08887@east1.biosym.com> Reply-To: biosym.com!chen@biosym.com NNTP-Posting-Host: net.bio.net unsubscribe chen@biosym.com =================================================================== Wenqiao Chen, Ph.D. BIOSYM Technologies Inc. 201-267-4476 Email address: chen@biosym.com =================================================================== From owner-structural-nmr@net.bio.net Thu Aug 25 23:00:00 1994 Path: biosci!CADMIUM.CSB.YALE.EDU!gardner From: gardner@CADMIUM.CSB.YALE.EDU (Kevin Gardner) Newsgroups: bionet.structural-nmr Subject: testing --- kindly ignore Date: 26 Aug 1994 13:21:18 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: <9408262021.AA19704@cadmium.csb.yale.edu> NNTP-Posting-Host: net.bio.net Sorry about the interruption, folks --- bionet.structural-nmr has been having some troubles at our site. Thanks, Kevin -- ************************************************************************* Kevin Gardner Yale University Dept. of Molecular Biophysics and Biochemistry Internet: gardner@zinc.csb.yale.edu Bitnet: gardner@yalemed ***I support the boycott of companies using mass Internet advertising*** From owner-structural-nmr@net.bio.net Mon Aug 29 23:00:00 1994 Path: biosci!MED.UNC.EDU!sheng From: sheng@MED.UNC.EDU (Sheng Zhong) Newsgroups: bionet.structural-nmr Subject: where to get GAMMA? Date: 30 Aug 1994 12:51:56 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <9408301951.AA06013@hasty.med.unc.edu> NNTP-Posting-Host: net.bio.net Hi. I'd like to know where to get the GAMMA from Ernst (JMR 106 75-105). I have tried anonymous at hertz.ethz.ch but got: Connected to hertz.ethz.ch. 220 hertz FTP server (Version wu-2.1c(3) Mon Mar 7 14:02:26 MET 1994) ready. Name (hertz.ethz.ch:sheng): anonymous 530 User anonymous unknown. Login failed. Help me. Please? Dr. Sheng Zhong Dept of Biochem & Biophys. UNC at Chapel Hill sheng@med.unc.edu From owner-structural-nmr@net.bio.net Tue Aug 30 23:00:00 1994 Path: biosci!UNMC.EDU!bgmeiner From: bgmeiner@UNMC.EDU (Dr. Bill Gmeiner) Newsgroups: bionet.structural-nmr Subject: LINSHA Date: 31 Aug 1994 05:42:05 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <9408311242.AA08907@molecular.unmc.edu> NNTP-Posting-Host: net.bio.net Could someone please provide me with the name and E-mail address of the appropriate person to contact regarding the SPHINX and LINSHA programs. I believe these originated in the Wuthrich group. Thanks. From owner-structural-nmr@net.bio.net Tue Aug 30 23:00:00 1994 Path: biosci!OTTER.BIOCHEM.UBC.CA!mcintosh From: mcintosh@OTTER.BIOCHEM.UBC.CA (Lawrence McIntosh) Newsgroups: bionet.structural-nmr Subject: (none) Date: 30 Aug 1994 22:12:55 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net I am curious how other labs deal with the problem of saving the massive amounts of 3D and 4D NMR data needed for assignments and structure determination. This includes long term archiving as well as storing data for frequent access. We have 3 SGI Indigos or IndigoIIs and currently use a 8 mm exabyte 8500 tape drive and a TahitaII MO drive. Although that should be great, in practice the Exabyte drive often fails to read/write tapes and the MO is plagued by over-heating (we have a "normal" computer room by most standards). In fact, both devices have been replaced or repaired several times by the manufacturers. A casual glance at the hardware usernets suggests that we might not be alone in our problems. I would appreciate any information or advice on a stable and convienent system to manage NMR data (short of buying disk drives every few months). Thanks! Lawrence McIntosh Univ. British Columbia mcintosh@otter.biochem.ubc.ca From owner-structural-nmr@net.bio.net Tue Aug 30 23:00:00 1994 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: (none) Date: 31 Aug 1994 04:23:16 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net We have relatively good experience with the DAT drive and 2GB tapes on our Indigo; the best solution we have found so far. It is not as great for frequent access but we use a 10GB hard disk system attached. Such devices are getting less and less expensive (the price is around few thousands and decreasing). Regards, Istvan ------------------------------- Istvan Pelczer, Ph.D. Res. Assist. Professor Chemistry Department, CST Bldg. Syracuse University Syracuse, NY 13244-4100 ph# 315 443 1023 fax# x-4070 ------------------------------- From owner-structural-nmr@net.bio.net Tue Aug 30 23:00:00 1994 Path: biosci!BIOC01.UTHSCSA.EDU!raman From: raman@BIOC01.UTHSCSA.EDU (C.S.RAMAN) Newsgroups: bionet.structural-nmr Subject: Re: LINSHA Date: 31 Aug 1994 12:46:11 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: <9408311910.AA07801@bioc01.uthscsa.edu> References: <9408311242.AA08907@molecular.unmc.edu> NNTP-Posting-Host: net.bio.net > Could someone please provide me with the name and E-mail address of the appropriate person to contact regarding the SPHINX and LINSHA programs. I believe these originated in the Wuthrich group. Thanks. > you may try contacting Dr. Christian Bartels regarding this: bartels@molbio.ethz.ch Cheers -raman -- C.S.Raman UNIX Programming & Administration SPARC & SGI Systems raman@bioc01.uthscsa.edu - INTERNET Department of Biochemistry raman@mintaka.chpc.utexas.edu - CHPC UTHSCSA c.raman@launchpad.unc.edu 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From owner-structural-nmr@net.bio.net Tue Aug 30 23:00:00 1994 Path: biosci!LAPLACE.CSB.YALE.EDU!abonvin From: abonvin@LAPLACE.CSB.YALE.EDU ("Alexandre Bonvin") Newsgroups: bionet.structural-nmr Subject: Re: xplor pdb format Date: 31 Aug 1994 13:50:19 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 63 Sender: daemon@net.bio.net Distribution: world Message-ID: <9408312050.AA28816@laplace.csb.yale.edu> NNTP-Posting-Host: net.bio.net Mogens Kjaer writes: > > We have previously deposited coordinates at PDB. This was done by sending > the X-PLOR PDB files to PDB, and they converted the atom names, etc., to > the right format. > > I was wondering, if a program/set of guidelines exists describing how to > do this. > > The differences between the X-PLOR coordinates and the PDB coordinates > were mainly: > > 1. Proton atoms names: HB1 -> 1HB > > 2. Stereospecificity: > > HB1, HB2 -> 2HB, 1HB > > 3. Order of methyl protons: > > HG11, HG12, HG13 -> 2HG1, 1HG1, 3HG1 > > 4. In some cases, the ordering of the carbon atoms were changed: > > CD1, CD2 -> CD2, CD1 > > 5. For Lys HZ#, the ordering was changed for some residues, for > some not! > > Does anyone have any information about this? > > 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 > In answer to this Prof. Axel Brunger ask me to forward the following: I have a collaboration with the PDB group in order the address the X-PLOR/PDB submission process for both X-ray and NMR structures. The next release of X-PLOR (spring '95?) will simplify this process. Axel ============================================================================== | Alexandre Bonvin PhD | Phone: (203) 432-5066 | | Dept. Mol. Biophys. & Biochemistry | Fax: (203) 432-6946 | | Yale University, 266 Whitney Avenue | Email: abonvin@laplace.csb.yale.edu | | New Haven CT 06511, USA | | =============================================================================== From owner-structural-nmr@net.bio.net Tue Aug 30 23:00:00 1994 Path: biosci!CS.Arizona.EDU!uunet!EU.net!sunic!news.uni-c.dk!unidhp.uni-c.dk!carlmk From: carlmk@unidhp.uni-c.dk (Mogens Kjaer) Newsgroups: bionet.structural-nmr Subject: X-PLOR PDB to PDB PDB? Date: 31 Aug 1994 13:02:42 GMT Organization: News Server at UNI-C, Danish Computing Centre for Research and Education. Lines: 44 Message-ID: <341v1i$7ul@news.uni-c.dk> NNTP-Posting-Host: unidhp.uni-c.dk Summary: How do I convert from X-PLOR PDB files to PDB PDB files? Keywords: X-PLOR, PDB X-Newsreader: TIN [version 1.2 PL1] We have previously deposited coordinates at PDB. This was done by sending the X-PLOR PDB files to PDB, and they converted the atom names, etc., to the right format. I was wondering, if a program/set of guidelines exists describing how to do this. The differences between the X-PLOR coordinates and the PDB coordinates were mainly: 1. Proton atoms names: HB1 -> 1HB 2. Stereospecificity: HB1, HB2 -> 2HB, 1HB 3. Order of methyl protons: HG11, HG12, HG13 -> 2HG1, 1HG1, 3HG1 4. In some cases, the ordering of the carbon atoms were changed: CD1, CD2 -> CD2, CD1 5. For Lys HZ#, the ordering was changed for some residues, for some not! Does anyone have any information about this? Mogens -- Mogens Kjaer Pronto Software - Development and Distribution Carlsberg Research Center Gamle Carlsberg Vej 10 DK-2500 Valby Denmark Phone: + 45 33 27 53 25 Fax: + 45 33 27 47 08 Email: carlmk@unidhp.uni-c.dk From owner-structural-nmr@net.bio.net Wed Aug 31 23:00:00 1994 Path: biosci!CS.Arizona.EDU!uunet!EU.net!sunic!news.uni-c.dk!unidhp.uni-c.dk!carlmk From: carlmk@unidhp.uni-c.dk (Mogens Kjaer) Newsgroups: bionet.structural-nmr Subject: Re: xplor pdb format Date: 1 Sep 1994 07:54:11 GMT Organization: News Server at UNI-C, Danish Computing Centre for Research and Education. Lines: 32 Distribution: world Message-ID: <3441b3$bh6@news.uni-c.dk> References: <9408312050.AA28816@laplace.csb.yale.edu> NNTP-Posting-Host: unidhp.uni-c.dk X-Newsreader: TIN [version 1.2 PL1] Alexandre Bonvin (abonvin@LAPLACE.CSB.YALE.EDU) wrote: : Mogens Kjaer writes: : > : > We have previously deposited coordinates at PDB. This was done by sending : > the X-PLOR PDB files to PDB, and they converted the atom names, etc., to : > the right format. : > : > I was wondering, if a program/set of guidelines exists describing how to : > do this. ........ : In answer to this Prof. Axel Brunger ask me to forward the following: : I have a collaboration with the PDB group in order the address the X-PLOR/PDB : submission process for both X-ray and NMR structures. The next release : of X-PLOR (spring '95?) will simplify this process. That sounds great, but of course that does not solve any current problems. Does anyone know, what PDB uses the convert/check atom names? Are these programs publicly available? -- 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