From owner-structural-nmr@net.bio.net Tue Apr 04 23:00:00 1995 Path: biosci!MUWAYF.UNIMELB.EDU.AU!sergio_scrofani From: sergio_scrofani@MUWAYF.UNIMELB.EDU.AU (Sergio Scrofani) Newsgroups: bionet.structural-nmr Subject: POSITIONS AVAILABLE (AUSTRA Date: 5 Apr 1995 16:05:58 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 73 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HP0HFQ8KWY002OFS@muwayb.ucs.unimelb.edu.au> NNTP-Posting-Host: net.bio.net POSITIONS AVAILABLE (AUSTRALIA) Dear users, Please forgive the cross-posting. We have a number of openings available in the Chemistry Department, University of Melbourne, Australia. The following ad describes three in particular. However, if you feel that you don't fit into the specified categories, feel free to make any enquiries to Prof. Tony Wedd (see below). ----------------------------------------------------------------------------------- The School of Chemistry is seeking applicants for the following positions: -Reader/Senior Lecturer in NMR Spectroscopy -Senior Lecturer/Lecturer in Mass Spectroscopy -Research Fellow in NMR Spectroscopy The School is seeking to strengthen its research and teaching capabilities in the fields of NMR spectroscopy and mass spectrometry. Applicants must have strong research backgrounds and the ability to initiate and foster major instrumentation improvements. For the Reader / Senior Lecturer / Lecturer positions, preference will be given to applicants with a background in bio-organic or biological chemistry who are willing to encourage interdisciplinary research and teaching initiatives both inside and outside the School. High resolution solution NMR instrumentation will include two 400 MHz and two 300 MHz instruments on site and access (20%) to a 500 MHz instrument. A 300 MHz CP/MAS attachment for solids will be available. Planning to gain access to higher field instruments has a high priority. The Reader / Senior Lecturer will be appointed director of the NMR facility and be responsible for overall planning and effective functioning. The Research Fellow, with the help of a Professional Officer, will be responsible for day-to-day functioning, technique development and training. The appointee will be encouraged to undertake independent and collaborative research. This appointment will be for up to three years in the first instance. Mass spectrometric instrumentation presently includes two high resolution instruments (VG and JEOL), one with FAB/EI/CI and GC capability. Funds are available to seed substantial expansion and the Senior Lecturer / Lecturer will exercise responsibility for that expansion and for further development and interaction with other groups within the University. The School has appointed Professor R.O. Watts as ICI-Masson Chair of Chemistry and Head of School from late June, 1995. It currently has 31 full time academic staff who undertake a range of internationally recognised research programs. The School also provides teaching programs for over 1800 undergraduate and some 90 postgraduate students and participates in a variety of community education programs. Applications should be sent, in duplicate, quoting reference number and three referees (including facsimile numbers) to the Director, Personnel Services, The University of Melbourne, Parkville, Victoria 3052, Victoria, Australia; fax +61-3-344-4694. Please include details of your research plans, your teaching philosophy and your vision for a School of Chemistry in the third millennium. Further information, position descriptions and the School Research Booklet can be obtained from Professor A.G. Wedd, Head of School: Tel. +61-3-344-7137; fax +61-3-347-5180; e-mail: Tony_Wedd.chemistry@muwayf.unimelb.edu.au Reference Numbers: Reader/Senior Lecturer: Y6100210 (salary: A$61,322 - 67,555/ $50,928 - 58,724) Senior Lecturer/Lecturer: Y9400485 (salary: A$50,928 - 58,724/ $41,574 - 49,370) Research Fellow Grade 1/2: Y0000431 (salary: A$29,539 - 40,087/ $42,198 - 50,111) Closing date: June 7, 1995. The University of Melbourne is an equal opportunity employer and has a smoke free work place policy. From owner-structural-nmr@net.bio.net Tue Apr 04 23:00:00 1995 Path: biosci!daresbury!trane.uninett.no!sunic!sunic.sunet.se!news.funet.fi!luotsi.uku.fi!usenet From: Matthias Niemitz Newsgroups: bionet.structural-nmr Subject: PERCH NMR software, new release Date: 5 Apr 1995 09:54:53 GMT Organization: University of Kuopio, Finland Lines: 19 Message-ID: <3ltpdd$hp8@luotsi.uku.fi> NNTP-Posting-Host: s3038.uku.fi Dear NMR Spectroscopist: We proudly announce the latest release of the PERCH NMR software package including new, unique features covering every-day routine tools to sophisticated procedures for deconvolution and simulation/iteration. A free tutorial is available via World Wide Web and anonymous FTP. For more information please check: World Wide Web: http://www.uku.fi/~niemitz/perch.htm Anonymous FTP: FTP.FUNET.FI in directory: /pub/sci/chem/nmr or contact: PERCH Project phone: + 358 71 163242 University of Kuopio, P.O.B. 1627 telefax: + 358 71 163259 FIN-70211 Kuopio, FINLAND e-mail: perch@kummeli.uku.fi From owner-structural-nmr@net.bio.net Wed Apr 05 23:00:00 1995 Path: biosci!agate!news.mindlink.net!news.bc.net!unixg.ubc.ca!news From: Newsgroups: bionet.structural-nmr Subject: protein-protein interactions Date: 6 Apr 1995 16:15:29 GMT Organization: The University of British Columbia Lines: 14 Message-ID: <3m1431$gma@nntp.ucs.ubc.ca> NNTP-Posting-Host: xray1.chem.ubc.ca Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1b2 (X11; I; IRIX 5.2 IP20) X-URL: news://news.ucs.ubc.ca/bionet.structural-nmr Dear all, I am not a nmr person. Can somebody point me to some good references for using nmr to study protein-protein interactions? I remember seeing one a while ago and it involves making one protein "invisible to nmr" by labelling with D2O and then imbolize one of them; and add the other one and see which protons are protected; something along these lines is what I am after. Thanks a lot. Yu Wai Chen Department of Biochemistry, University of British Columbia, Vancouver BC, CANADA Please reply to ywchen@laue.biochem.ubc.ca From owner-structural-nmr@net.bio.net Thu Apr 06 23:00:00 1995 Path: biosci!bcm!news.msfc.nasa.gov!sol.ctr.columbia.edu!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!bioc.cam.ac.uk!zx From: zx@bioc.cam.ac.uk Newsgroups: bionet.structural-nmr Subject: stability of proteins Date: 7 Apr 1995 16:14:56 GMT Organization: Somewhere in the University of Cambridge Lines: 16 Distribution: world Message-ID: <3m3oe0$pen@lyra.csx.cam.ac.uk> NNTP-Posting-Host: eden.bioc.cam.ac.uk Keywords: stability, nmr, structural analysis Dear netters, Structural determination by NMR requires very stable proteins, which probably are not feasible for many proteins. I am now working on a protein in PSI reaction center, which shows degradation after one or two days incubation at room temperature. A 3D NOESY experiment takes at least three days! Can the protein be stabilized without using mutagenesis? Any suggestions are highly appreciated! zx. -- From: Dr. Xia Zhicheng Department of Biochemistry University of Cambridge Tennis Court Road Cambridge CB2 1QW E-mail zx@mole.bio.cam.ac.uk From owner-structural-nmr@net.bio.net Thu Apr 06 23:00:00 1995 Path: biosci!ERE.UMontreal.CA!beausole From: beausole@ERE.UMontreal.CA (Beausoleil Eric) Newsgroups: bionet.structural-nmr Subject: Inversion transfer Date: 7 Apr 1995 14:32:41 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <9504072131.AA20862@tornade.ERE.UMontreal.CA> NNTP-Posting-Host: net.bio.net To whom it may concern I would like to know if anybody have program for analyzing selective saturation exchange experiment according to Campbell J.Magn. Res. vol 21 p397. In advance thank you. Eric Beausoleil Etudiant Ph.D. Email:beausole@ere.umontreal.ca Chimie Organique Local:G-629 Universite de Montreal Tel:1-514-343-6111 (#3954) From owner-structural-nmr@net.bio.net Sat Apr 08 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: bryan@freja.fkem2.lth.se (Bryan Finn) Newsgroups: bionet.structural-nmr Subject: Re: stability of proteins Date: 8 Apr 1995 18:16:03 +0100 Lines: 44 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3m6gcj$c1e@mserv1.dl.ac.uk> Original-To: str-nmr@dl.ac.uk > Dear netters, > Structural determination by NMR requires very stable proteins, which probably are not feasible for many proteins. I am now working on a protein in PSI reaction center, which shows degradation after one or two days incubation at room temperature. A 3D NOESY experiment takes at least three days! Can the protein be stabilized without using mutagenesis? Any suggestions are highly appreciated! > zx. > > From: > > Dr. Xia Zhicheng Xia, First, check the stability of unfolding with a simple unfolding expt (e.g. a series of 1D's at different temps or by other means such as UV absorance or CD spectroscopy). If the problem is unfolding, change the solvent conditions with respect to pH, temperature or addition of additives (e.g. salt). If the problem is instability against degradation by microorganisms, try adding a little sodium azide to the sample (0.02%). Good luck! Bryan ___________________________________________________________________ | | | Dr. Bryan Finn | | Department of Physical Chemistry 2 Tel: +46-46-222-8254 | | Chemical Center Fax: +46-46-222-4543 | | University of Lund | | POB 124 | | S-221 00 Lund Sweden e-mail: Bryan.Finn@fkem2.lth.se | | WWW: http://www.fkem2.lth.se/personnel/bryan/finn.html | |_________________________________________________________________| From owner-structural-nmr@net.bio.net Sun Apr 09 23:00:00 1995 Path: biosci!rutgers!oitnews.harvard.edu!das-news2.harvard.edu!news2.near.net!news3.near.net!yale!usenet From: abonvin@volta.csb.yale.edu ("Alexandre Bonvin") Newsgroups: bionet.structural-nmr Subject: X-PLOR www pages (correction) Date: 10 Apr 1995 17:53:23 GMT Organization: Yale University, Department of Computer Science, New Haven, CT Lines: 17 Message-ID: <3mbrak$iju@babyblue.cs.yale.edu> NNTP-Posting-Host: volta.csb.yale.edu Dear netters, Xplor has now a www home page featuring the X-PLOR manual and tutorial files on-line. The official address is: http://xplor.csb.yale.edu (pauli in the previous posting should work as well) Alexandre ========================================================================== | 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 Sun Apr 09 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!news2.near.net!news3.near.net!yale!usenet From: abonvin@volta.csb.yale.edu ("Alexandre Bonvin") Newsgroups: bionet.structural-nmr Subject: X-PLOR www pages Date: 10 Apr 1995 17:48:09 GMT Organization: Yale University, Department of Computer Science, New Haven, CT Lines: 17 Message-ID: <3mbr0p$iiu@babyblue.cs.yale.edu> NNTP-Posting-Host: volta.csb.yale.edu Dear netters, Xplor has now a www home page featuring the X-PLOR manual and tutorial files on-line. The address is: http://pauli.csb.yale.edu Alexandre ========================================================================== | Alexandre Bonvin PhD | Phone: (203) 432-5066 | | Mol. Biophys. & Biochemistry | Fax: (203) 432-6946 | | Yale University, PO Box 208114 | Email: abonvin@laplace.csb.yale.edu | | New Haven CT 06511, USA | | ========================================================================== From owner-structural-nmr@net.bio.net Sun Apr 09 23:00:00 1995 Path: biosci!LARRY.BIOP.UMICH.EDU!wang From: wang@LARRY.BIOP.UMICH.EDU Newsgroups: bionet.structural-nmr Subject: Re: stability of proteins Date: 10 Apr 1995 09:21:13 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 33 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <3m3oe0$pen@lyra.csx.cam.ac.uk> NNTP-Posting-Host: net.bio.net How about try some co-solvent. We once used some acetylnitril to help stablize some protein. It worked fine for two protein studied in our lab. On 7 Apr 1995 zx@bioc.cam.ac.uk wrote: > Dear netters, > Structural determination by NMR requires very stable proteins, which probably are not feasible for many proteins. I am now working on a protein in PSI reaction center, which shows degradation after one or two days incubation at room temperature. A 3D NOESY experiment takes at least three days! Can the protein be stabilized without using mutagenesis? Any suggestions are highly appreciated! > zx. > > -- > > From: > > Dr. Xia Zhicheng > Department of Biochemistry > University of Cambridge > Tennis Court Road > Cambridge CB2 1QW > > E-mail zx@mole.bio.cam.ac.uk > > ################################################################### Hong Wang Phone: (313) 763-8972 Univ. Michigan Email: wang@larry.biop.umich.edu ################################################################### From owner-structural-nmr@net.bio.net Sun Apr 09 23:00:00 1995 Path: biosci!SNEEZY.FHIS.NET!barry From: barry@SNEEZY.FHIS.NET ("Barry Schweitzer") Newsgroups: bionet.structural-nmr Subject: Post-doctoral Position Available Date: 10 Apr 1995 07:56:57 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 43 Sender: daemon@net.bio.net Distribution: world Message-ID: <9504101055.ZM3199@sneezy.fhis.net> NNTP-Posting-Host: net.bio.net POST-DOCTORAL POSITION AVAILABLE A post-doctoral position is available starting July 1, 1995 in the Laboratory of Structural Biology at the Walt Disney Memorial Cancer Institute (WDMCI) at Florida Hospital, a not-for-profit 1500-bed acute care research hospital in Orlando, Florida. Research in the Laboratory of Structural Biology is focused on the development of new anti-cancer agents through the use of Nuclear Magnetic Resonance (NMR) and computer modeling. Specific areas of interest include: (1) Structure- function relationships in proteins involved in blood coagulation and fibrinolysis, (2) Effects of anti-cancer drugs on DNA structure, and (3) DNA-protein interactions. The successful candidate should be highly motivated and must have a strong background in the application of solution-state multi- dimensional triple resonance NMR to isotopically-labeled proteins. Experience in pulse sequence design, molecular biology (PCR, cloning, protein overexpression/purification), and structure calculations/molecular modeling is also desirable, but optional. Salary rate is negotiable and will be set commensurate with experience. The Laboratory of Structural Biology is located in a new 16,000 sq. ft. research facility that houses the Cancer Research Division of the WDMCI. Our laboratory has exclusive use of a Varian UnityPlus 600 MHz spectrometer with triple resonance and gradient capabilities and several SUN and SGI workstations. The Cancer Research Division also has excellent facilities for cellular and molecular biology, tissue culture, and protein chemistry. WDMCI is affiliated with the University of Central Florida, a 25,000-student research university located 2 minutes away. Send curriculum vitae and names of three references to: Dr. Barry Schweitzer Director, Division of Structural Biology Walt Disney Memorial Cancer Institute 12722 Research Parkway Orlando, FL 32826 email: barry@sneezy.fhis.net From owner-structural-nmr@net.bio.net Mon Apr 10 23:00:00 1995 Path: biosci!SNEEZY.FHIS.NET!barry From: barry@SNEEZY.FHIS.NET ("Barry Schweitzer") Newsgroups: bionet.structural-nmr Subject: 15N labeling in yeast Date: 11 Apr 1995 15:57:02 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 24 Sender: daemon@net.bio.net Distribution: world Message-ID: <9504111856.ZM5178@sneezy.fhis.net> NNTP-Posting-Host: net.bio.net Hi Out There! Collaborators of ours have a protein cloned and expressed in the P. pastoris yeast system. It shouldn't be hard (or expensive) to 13C-label the protein; the bugs grow on methanol as their sole carbon source. However, all the protocols that I have seen call for yeast nitrogen base as the nitrogen source. I haven't seen anyone selling this in 15N-form. Does anyone have a recipe for 15N labeling (e.g. using 15N-ammonium) in this system? Thanks in advance. -- Barry Schweitzer, Ph.D. Director Assistant Professor Division of Structural Biology Department of Chemistry Walt Disney Memorial Cancer Institute University of Central Florida at Florida Hospital 12722 Research Parkway Orlando, FL 32826 Phone: (407) 380-9977 FAX: (407) 380-9978 email: barry@sneezy.fhis.net From owner-structural-nmr@net.bio.net Mon Apr 10 23:00:00 1995 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: C13 NMR chemical shifts Date: 11 Apr 1995 16:26:58 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <199504111910.QAA13635@styx.iqm.unicamp.br> NNTP-Posting-Host: net.bio.net I believe Sadtler offers the best collection of data and a software (C-SEARCH) at the time, however, Aldrich has 13C spectrum collection, too (probably others as well), and Bruker also offers software which calculates 13C chemical shifts. Good luck, Istvan ================================ Istvan Pelczer, Ph.D. Res. Assist. Professor Chemistry Department, CST Bldg. Syracuse University Syracuse, NY 13244-4100 ph: (315) 443 1023 or x-5932 fax: x-1022(lab) or x-4070(dept) From owner-structural-nmr@net.bio.net Mon Apr 10 23:00:00 1995 Path: biosci!IQM.UNICAMP.BR!elcana From: elcana@IQM.UNICAMP.BR (Anselmo Elcana de Oliveira) Newsgroups: bionet.structural-nmr Subject: C13 NMR chemical shifts Date: 11 Apr 1995 12:22:45 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <199504111910.QAA13635@styx.iqm.unicamp.br> NNTP-Posting-Host: net.bio.net Hi netters, Does anybody know where I can find a program to calculate the C13 NMR chemical shifts? I'm also looking for a data bank of chemical shifts. Please, send the answers to me, not to the list. Thanks in advance, Elcana elcana@iqm.unicamp.br From owner-structural-nmr@net.bio.net Tue Apr 11 23:00:00 1995 Path: biosci!HWS.IPC.HIROSHIMA-U.AC.JP!kazz From: kazz@HWS.IPC.HIROSHIMA-U.AC.JP (Kazuhiro OHTANI) Newsgroups: bionet.structural-nmr Subject: help Date: 11 Apr 1995 19:56:55 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: <9504120257.AA28245@hws.ipc.hiroshima-u.ac.jp> NNTP-Posting-Host: net.bio.net help OHTANI, Kazuhiro Dpt. of Pharm. Sci., Schl of Medicine, Hiroshima Univ. e-mail : kazz@ue.ipc.hiroshima-u.ac.jp Nifty : GHB03031 From owner-structural-nmr@net.bio.net Tue Apr 11 23:00:00 1995 Path: biosci!cc.uoi.gr!astavrak From: astavrak@cc.uoi.gr (Athanasios Stavrakoudis) Newsgroups: bionet.structural-nmr Subject: help on assignment Date: 12 Apr 1995 08:06:44 -0700 Organization: University of Ioannina Computer Center Dourouti, Ioannina, Greece 451 10 tel: +30-651-45298, fax: +30-651-45298 Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <9504121748.AA04104@apollon.cc.uoi.gr> NNTP-Posting-Host: net.bio.net Hello everybody I am looking for a DOS/SGI program to do manual assignment of small peptides. Does anyone use such programs ? Or, have you an idea where can l find something usefull ? thanks, Athanassios Stavrakoudis Un. Ioannina Dep. Chemistry Ioannina-Greece e-mail : astavrak@cc.uoi.gr From owner-structural-nmr@net.bio.net Tue Apr 11 23:00:00 1995 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: help on assignment Date: 12 Apr 1995 09:01:08 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 43 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <9504121748.AA04104@apollon.cc.uoi.gr> NNTP-Posting-Host: net.bio.net On 12 Apr 1995, Athanasios Stavrakoudis wrote: > > Hello everybody > > I am looking for a DOS/SGI program to do > manual assignment of small peptides. Does > anyone use such programs ? > Or, have you an idea where can l find > something usefull ? > > thanks, > > Athanassios Stavrakoudis > Un. Ioannina > Dep. Chemistry > Ioannina-Greece > e-mail : astavrak@cc.uoi.gr > > A possible choice for PC would be PIXI (you can read about it in JMR 88(1990)511-522), which you can download from gopher.nmrfam.wisc.edu. Workstation-level assignment/analysis software packages are NMRView, PIPP, or ANSIG; all available over the net in one way or another (see some earlier news in the str-nmr@net.bio.net). There are commercial packages, too, but I believe you look for something which does not cost a lot. Good luck, Istvan ================================ Istvan Pelczer, Ph.D. Res. Assist. Professor Chemistry Department, CST Bldg. Syracuse University Syracuse, NY 13244-4100 ph: (315) 443 1023 or x-5932 fax: x-1022(lab) or x-4070(dept) From owner-structural-nmr@net.bio.net Tue Apr 11 23:00:00 1995 Path: biosci!daresbury!trane.uninett.no!sunic!sunic.sunet.se!seunet!news2.swip.net!doc.news.pipex.net!pipex!lyra.csx.cam.ac.uk!bioc.cam.ac.uk!bos From: bos@bioc.cam.ac.uk (Brian Smith (Bioc)) Newsgroups: bionet.structural-nmr Subject: Re: 15N labeling in yeast Date: 12 Apr 1995 09:16:08 GMT Organization: Somewhere in the University of Cambridge Lines: 13 Distribution: world Message-ID: <3mg5oo$gpd@lyra.csx.cam.ac.uk> References: <9504111856.ZM5178@sneezy.fhis.net> NNTP-Posting-Host: nirvana.bioc.cam.ac.uk In article <9504111856.ZM5178@sneezy.fhis.net>, barry@SNEEZY.FHIS.NET ("Barry Schweitzer") writes: > Collaborators of ours have a protein cloned and expressed in the P. pastoris > yeast system. It shouldn't be hard (or expensive) to 13C-label the protein; > the bugs grow on methanol as their sole carbon source. However, all > the protocols that I have seen call for yeast nitrogen base as the nitrogen > source. I haven't seen anyone selling this in 15N-form. Does anyone I have 15N labelled in S.cerevisiae using bought YNB without ammonium sulphate supplemented with 15N ammonium sulphate. Results were good. I see no reason why this shouldn't work for pichia too. -- Brian Smith Dept. of Biochemistry, email: bos@bioc.cam.ac.uk University of Cambridge, Tel: +44 01223 333744/679/499 Cambridge. CB2 1QW. From owner-structural-nmr@net.bio.net Wed Apr 12 23:00:00 1995 Path: biosci!agate!holonet!colossus.holonet.net!NewsWatcher!user From: g_ashley@holonet.net (Gary W. Ashley) Newsgroups: bionet.structural-nmr Subject: Re: looking for Le x Date: Thu, 13 Apr 1995 12:06:47 -0800 Organization: HoloNet National Internet Access System: 510-704-1058/modem Lines: 16 Distribution: world Message-ID: References: <199504122051.NAA16698@net.bio.net> NNTP-Posting-Host: gashley.ip.holonet.net In article , anlackey@BLUE.WEEG.UIOWA.EDU ("A. Lackey") wrote: > I am currently looking for the molecular quardinents of the published > structures of Le x, sLe x and the sulfated Le x. Is the structure of > any ( or all) of these compounds in a database accessable to the public ? > > If not what is the best way to obtain these structures. Should one > write the author ? > I think it is always a good idea to first try and get the coordinates from the people who published them. You stand a good chance of getting the latest updated data, and it lets them know that someone out there appreciates and can use their hard-earned results. GW Ashley From owner-structural-nmr@net.bio.net Wed Apr 12 23:00:00 1995 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!news.sprintlink.net!holonet!colossus.holonet.net!NewsWatcher!user From: g_ashley@holonet.net (Gary W. Ashley) Newsgroups: bionet.structural-nmr Subject: Re: C13 NMR chemical shifts Date: Wed, 12 Apr 1995 20:43:31 -0800 Organization: HoloNet National Internet Access System: 510-704-1058/modem Lines: 15 Distribution: world Message-ID: References: <199504111910.QAA13635@styx.iqm.unicamp.br> NNTP-Posting-Host: gashley.ip.holonet.net In article <199504111910.QAA13635@styx.iqm.unicamp.br>, elcana@IQM.UNICAMP.BR (Anselmo Elcana de Oliveira) wrote: > Hi netters, > > Does anybody know where I can find a program to calculate the C13 NMR > chemical shifts? I'm also looking for a data bank of chemical shifts. > I would suggest the book by Breitmaier for a fairly comprehensive tabulation of 13C chemical shifts, at least of small molecules. I don't know if such a tabulation exists for proteins. Calculation of 13C shifts is somewhat problematic, if not an outright art form. GW Ashley From owner-structural-nmr@net.bio.net Wed Apr 12 23:00:00 1995 Path: biosci!BLUE.WEEG.UIOWA.EDU!anlackey From: anlackey@BLUE.WEEG.UIOWA.EDU ("A. Lackey") Newsgroups: bionet.structural-nmr Subject: Re: C13 NMR chemical shifts Date: 13 Apr 1995 08:02:50 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net On Wed, 12 Apr 1995, Gary W. Ashley wrote: > Date: Wed, 12 Apr 1995 20:43:31 -0800 > From: Gary W. Ashley > To: str-nmr@net.bio.net > Subject: Re: C13 NMR chemical shifts > > > Does anybody know where I can find a program to calculate the C13 NMR > > chemical shifts? I'm also looking for a data bank of chemical shifts. > > There is no database that I am aware of but there are plenty of good listings that have been published. There is a good account of many of the smaller molecules through 13C shifts but probably not so much in the way of large molecules ( protiens ). Also the shifts of 13C are exquisidly sensitive to solvent and temperature which may cause some listings to be problamatic. sorry I was not more help, Anthony lackey From owner-structural-nmr@net.bio.net Wed Apr 12 23:00:00 1995 Path: biosci!BLUE.WEEG.UIOWA.EDU!anlackey From: anlackey@BLUE.WEEG.UIOWA.EDU ("A. Lackey") Newsgroups: bionet.structural-nmr Subject: looking for Le x Date: 13 Apr 1995 07:52:00 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <199504122051.NAA16698@net.bio.net> NNTP-Posting-Host: net.bio.net I am currently looking for the molecular quardinents of the published structures of Le x, sLe x and the sulfated Le x. Is the structure of any ( or all) of these compounds in a database accessable to the public ? If not what is the best way to obtain these structures. Should one write the author ? Anthony Lackey anlackey@blue.weeg.uiowa.edu From owner-structural-nmr@net.bio.net Wed Apr 12 23:00:00 1995 Path: biosci!daresbury!trane.uninett.no!Norway.EU.net!EU.net!Germany.EU.net!zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!ipp-garching.mpg.de!kaki!cieslar From: cieslar@mango.biochem.mpg.de () Newsgroups: bionet.structural-nmr Subject: Software for 3D and 2D available for SGI Machines Date: 13 Apr 1995 11:19:57 GMT Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 22 Message-ID: <3mj1ct$qoq@sat.ipp-garching.mpg.de> NNTP-Posting-Host: kaki.biochem.mpg.de X-Newsreader: TIN [version 1.2 PL2] In the last years the program ccnmr was developed for processing display (and assignment to some degree) was developed. It was implemented on CONVEX and Silicon Graphics workstations, where it also available in parallelized version for multiprocessor Systems. It can process serial files from Bruker and Varian Spectrometers, and is able to read processed Bruker files. The processing program may make an online connection to an other SGI workstation for graphic display. It is available via anonymous ftp from mango.biochem.mpg.de You may test the capabilties of the graphic program by getting the files in: pub/nmrdemo The program as well as Testspectra are included. README contains instructions. The executables for the rest of the ccnmr program are in pub/ccnmr along with the users manual. From owner-structural-nmr@net.bio.net Thu Apr 13 23:00:00 1995 Path: biosci!agate!holonet!colossus.holonet.net!NewsWatcher!user From: g_ashley@holonet.net (Gary W. Ashley) Newsgroups: bionet.structural-nmr Subject: Re: C13 NMR chemical shifts Date: Thu, 13 Apr 1995 20:41:12 -0800 Organization: HoloNet National Internet Access System: 510-704-1058/modem Lines: 27 Distribution: world Message-ID: References: NNTP-Posting-Host: gashley.ip.holonet.net In article , anlackey@BLUE.WEEG.UIOWA.EDU ("A. Lackey") wrote: > On Wed, 12 Apr 1995, Gary W. Ashley wrote: > > > Date: Wed, 12 Apr 1995 20:43:31 -0800 > > From: Gary W. Ashley > > To: str-nmr@net.bio.net > > Subject: Re: C13 NMR chemical shifts > > > > > Does anybody know where I can find a program to calculate the C13 NMR > > > chemical shifts? I'm also looking for a data bank of chemical shifts. > > > > There is no database that I am aware of but there are plenty of good > listings that have been published. There is a good account of many of > the smaller molecules through 13C shifts but probably not so much in the > way of large molecules ( protiens ). Also the shifts of 13C are > exquisidly sensitive to solvent and temperature which may cause some > listings to be problamatic. > sorry I was not more help, > Anthony lackey Sorry, but I did not post the above-mentioned message...I did, however, post a reply to the message. I am *not* looking for info on 13C chemical shifts. GW Ashley From owner-structural-nmr@net.bio.net Fri Apr 14 23:00:00 1995 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!news.sprintlink.net!uunet!in1.uu.net!fonorola!news.compulink.com!cedrick From: cedrick@cml.com (Lee Boros) Newsgroups: bionet.structural-nmr Subject: Help On Gortex Date: 14 Apr 1995 16:58:20 GMT Organization: ComputerLink Online Inc. Lines: 14 Message-ID: <3mm9jc$o71@news.compulink.com> NNTP-Posting-Host: cml.com X-Newsreader: TIN [version 1.2 PL2] Hi, I'm doing a Chemistry Project on Gortex. I am in Grade 12 and I am trying to find some informtaion on the internet but am having great difficulties. Does anyone know where I can search for information on this molecule? -Lee ------------------------------------------------------------------- : ComputerLink Online Inc. Realms of Despair! : : (416)233-5410, 232 lines telnet realms.game.org 4000 : : T1 bandwidth, 300-28,800 bps endless medieval enjoyment! : : : : Join our International Teleconference: chat.compulink.com 9000 : ------------------------------------------------------------------- From owner-structural-nmr@net.bio.net Mon Apr 17 23:00:00 1995 Path: biosci!rutgers!uwm.edu!psuvax1!news.cc.swarthmore.edu!netnews.upenn.edu!elmo.tju.edu!usenet From: James Varnum Newsgroups: bionet.structural-nmr Subject: Circular Dichroism on a Dichro CD6 Date: 18 Apr 1995 17:52:30 GMT Organization: Thomas Jefferson University Lines: 5 Message-ID: <3n0u8u$9er@elmo.tju.edu> NNTP-Posting-Host: lennon.jci.tju.edu I need help fixing a problem on a CD6 . Recently the signal to noise below 200 nm has gotten terrible ! The manufacturer only suggestion is to replace the mirrors , yet the machine is only 3 years old. Any help or suggestions willl be greatly appreciated. J. M. Varnum Thomas Jefferson University , NMR Facility From owner-structural-nmr@net.bio.net Mon Apr 17 23:00:00 1995 Path: biosci!RISC1.LRM.FI.CNR.IT!isabella From: isabella@RISC1.LRM.FI.CNR.IT Newsgroups: bionet.structural-nmr Subject: help on e-cosy Date: 18 Apr 1995 01:30:24 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <9504180818.AA17354@risc1.lrm.fi.cnr.it> NNTP-Posting-Host: net.bio.net Help!!! I am trying to perform an e-cosy type spectrum to measure 3JHNHA couplings, but I have not succeded yet.... I have not idea where are my mistakes.. I am working with a Bruker instrument. Can anyone send me a beautiful, mistake-less sequence with instructions for beginners? Fast help is appreciated because my NMR time expires soon! Thanks a lot Isabella isabella@risc1.lrm.fi.cnr.it From owner-structural-nmr@net.bio.net Tue Apr 18 23:00:00 1995 Path: biosci!agate!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: bryan@freja.fkem2.lth.se (Bryan Finn) Newsgroups: bionet.structural-nmr Subject: Re: Circular Dichroism on a Dichro CD6 Date: 19 Apr 1995 09:00:02 +0100 Lines: 37 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3n2fu2$s47@mserv1.dl.ac.uk> Original-To: str-nmr@dl.ac.uk J.M., If cleaning the mirrors doesn't help, then the problem is probably caused by too much oxygen in the system. This oxygen is converted to ozone by the Xenon lamp and this ozone is what is degrading the mirrors. Most manufacturers (e.g. Jasco and Aviv) usually recommend using ultra-pure N2 to purge the entire system of oxygen during use. Unfortunately, your manufacturer is correct in that the only remedy is replacing the mirrors if this is the case. After the mirror replacement, you should make sure that you have a source of nitrogen to flush the system with (e.g. ultrapure N2 gas or boil-off from a liquid N2 tank). An adequate N2 flow rate should prolong the life of your new mirrors by at least 2-3 fold. Ask your manufacturer or even another manufacturer for details. (It's surprising that they didn't stress this when installing the machine). Bryan Finn ___________________________________________________________________ | | | Dr. Bryan Finn | | Department of Physical Chemistry 2 Tel: +46-46-222-8254 | | Chemical Center Fax: +46-46-222-4543 | | University of Lund | | POB 124 | | S-221 00 Lund Sweden e-mail: bryan@freja.fkem2.lth.se | | WWW: http://www.fkem2.lth.se/personnel/bryan/finn.html | |_________________________________________________________________| From owner-structural-nmr@net.bio.net Tue Apr 18 23:00:00 1995 Path: biosci!ANDREW.CMU.EDU!ar1z+ From: ar1z+@ANDREW.CMU.EDU ("Alexander J. Ropelewski") Newsgroups: bionet.structural-nmr Subject: CCL:STRUCTURE DETERMINATION FROM NMR Date: 19 Apr 1995 13:54:59 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 98 Sender: daemon@net.bio.net Distribution: world Message-ID: <8jZLUIi00WB88DHVkO@andrew.cmu.edu> 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 AFFILIATED 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 Apr 18 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!swrinde!cs.utexas.edu!news.sprintlink.net!noc.netcom.net!usenet.eel.ufl.edu!news-feed-1.peachnet.edu!news.duke.edu!godot.cc.duq.edu!newsfeed.pitt.edu!uunet!newstf01.news.aol.com!newsbf02.news.aol.com!not-for-mail From: chemotaxis@aol.com (Chemotaxis) Newsgroups: bionet.structural-nmr Subject: Re: Circular Dichroism on a Dichro CD6 Date: 19 Apr 1995 02:16:09 -0400 Organization: America Online, Inc. (1-800-827-6364) Lines: 7 Sender: root@newsbf02.news.aol.com Message-ID: <3n29r9$ih8@newsbf02.news.aol.com> References: <3n0u8u$9er@elmo.tju.edu> Reply-To: chemotaxis@aol.com (Chemotaxis) I have heard that that mirrors may need cleaning over a period of time. Depending on the conditions of use and the evirons, the mirrors may get a dust film coverage - which when cleaned (carefully) may improve on the noise level at lower wavelengths. (I suppose you have checked the light source?) G.DeKoster From owner-structural-nmr@net.bio.net Fri Apr 21 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!newsfeed.pitt.edu!ehdup-i-6.rmt.net.pitt.edu!user From: pxpst2@pitt.edu (Peter Pediaditakis) Newsgroups: bionet.structural-nmr Subject: Re: Help On Gortex Date: Sat, 22 Apr 1995 00:15:11 -0600 Organization: Scientist Lines: 7 Message-ID: References: <3mm9jc$o71@news.compulink.com> NNTP-Posting-Host: ehdup-i-6.rmt.net.pitt.edu If you want to learn more about this molecule start with a college library. If you do a archie search you might find something. Also check with dupont's computor because they have the patent on it. All I know about gortex is that it is teflon that is streched at a specific force and temperature thus forming gortex. It has a unique property in that it allows water to pas in only one direction. It was invented by accident/hapistance. From owner-structural-nmr@net.bio.net Sat Apr 22 23:00:00 1995 Path: biosci!gandalf.psf.sickkids.on.ca!ouwen From: ouwen@gandalf.psf.sickkids.on.ca (ouwen) Newsgroups: bionet.structural-nmr Subject: subscribe Date: 23 Apr 1995 09:38:01 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: <9504231638.AA09304@elrond.psf.sickkids.on.ca> NNTP-Posting-Host: net.bio.net subscribe Ouwen Zhang From owner-structural-nmr@net.bio.net Sun Apr 23 23:00:00 1995 Path: biosci!adam.cc.sunysb.edu!news.sprintlink.net!pipex!howland.reston.ans.net!gatech!newsjunkie.ans.net!inet.d48.lilly.com!sherwood.d46.lilly.com!gfn Newsgroups: bionet.structural-nmr Subject: Re: Circular Dichroism on a Dichro CD6 Message-ID: <1995Apr24.133244.4616@inet.d48.lilly.com> From: Greg Needham Date: 24 Apr 95 13:32:43 EST References: <3n0u8u$9er@elmo.tju.edu> Distribution: world Organization: Eli Lilly and Co. Nntp-Posting-Host: sherwood.d46.lilly.com X-UserAgent: Version 1.1.3 X-XXMessage-ID: X-XXDate: Mon, 24 Apr 95 13:34:16 GMT Lines: 11 varnum@lac.jci.tju.edu (James Varnum) I would echo the last post. Replace (and align) the lamp before I would touch the mirrors. My problems with light intensity (S/N) usually go away with a new lamp. ************************************************************************ gfn@lilly.com All opinions are my own and do not represent my company ************************************************************************ From owner-structural-nmr@net.bio.net Sun Apr 23 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!msunews!netnews.upenn.edu!elmo.tju.edu!usenet From: James Varnum Newsgroups: bionet.structural-nmr Subject: Oxford Magnet Date: 24 Apr 1995 20:05:39 GMT Organization: Thomas Jefferson University Lines: 4 Message-ID: <3nh0aj$7ks@elmo.tju.edu> NNTP-Posting-Host: watson.jci.tju.edu Does anyone have the E-mail address or phone number for Oxford Magnets? Thanks , J. Varnum From owner-structural-nmr@net.bio.net Mon Apr 24 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.cac.psu.edu!news.pop.psu.edu!psuvax1!news.cc.swarthmore.edu!netnews.upenn.edu!elmo.tju.edu!usenet From: James Varnum Newsgroups: bionet.structural-nmr Subject: Nucleic Structure Parameters Date: 25 Apr 1995 19:52:20 GMT Organization: Thomas Jefferson University Lines: 3 Message-ID: <3njjtk$1lm@elmo.tju.edu> NNTP-Posting-Host: watson.jci.tju.edu I need help in obtaining software that will assist in determining nucleic acid structure parameters , i.e. propeller twist etc. Thanks jim varnum From owner-structural-nmr@net.bio.net Tue Apr 25 23:00:00 1995 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: two water signals Date: 26 Apr 1995 08:09:29 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Netters, In DMSO there are usually two water signals; the main signal is accompanied by another smaller water resonance at somewhat higher fields. I don't remember what is this second signal about -- is it the fraction of the water which is strongly interacting with DMSO, or something else? I appreciate your comments, Istvan ================================ Istvan Pelczer, Ph.D. Res. Assist. Professor Chemistry Department, CST Bldg. Syracuse University Syracuse, NY 13244-4100 ph: (315) 443 1023 or x-5932 fax: x-1022(lab) or x-4070(dept) From owner-structural-nmr@net.bio.net Tue Apr 25 23:00:00 1995 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: CD-R/W Date: 26 Apr 1995 08:03:58 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Netters, We are considering to purchase a read-write EOM unit for archiving our data. I would appreciate if you could share with me your experience on such devices and give an advise which model(s) are most reliable and cost-efficient. Thank you, Istvan ================================ Istvan Pelczer, Ph.D. Res. Assist. Professor Chemistry Department, CST Bldg. Syracuse University Syracuse, NY 13244-4100 ph: (315) 443 1023 or x-5932 fax: x-1022(lab) or x-4070(dept) From owner-structural-nmr@net.bio.net Wed Apr 26 23:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!news.sprintlink.net!holonet!colossus.holonet.net!NewsWatcher!user From: g_ashley@holonet.net (Gary W. Ashley) Newsgroups: bionet.structural-nmr Subject: Re: two water signals Date: Wed, 26 Apr 1995 18:09:08 -0800 Organization: HoloNet National Internet Access System: 510-704-1058/modem Lines: 21 Distribution: world Message-ID: References: NNTP-Posting-Host: gashley.ip.holonet.net In article , ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) wrote: > Dear Netters, > > In DMSO there are usually two water signals; the main signal is > accompanied by another smaller water resonance at somewhat higher fields. I > don't remember what is this second signal about -- is it the fraction of the > water which is strongly interacting with DMSO, or something else? My thought is that the second signal is due to residual HOD from the exchange reaction used to make the d6-DMSO. As OH/OD exchange is so slow in DMSO, especially at the low water concentrations we're talking about, one can observe the isotope-shifted water signal. It seems highly unlikely that differential H-bonding is responsible, given the vast molar excess of DMSO over water in these samples - there is plenty of DMSO around to coordinate all the water, I would think. That's my $0.02 worth... Gary Ashley From owner-structural-nmr@net.bio.net Wed Apr 26 23:00:00 1995 Newsgroups: bionet.structural-nmr Path: biosci!ns1.faseb.org!darwin.sura.net!nih-csl!rvenable From: rvenable@deimos.cber.nih.gov (Rick Venable) Subject: Re: Nucleic Structure Parameters Message-ID: <1995Apr26.230540.23732@alw.nih.gov> Sender: postman@alw.nih.gov (AMDS Postmaster) Nntp-Posting-Host: deimos.cber.nih.gov Organization: FDA/CBER Biophysics Lab X-Newsreader: TIN [version 1.2 PL2] References: <3njjtk$1lm@elmo.tju.edu> Date: Wed, 26 Apr 1995 23:05:40 GMT Lines: 15 On 25 Apr 1995 19:52:20 GMT James Varnum pontificated: > I need help in obtaining software that will assist in determining > nucleic acid structure parameters , i.e. propeller twist etc. > Thanks jim varnum There's a program contributed to Brookhaven (home of the PDB) which does just that, using PDB formatted files. I believe it's called dnageom or dnaparm or something similar. Check their gopher server, or their ftp site. -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| / Not an official statement \ rvenable@deimos.cber.nih.gov \/ |=| \ or position of the FDA. / From owner-structural-nmr@net.bio.net Wed Apr 26 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!sunic!sunic.sunet.se!news.funet.fi!ousrvr.oulu.fi!eha From: eha@paju.oulu.fi (Esa Haapaniemi) Newsgroups: bionet.structural-nmr Subject: Re: two water signals Date: 27 Apr 1995 16:39:50 GMT Organization: University of Oulu Lines: 14 Distribution: world Message-ID: <3nohcm$mst@ousrvr.oulu.fi> References: NNTP-Posting-Host: ernst.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] : In DMSO there are usually two water signals; the main signal is : accompanied by another smaller water resonance at somewhat higher fields. I : don't remember what is this second signal about -- is it the fraction of the : water which is strongly interacting with DMSO, or something else? : I appreciate your comments, Isn't that the HDO ? One proton has changed to deuterium and thus the remaining proton gives shifted signal. -- Esa Haapaniemi University of Oulu Department of Chemistry Finland From owner-structural-nmr@net.bio.net Wed Apr 26 23:00:00 1995 Path: biosci!CHEMF.RUTGERS.EDU!MARLA From: MARLA@CHEMF.RUTGERS.EDU (Marla Babcock) Newsgroups: bionet.structural-nmr Subject: Nucleic Acid Parameters Date: 26 Apr 1995 20:13:22 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <085455FA1EFF2007A6@chemf.rutgers.edu> NNTP-Posting-Host: net.bio.net There are six programs for calculating nucleic acid parameters that are readily distributed: Newhelib from Dickerson at UCLA (red@uclaue.mbi.ucla.edu) NUPARM from Bansal available from Brookhaven Curves 4 from Lavery (France) and Sklenar incorporated into Dials and Windows from Beveridge (in the Toolbox) NGEOM from Tung at los Alamos (cst@t10.lanl.gov) BasePair from E. von Kitzing (Germany) and mine which has been sent to the author of the request. Good luck Marla Babcock (Marla@chemf.rutgers.edu) From owner-structural-nmr@net.bio.net Thu Apr 27 23:00:00 1995 Path: biosci!NEUTRON.CHEM.YALE.EDU!rife From: rife@NEUTRON.CHEM.YALE.EDU (Jason Rife) Newsgroups: bionet.structural-nmr Subject: two water peaks Date: 27 Apr 1995 17:30:29 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <199504280030.UAA06609@neutron.chem.yale.edu> NNTP-Posting-Host: net.bio.net Regarding the two water peaks in DMSO: Esa Haapaniemi wrote: Isn't that the HDO ? One proton has changed to deuterium and thus the remaining proton gives shifted signal. My question is where does the deuterium come from to form HDO? Is the system under discussion a mix of DMSO and D20 with the water signals coming from residual water? Otherwise I don't see how HDO could be formed and the answer is more complicated. Jason Rife. From owner-structural-nmr@net.bio.net Fri Apr 28 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!pipex!sunic!sunic.sunet.se!news.funet.fi!ousrvr.oulu.fi!mattisoi From: mattisoi@paju.oulu.fi (Matti Soininen) Newsgroups: bionet.structural-nmr Subject: Re: two water peaks Date: 29 Apr 1995 11:03:36 GMT Organization: Univ. of Oulu , Dept. of Chemistry Lines: 22 Distribution: world Message-ID: <3nt6e8$j68@ousrvr.oulu.fi> References: <199504280030.UAA06609@neutron.chem.yale.edu> NNTP-Posting-Host: raita.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] Jason Rife (rife@NEUTRON.CHEM.YALE.EDU) wrote: : My question is where does the deuterium come from to form HDO? Is the : system under discussion a mix of DMSO and D20 with the water signals : coming from residual water? Otherwise I don't see how HDO could be : formed and the answer is more complicated. : : Jason Rife. : If you are using deuterated DMSO (DMSO-d6) the deuterium comes from there and exhanges with water protons to form HDO. -- ######################################################################### # Matti Soininen # # Yliopistokatu 24 A 102 # # 90570 OULU # # p.981-5567 509 # # e-mail: mattisoi@phoenix.oulu.fi # # http://phoenix.oulu.fi/~mattisoi # ######################################################################### From owner-structural-nmr@net.bio.net Sat Apr 29 23:00:00 1995 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: two water signals Date: 30 Apr 1995 06:14:22 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 28 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net Dear Netters, Thank you all who commented on the existence of a second water signal in DMSO-d6. Most responded that it is the signal of HDO, while the main resonance belongs to H2O. We have made a simple experiment which proves this option: with a tiny fraction of D2O added the second signal increases significantly, which is not expected if it was a solvation phenomenon. The spectra look pretty; we'll show them in The NMR Newsletter (formerly TAMU Newsletter). The origin of the D is still not clear, however. Either it comes form the production of the DMSO-d6, or, I guess, some tautomeric process should be involved -- otherwise breaking a covalent C-D bond should be necessary. Thanks again, I wish good sailing on the net, Istvan ================================ Istvan Pelczer, Ph.D. Res. Assist. Professor Chemistry Department, CST Bldg. Syracuse University Syracuse, NY 13244-4100 ph: (315) 443 1023 or x-5932 fax: x-1022(lab) or x-4070(dept) From owner-structural-nmr@net.bio.net Sun Apr 30 23:00:00 1995 Path: biosci!CHEM0SUN.CALSTATELA.EDU!glee From: glee@CHEM0SUN.CALSTATELA.EDU (Ging Lee 12-06-90) Newsgroups: bionet.structural-nmr Subject: (none) Date: 30 Apr 1995 22:40:38 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: <9505010536.AA12356@chem0sun.calstatela.edu> NNTP-Posting-Host: net.bio.net subscribe and forward to glee@spartan2.calstatela.edu From owner-structural-nmr@net.bio.net Sun Apr 30 23:00:00 1995 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: two water signals Date: 1 May 1995 07:28:36 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 64 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <9504301638.AA13715@bioc01.uthscsa.edu> NNTP-Posting-Host: net.bio.net Dear Raman, I believe the answer could be a matter of interest for others on the net, too, so let me post it to them as well. The NMR Newsletter, which functioned as TAMU Newsletter for a while has gained independency recently -- that's why the change in the name. Contribution is a requirement, yes. For more information and subscription please, contact Professor Barry L. Shapiro at: 966 Elsinore Court, Palo Alto, CA 94303, or by fax: (415) 493 1348. Daytime phone (8am-10pm, PT): (415) 493 5971. Sincerely, Istvan ================================ Istvan Pelczer, Ph.D. Res. Assist. Professor Chemistry Department, CST Bldg. Syracuse University Syracuse, NY 13244-4100 ph: (315) 443 1023 or x-5932 fax: x-1022(lab) or x-4070(dept) On Sun, 30 Apr 1995, C.S.RAMAN wrote: > Dear Istvan: > > > phenomenon. The spectra look pretty; we'll show them in The NMR > > Newsletter (formerly TAMU Newsletter). > > Since you brought it up, I was wondering how one can obtain a > subscription to the NMR newsletter? I used to receive it in the past > but since the operation moved to Stanford (or CA?), I haven't had much > contact. What is the current status of the newsletter? Do you still > need to contribute to retain a subscription? > > Thanks for your time. > Best regards > -raman > -- > _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ > _/ _/ > _/ C.S.RAMAN _/ > _/ Department of Biochemistry _/ > _/ University of Texas Health Science Center _/ > _/ 7703 Floyd Curl Drive _/ > _/ San Antonio, TX 78284-7760 _/ > _/ USA _/ > _/ _/ > _/ Tel: (210) 567-6623 _/ > _/ Fax: (210) 567-6595 _/ > _/ E-mail: raman@bioc01.uthscsa.edu _/ > _/ _/ > _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ > _/ _/ > _/ How can it be that mathematics, a product of human thought _/ > _/ independent of experience, is so admirably adapted to the _/ > _/ objects of reality? -Albert Einstein _/ > _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ > >