From owner-structural-nmr@net.bio.net Mon May 01 23:00:00 1995 Path: biosci!PICARD.NIEHS.NIH.GOV!rachelle From: rachelle@PICARD.NIEHS.NIH.GOV (Rachelle J. Bienstock) Newsgroups: bionet.structural-nmr Subject: Questions concerning preparation of protein NMR sample Date: 2 May 1995 07:26:30 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 33 Sender: daemon@net.bio.net Distribution: world Message-ID: <9505021427.AA19683@picard.niehs.nih.gov> NNTP-Posting-Host: net.bio.net Hi- I am going to begin some studies of a small protein (app 10 KDa) and have some questions concerning sample preparation. Do people typically purchase deuterated buffers to prepare samples in, or do they just prepare samples in d2o and then adjust pH with deuterated reagents? Also, what pH and buffers would people recommend using? If someone is preparing a protein for you and expresses it in E.Coli and then just runs in down an antibody column what other steps do people usually do to obtain a sample pure enough for NMR experiments? If anyone could suggest a good current reference on preparing a protein sample for proton NMR I would greatly appreciate it... Thanks, Rachelle (rachelle@picard.niehs.nih.gov) ##### (o o) +------------------------oooO---(__)---Oooo----------------------------+ | | | Dr. Rachelle Bienstock INTERNET :rachelle@picard.niehs.nih.gov | | National Institute of | | Environmental Health Sciences | | P.O. Box 12233 Mail Drop 10-03 Telephone : 919-541-3397 | | Research Triangle Park, NC 27709 Fax : 919-541-1578 | +----------------------------------------------------------------------+ || || (__) (__) From owner-structural-nmr@net.bio.net Mon May 01 23:00:00 1995 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: Questions concerning preparation of protein NMR sample Date: 2 May 1995 08:20:35 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <9505021427.AA19683@picard.niehs.nih.gov> NNTP-Posting-Host: net.bio.net There is a good reference for sample preparation: N. J. Oppenheimer; Methods in Enzymology, 176(1989)78-89. 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 May 01 23:00:00 1995 Path: biosci!PILLER.PHARM.UTAH.EDU!durant From: durant@PILLER.PHARM.UTAH.EDU (Phil Durant) Newsgroups: bionet.structural-nmr Subject: heterotocsynosy pulse sequence Date: 2 May 1995 14:18:50 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: <9505022021.AA00950@piller.pharm.utah.edu> NNTP-Posting-Host: net.bio.net Hi bionetters, I am a graduate student doing NMR on RNA hairpins and would like to run a heterotocsynosy or heterotocsytocsy experiment on our Varian instrument. Most people seem to be doing this type of experiment on Bruker instruments so I am having trouble finding a pulse sequence written for Varian use. I have already checked the Varian userlib directory. If anyone has this pulse sequence or knows where I can find it please let me know. Thanks, Phil Durant Univ. of Utah - Dept. of Medicinal Chemistry durant@piller.pharm.utah.edu From owner-structural-nmr@net.bio.net Tue May 02 23:00:00 1995 Path: biosci!rutgers!gatech!swrinde!pipex!sunic!sunic.sunet.se!trane.uninett.no!due.uninett.no!nkjem.kj.uib.no!user From: Erlend.Moldrheim@kj.uib.no (Erlend Moldrheim) Newsgroups: bionet.structural-nmr Subject: Dust particles in D20 Followup-To: bionet.structural-nmr Date: 3 May 1995 09:25:53 GMT Organization: Dept. of Chem., Univ. of Bergen Lines: 8 Message-ID: NNTP-Posting-Host: nkjem.kj.uib.no We have discovered dust particles in ampoules containing 99.996 % and 99.96 % D2O from Cambridge Isotope Lab. and Euriso-top respectively. This will cause line-broadening and reduce the resolution of the spectra ( we are working with oligonucleotides). I wonder : has anyone else had this problem ? I am sure this question is of interest to users of this group. Erlend Moldrheim From owner-structural-nmr@net.bio.net Tue May 02 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: bryan@freja.fkem2.lth.se (Bryan Finn) Newsgroups: bionet.structural-nmr Subject: Re: Dust particles in D20 Date: 3 May 1995 11:35:45 +0100 Lines: 34 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3o7ma1$4du@mserv1.dl.ac.uk> Original-To: str-nmr@dl.ac.uk > We have discovered dust particles in ampoules containing 99.996 % and 99.96 > % D2O from Cambridge Isotope Lab. and Euriso-top respectively. This will > cause line-broadening and reduce the resolution of the spectra ( we are > working with oligonucleotides). > I wonder : has anyone else had this problem ? > I am sure this question is of interest to users of this group. > > Erlend Moldrheim > Have you contacted Cambridge Isotope Lab. and Euriso-top? What do they say about this? 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@freja.fkem2.lth.se | | WWW: http://www.fkem2.lth.se/personnel/bryan/finn.html | |_________________________________________________________________| From owner-structural-nmr@net.bio.net Tue May 02 23:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!news.sprintlink.net!sundog.tiac.net!cil.tiac.net!lynneb From: lynneb@isotope.com (Lynne S. Batchelder) Newsgroups: bionet.structural-nmr Subject: dust particles in D2O and other issues Date: Wed, 3 May 1995 15:10:08 Organization: Cambridge Isotope Laboratories Lines: 22 Message-ID: NNTP-Posting-Host: cil.tiac.net X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] I wanted to make you all aware that Cambridge Isotope Laboratories is on the Net and I also wanted to respond to the postings about dust particles in D2O. (See May 3 posting from Erlend.Moldrheim@kj.uib.no and responses) CIL has a formal procedure to investigate and solve all issues regarding product quality as well as general technical inquiries. Since we are available on the Net your questions may be directed to me or you may also contact the CIL Sales Rep in your area. We shall respond to your questions in the most efficient manner. If you have questions about one of our products, please provide the following information: description of problem, catalog no. of product, quantity, lot no., purchase order no., date purchased and of course your full name and address If you have any comments or suggestions please let us know. Lynne S. Batchelder, Ph.D. Technical Services Manager Cambridge Isotope Laboratories, Inc. 50 Frontage Road Andover, Massachusetts 01810 508 749 8000 508 749 2768 (FAX) From owner-structural-nmr@net.bio.net Tue May 02 23:00:00 1995 Path: biosci!adam.cc.sunysb.edu!news.sprintlink.net!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: ulf@cis.biochemtech.uni-halle.de (Ulf Reimer) Newsgroups: bionet.structural-nmr Subject: Re:_Dust_particles_in_D2O Date: 3 May 1995 15:15:41 +0100 Lines: 25 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3o836d$e0o@mserv1.dl.ac.uk> Original-To: str-nmr@dl.ac.uk > We have discovered dust particles in ampoules containing 99.996 % and 99.96 > % D2O from Cambridge Isotope Lab. and Euriso-top respectively. This will > cause line-broadening and reduce the resolution of the spectra ( we are > working with oligonucleotides). > I wonder : has anyone else had this problem ? > I am sure this question is of interest to users of this group. > > Erlend Moldrheim > The dust is to be seen in the intact ampules. They were already contaminated when I got them! Sincerely, Ulf Reimer | ulf@cis.biochemtech.uni-halle.de Ulf Reimer | Phone: +49 0345 617-246 | Fax: +49 0345 5511972 Weinbergweg 16a | Max Planck-Gesellschaft e.V. D-06120 Halle (Saale) | AG "Enzymologie der Peptidbindung" Germany From owner-structural-nmr@net.bio.net Tue May 02 23:00:00 1995 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: Dust particles in D20 Date: 3 May 1995 06:10:31 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 42 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net On 3 May 1995, Erlend Moldrheim wrote: > We have discovered dust particles in ampoules containing 99.996 % and 99.96 > % D2O from Cambridge Isotope Lab. and Euriso-top respectively. This will > cause line-broadening and reduce the resolution of the spectra ( we are > working with oligonucleotides). > I wonder : has anyone else had this problem ? > I am sure this question is of interest to users of this group. > > Erlend Moldrheim > > Excuse me if I ask about an obvious thing, which you have checked already; do you see the dust particles in the intact ampules? There are other ways how dust can contaminate your samples. In our practice (we work with oligonucleotides, too, beside other samples) we use liofilization, when breaking the vacuum is likely to suck in dust. Also, the sample tube itself carries dust particles on the inside wall surface (also outside, but it is not that much of a danger), due to the electrostatic attraction. As such particles are likely to broaden lines and degrade homogeneity we take careful measures to keep them away. We rinse the tubes well several times, filter all samples through microfilters and usually make up the samples in a glovebag under nitrogen or argone. The latter ensures that no (or at least much less) oxigen will be in the sample which improves lineshape further. 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) From owner-structural-nmr@net.bio.net Tue May 02 23:00:00 1995 Path: biosci!SNEEZY.FHIS.NET!barry From: barry@SNEEZY.FHIS.NET ("Barry Schweitzer") Newsgroups: bionet.structural-nmr Subject: Borate buffer? Date: 3 May 1995 13:52:13 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 28 Sender: daemon@net.bio.net Distribution: world Message-ID: <9505031651.ZM5292@sneezy.fhis.net> NNTP-Posting-Host: net.bio.net Hi there: Does anyone know any reason why using a borate buffer for an NMR sample should cause a problem? Someone wants to send us a sample in a borate/NaCl buffer. I can't recall seeing this used before so I thought I would ask the group first. This is a probably a low interest question so replies can be sent directly to me instead of using up valuable bandwidth. Thanks in advance! Barry -- 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 Tue May 02 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: ulf@cis.biochemtech.uni-halle.de (Ulf Reimer) Newsgroups: bionet.structural-nmr Subject: Re:_Dust_particles_in_D2O Date: 3 May 1995 13:35:59 +0100 Lines: 30 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3o7tbf$9gh@mserv1.dl.ac.uk> Original-To: str-nmr@dl.ac.uk > We have discovered dust particles in ampoules containing 99.996 % and 99.96 > % D2O from Cambridge Isotope Lab. and Euriso-top respectively. This will > cause line-broadening and reduce the resolution of the spectra ( we are > working with oligonucleotides). > I wonder : has anyone else had this problem ? > I am sure this question is of interest to users of this group. > > Erlend Moldrheim > I`ve got D2O 99.96 % from euroiso-top. When I read the message I looked for dust particles in it and I found some! I still not used this charge of D2O, thats why I cannot say anything about occuring problems. Sincerely Ulf Reimer | ulf@cis.biochemtech.uni-halle.de Ulf Reimer | Phone: +49 0345 617-246 | Fax: +49 0345 5511972 Weinbergweg 16a | Max Planck-Gesellschaft e.V. D-06120 Halle (Saale) | AG "Enzymologie der Peptidbindung" Germany From owner-structural-nmr@net.bio.net Wed May 03 23:00:00 1995 Path: biosci!biophy.jussieu.fr!michel From: michel@biophy.jussieu.fr (Michel SEIGNEURET) Newsgroups: bionet.structural-nmr Subject: Re: Dust particles in D20 Date: 3 May 1995 23:53:29 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: <9505040701.AA08201@mood.biophy.jussieu.fr> NNTP-Posting-Host: net.bio.net Suppliers usually warrant the chemical and isotopic purity of their D2O but not the microbiological one i.e. the D2O is not sterilized. I have in fact noticed bacterial growth which visually can appear as dust in several D2O ampules from several supplier. A consequence may be the digestion of your favorite protein by bacterial proteases. A routine precaution is to store D2O at low temperature. A safer way would be to autoclave the D2O but I do not know whether the ampule might explode or not. Maybe a volunteer netter might try and tell us... Michel Seigneuret Universite Paris 7 Lab. de Biophysique Cellulaire France From owner-structural-nmr@net.bio.net Wed May 03 23:00:00 1995 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: Questions concerning preparation of protein NMR sample Date: 4 May 1995 09:34:52 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <9505021427.AA19683@picard.niehs.nih.gov> NNTP-Posting-Host: net.bio.net There is another excellent chapter about sample preparation: W. U. Primrose, Sample preparation Chapter 2 in: NMR of Macromolecules, A Practical Approach Ed.: G. C. K. Roberts, Oxford Univ. Press., 1993. 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) From owner-structural-nmr@net.bio.net Thu May 04 23:00:00 1995 Path: biosci!jk.uni-linz.ac.at!Alexej.Jerschow From: Alexej.Jerschow@jk.uni-linz.ac.at (Alexej Jerschow) Newsgroups: bionet.structural-nmr Subject: Polymers T1 and T2-measurements ? Date: 5 May 1995 00:53:22 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <199505050750.AA16489@alijku06.edvz.uni-linz.ac.at> NNTP-Posting-Host: net.bio.net Hi ! I need a practicable sample preparation technique for removing oxygen in polymer samples (polypropylene) dissolved in tetrachloroethane-d4 (or a mixture of trichlorobenzene/benzene) for T1 and T2-measurements. A severe problem is that the sample itself contains air occlusions. The resultant solution (10 wt%) is very viscous and so common techniques like N2 purging or evacuation/N2 filling seem not to be appropriate. I would very much appreciate if someone could help me. AJ From owner-structural-nmr@net.bio.net Thu May 04 23:00:00 1995 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: Q: stable peptide conformation in aqueous solution? Date: 5 May 1995 07:12:02 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 31 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net Let me have one more comment on this issue. The transition between "stable" and "dynamic" is not only extremely fuzzy based on individual properties of the molecules and their environment, but this classification is questionable for all systems we study. The term "dynamic" has different meaning for various spectroscopy methods with different time scale. Also, it is usually our -- wishful -- expectation to find THE structure even for large molecules with lots of constraints. In reality the whole (or segments of the) molecule is largely mobile, and there are several structures which satisfy the measured parameters. There are plenty of examples of such behaviour in the current literature; eglin c is a nice example from Gerhard Wagner's lab, among many others. Warnings have been presented several times (from Oleg Jardetzky, for example) about the dangers of the "static" description of such structures. We also experienced extended local mobility of the loop region in a 24-mer RNA hairpin recently -- it will appear in the May-23st issue of Biochemistry. 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) From owner-structural-nmr@net.bio.net Thu May 04 23:00:00 1995 Newsgroups: bionet.structural-nmr Path: biosci!rutgers!gatech!swrinde!cs.utexas.edu!uunet!nih-csl!loglady.ninds.nih.gov!johnk From: johnk@spasm.niddk.nih.gov (John Kuszewski) Subject: Re: Q: stable peptide conformation in aqueous solution? Message-ID: <1995May5.155108.6679@alw.nih.gov> Sender: postman@alw.nih.gov (AMDS Postmaster) Nntp-Posting-Host: spasm.niddk.nih.gov Reply-To: johnk@spasm.niddk.nih.gov (John Kuszewski) Organization: National Insts. of Health References: Date: Fri, 5 May 1995 15:51:08 GMT Lines: 34 |>My question is: |> |>WERE (AT WHICH SIZE) IS THE APPROXIMATE TRANSITION "DYNAMIC - STABLE"? |> (aqueous solution no detergents etc., room-temperature) Using calorimetry to look for cooperative folding/unfolding transitions, Privalov has found that the minimum length of a peptide that has a "folded" state is (depending on sequence, of course) about 50 residues. Of course, there are exceptions (eg. BPTI), but these tend to "cheat" by having large numbers of disulphides or cyclic backbones. And also there have been plenty of "structures" done of small ordinary peptides by NMR, but these are uniformly found to be rather flexible. -- _____________ | ___/_ | |/ / -- /\ // /-- || || / /|| || || / / || || ||/ / || John Kuszewski || |/ /| || johnk@spasm.niddk.nih.gov || / /|| || \/ / / || \/ that's MISTER protein G to you! |/__/| | /_________| "Biophysics has driven me to an attitude of apocalyptic doom" --Frank Delaglio From owner-structural-nmr@net.bio.net Thu May 04 23:00:00 1995 Path: biosci!LAPLACE.CSB.YALE.EDU!abonvin From: abonvin@LAPLACE.CSB.YALE.EDU ("Alexandre Bonvin") Newsgroups: bionet.structural-nmr Subject: Re: Q: stable peptide conformation in aqueous solution? Date: 5 May 1995 08:14:23 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 60 Sender: daemon@net.bio.net Distribution: world Message-ID: <9505051514.AA15497@laplace.csb.yale.edu> NNTP-Posting-Host: net.bio.net > > Let me have one more comment on this issue. The transition between > "stable" and "dynamic" is not only extremely fuzzy based on individual > properties of the molecules and their environment, but this > classification is questionable for all systems we study. The term > "dynamic" has different meaning for various spectroscopy methods with > different time scale. Also, it is usually our -- wishful -- expectation > to find THE structure even for large molecules with lots of constraints. > In reality the whole (or segments of the) molecule is largely mobile, and > there are several structures which satisfy the measured parameters. > There are plenty of examples of such behaviour in the current > literature; eglin c is a nice example from Gerhard Wagner's lab, among > many others. Warnings have been presented several times (from Oleg > Jardetzky, for example) about the dangers of the "static" description of > such structures. ... > Istvan I agree with Istvan comments and his warnings about the dangers of the "static" description of such structures". More appropriate approches can be used in case of conformational variability or dynamical character of proteins (or parts of it (e.g. loops)). Basically, two methods can be used in the structure calculations to account for such processes: time- or ensemble-averaged constraints. The choice will depend on the time scale of the averaging processes in solution. A danger of such approaches, however, is that we introduce more parameters when fitting our NMR data and might end up overfitting them. I have been working on developing methods to assess the validity of multi-conformer (or ensemble-averaged) refinement in NMR structure determination. Cross-validation can be used for this purporse (the idea the crystallographic free R-factor applied to NMR). These results will appear in JMB, but I also intend to present a poster in the "NET SUMMER POSTER SESSION on NMR" on the web. For information about this poster session contact one of the following persons: Bryan Finn, bryan@freja.fkem2.lth.se Kevin Gardner, gardner@zinc.csb.yale.edu Barry Hardy, bhardy@convex.ox.ac.uk Alexandre ========================================================================== | Alexandre Bonvin PhD | Phone: (203) 432-5066 | | Mol. Biophys. & Biochemistry | Fax: (203) 432-6946 | | Yale University | Email: abonvin@laplace.csb.yale.edu | | New Haven CT 06520-8114, USA | | ========================================================================== From owner-structural-nmr@net.bio.net Thu May 04 23:00:00 1995 Path: biosci!rutgers!gatech!swrinde!hookup!rover.ucs.ualberta.ca!news From: DWHYTE@pharmacy.ualberta.ca (Don Whyte) Newsgroups: bionet.structural-nmr Subject: looking for non-magnetic chairs Date: 5 May 1995 14:43:10 GMT Organization: University of Alberta Lines: 11 Message-ID: <3oddhu$19cu@rover.ucs.ualberta.ca> Reply-To: DWHYTE@Pharmacy.ualberta.ca NNTP-Posting-Host: ptarmigan.pharmacy.ualberta.ca X-Newsreader: WinVN 0.92.4 Dear Netters We would like to find where to buy office chairs made of non-magnetic material to use in our 300 mhz NMR room. The NMR field is affected by movement of steel chairs. Please respond to above address. Thanks Don Whyte From owner-structural-nmr@net.bio.net Thu May 04 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!howland.reston.ans.net!news-e1a.megaweb.com!newstf01.news.aol.com!uunet!EU.net!Germany.EU.net!zib-berlin.de!fu-berlin.de!novell-compaq.rz-berlin.mpg.DE!not-for-mail From: Schnibbe@MPIMG-Berlin-Dahlem.MPG.DE (Thomas Schnibbe) Newsgroups: bionet.structural-nmr Subject: Q: stable peptide conformation in aqueous solution? Date: Thu, 4 May 1995 14:12:20 GMT +0100 Organization: Max Planck Institut fuer molekulare Genetik, Berlin Lines: 45 Message-ID: NNTP-Posting-Host: novell-compaq.rz-berlin.mpg.de (141.14.129.150) X-Access: 16 25 816 X-Newsreader: Trumpet for Windows [Version 1.0 Rev B] Dear Netters, I have a question concerning peptide conformation in aqueous solution. It has been shown that secondary structure formation in aqueous solution should be negligible for all short peptides (shorter than 13 - 15 aa or so). Increased chain length moves along with secondary structure formation: Medium size peptides may present a population with secondary structure in a rapid equilibrium with random, mainly extended, conformations. Large peptides/proteins beyond a certain chain length show stable (super-) secondary and tertiary structures (quite stable and somehow dynamic, too). My question is: WERE (AT WHICH SIZE) IS THE APPROXIMATE TRANSITION "DYNAMIC - STABLE"? (aqueous solution no detergents etc., room-temperature) (Of course, secondary/tertiary structure formation strongly depends on physico-chemical properties of the bulk solution, the primary structure, temperature etc., too) Since I'm working on synthetic peptides you would help me a lot. Thank you for your time, Thomas ___ Thomas Schnibbe ___ Max-Planck-Institute for Molecular Genetics ___ Ihnestr. 73 tel (0)30-84131280 14195 Berlin fax (0)30-84131385 Germany email Schnibbe@MPIMG-Berlin-Dahlem.MPG.DE From owner-structural-nmr@net.bio.net Thu May 04 23:00:00 1995 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: Q: stable peptide conformation in aqueous solution? Date: 5 May 1995 04:38:34 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 70 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net I believe there is no general answer to your question. The behaviour of the peptide is a function of individual character of the structure, and other parameters not listed yet, such as pH, ionic strength, etc. Also, in some cases the population of various conformations can be mapped out by careful analysis of the NMR information (see papers from Ernst's lab on antamanide, and Renzo Bazzo has developed some tools for thi to my best knowledge, too). 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 Thu, 4 May 1995, Thomas Schnibbe wrote: > > Dear Netters, > > I have a question concerning peptide conformation in aqueous > solution. > > It has been shown that secondary structure formation in aqueous > solution should be negligible for all short peptides (shorter than 13 - 15 aa > or so). > Increased chain length moves along with secondary structure formation: Medium > size peptides may present a population with secondary structure in a rapid > equilibrium with random, mainly extended, conformations. > Large peptides/proteins beyond a certain chain length show stable > (super-) secondary and tertiary structures (quite stable and somehow > dynamic, too). > > My question is: > > WERE (AT WHICH SIZE) IS THE APPROXIMATE TRANSITION "DYNAMIC - STABLE"? > (aqueous solution no detergents etc., room-temperature) > > (Of course, secondary/tertiary structure formation strongly depends on > physico-chemical properties of the bulk solution, the primary structure, > temperature etc., too) > > Since I'm working on synthetic peptides you would help me a lot. > > Thank you for your time, > > Thomas > > > > > > > ___ > Thomas Schnibbe > ___ > Max-Planck-Institute for Molecular Genetics > ___ > Ihnestr. 73 tel (0)30-84131280 > 14195 Berlin fax (0)30-84131385 > Germany email Schnibbe@MPIMG-Berlin-Dahlem.MPG.DE > > > From owner-structural-nmr@net.bio.net Thu May 04 23:00:00 1995 Path: biosci!jk.uni-linz.ac.at!Alexej.Jerschow From: Alexej.Jerschow@jk.uni-linz.ac.at (Alexej Jerschow) Newsgroups: bionet.structural-nmr Subject: Polypropylene/T1,T2-measurements Date: 5 May 1995 03:39:53 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <199505051037.AA24580@alijku06.edvz.uni-linz.ac.at> NNTP-Posting-Host: net.bio.net Hi ! I need a practicable sample preparation technique for removing oxygen in polymer samples (polypropylene) dissolved in tetrachloroethane-d4 (or a mixture of trichlorobenzene/benzene) for T1 and T2-measurements. A severe problem is that the sample itself contains air occlusions. The resultant solution (10 wt%) is very viscous and so common techniques like N2 purging or evacuation/N2 filling seem not to be appropriate. I would very much appreciate if someone could help me. AJ ---------------------------------------- Alexej Jerschow Organic Chemistry Johannes Kepler University Linz, Austria Tel: (732) 2468-777 or (732) 246202 From owner-structural-nmr@net.bio.net Fri May 05 23:00:00 1995 Path: biosci!rutgers!gatech!bloom-beacon.mit.edu!news.bu.edu!news3.near.net!yale!news.ycc.yale.edu!cadmium.csb.yale.edu!gardner From: gardner@cadmium.csb.yale.edu (Kevin Gardner) Newsgroups: bionet.structural-nmr Subject: Re: Q: stable peptide conformation in aqueous solution? Date: 6 May 1995 01:09:42 GMT Organization: Yale University Lines: 33 Distribution: world Message-ID: <3oei8m$j33@news.ycc.yale.edu> References: <9505051514.AA15497@laplace.csb.yale.edu> NNTP-Posting-Host: cadmium.csb.yale.edu X-Newsreader: TIN [version 1.2 PL2] Alexandre Bonvin (abonvin@LAPLACE.CSB.YALE.EDU) wrote: : crystallographic free R-factor applied to NMR). These results will : appear in JMB, but I also intend to present a poster in the "NET : SUMMER POSTER SESSION on NMR" on the web. For information about : this poster session contact one of the following persons: : Bryan Finn, bryan@freja.fkem2.lth.se : Kevin Gardner, gardner@zinc.csb.yale.edu : Barry Hardy, bhardy@convex.ox.ac.uk Thanks to Alexandre for the free publicity; I'll have to walk upstairs to thank him again in person and buy him a beer. I'd like to take this opportunity to encourage any interested people to check out a preliminary set of posters that we already have on the Web (Alexandre's is coming soon): http://zinc.csb.yale.edu/nmr/poster.html An additional site at Oxford will be coming on-line soon to offer faster responses to European participants. We're still looking for participants for this session, due to run in early June. Check out our site or contact one of the organizers (addresses above) for more information. Thanks, Kevin -- ************************************************************************* Kevin Gardner Yale University Dept. of Molecular Biophysics and Biochemistry Internet: gardner@zinc.csb.yale.edu Bitnet: gardner@yalemed http://zinc.csb.yale.edu/~gardner From owner-structural-nmr@net.bio.net Fri May 05 23:00:00 1995 Path: biosci!WEIZMANN.WEIZMANN.AC.IL!CSMLN From: CSMLN@WEIZMANN.WEIZMANN.AC.IL ("m.lakshmi narayanan") Newsgroups: bionet.structural-nmr Subject: crystallography position (fwd) (fwd) Date: 6 May 1995 01:17:47 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 29 Sender: daemon@net.bio.net Distribution: world Message-ID: <950506.111817.+0300.CSMLN@WEIZMANN.WEIZMANN.AC.IL> NNTP-Posting-Host: net.bio.net Dear Sir/Madam, I am a chemist(M.Sc.)- cum - crystallographer(Ph.d.) Looking for a suitable position in a research laboratory. Those who have positions available may please ask for cv/biodata. Research Interest: 1. Crystallography (Macromolecular/Small molecular) 2. drug designing 3. molecular modelling 4. Protein, DNA structure analysis expecting an earlier response thanking you sincerely yours M. Lakshmi Narayanan Department of Structural Biology Weizmann Institute of Science Rehovot 76100 ISRAEL From owner-structural-nmr@net.bio.net Fri May 05 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!usenet.eel.ufl.edu!noc.netcom.net!news.sprintlink.net!pipex!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!smb18 From: smb18@mole.bio.cam.ac.uk (Simon Brocklehurst (Bioc)) Newsgroups: bionet.structural-nmr Subject: Re: Q: stable peptide conformation in aqueous solution? Date: 6 May 1995 11:57:53 GMT Organization: University of Cambridge, England Lines: 32 Message-ID: <3ofo81$i1a@lyra.csx.cam.ac.uk> References: NNTP-Posting-Host: mole.bio.cam.ac.uk Schnibbe@MPIMG-Berlin-Dahlem.MPG.DE (Thomas Schnibbe) writes: >WERE (AT WHICH SIZE) IS THE APPROXIMATE TRANSITION "DYNAMIC - STABLE"? > (aqueous solution no detergents etc., room-temperature) At present, the transition is probably about 30-50 residues. The smallest stable protein fold (with no ligands, disulphides, co-factors etc to help stabilization) yet discovered is that of the peripheral subunit-binding domain of 2-oxo acid dehydrogenase multienzyme complexes - the structure of a fragment of this multidomain "domain-and-linker" protein indicated that 33 residues were highly ordered, with hints of looser structure extending a few residues towards the N-terminus. See: AU: BROCKLEHURST_SM, KALIA_YN, PERHAM_RN JN: TRENDS IN BIOCHEMICAL SCIENCES 1994 Vol.19 No.9 pp.360-361 AU: KALIA_YN, BROCKLEHURST_SM, HIPPS_DS, APPELLA_E, SAKAGUCHI_K, PERHAM_RN JN: JOURNAL OF MOLECULAR BIOLOGY 1993 Vol.230 No.1 pp.323-341 The protein described in these references keeps pretty much all its structure until about 55 degrees I think - and if, I recall correctly, has a Tm of about 65 degrees. _________________________________________________________________________ | | ,_ o Simon M. Brocklehurst, | / //\, Oxford Centre for Molecular Sciences | \>> | Department of Biochemistry, University of Oxford, | \\, Oxford, UK. | E-mail: smb@bioch.ox.ac.uk |________________________________________________________________________ From owner-structural-nmr@net.bio.net Fri May 05 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!gatech!bloom-beacon.mit.edu!uhog.mit.edu!rutgers!uwm.edu!vixen.cso.uiuc.edu!prairienet.org!glturner From: glturner@prairienet.org (Gary L. Turner) Newsgroups: bionet.structural-nmr Subject: Re: looking for non-magnetic chairs Date: 6 May 1995 02:34:00 GMT Organization: University of Illinois at Urbana Lines: 18 Message-ID: <3oen6o$rat@vixen.cso.uiuc.edu> NNTP-Posting-Host: firefly.prairienet.org >Dear Netters > >We would like to find where to buy office chairs made of >non-magnetic material to use in our 300 mhz NMR room. >The NMR field is affected by movement of steel chairs. > >Please respond to above address. > >Thanks > >Don Whyte At most lawn/garden centers, plastic lawn chairs are available. They work extremely well, are totally plastic, and typically cost about $10. Gary Turner Spectral Data Services, Inc -- From owner-structural-nmr@net.bio.net Sat May 06 23:00:00 1995 Path: biosci!NODDY.CM.UTEXAS.EDU!jarle From: jarle@NODDY.CM.UTEXAS.EDU (Jarle Lillemoen) Newsgroups: bionet.structural-nmr Subject: (none) Date: 7 May 1995 14:08:28 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: <9505072108.AA07046@noddy.cm.utexas.edu> NNTP-Posting-Host: net.bio.net subscribe From owner-structural-nmr@net.bio.net Sun May 07 23:00:00 1995 Path: biosci!rutgers!gatech!newsjunkie.ans.net!inet.d48.lilly.com!sherwood.d46.lilly.com!gfn Newsgroups: bionet.structural-nmr Subject: Re: Polymers T1 and T2-measurements ? Message-ID: <1995May8.164752.4769@inet.d48.lilly.com> From: Greg Needham Date: 8 May 95 16:47:51 EST References: <199505050750.AA16489@alijku06.edvz.uni-linz.ac.at> 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, 8 May 95 16:49:26 GMT Lines: 15 Alexej.Jerschow@jk.uni-linz.ac.at (Alexej Jerschow) It has been a very long time since I had to worry about such things, but.... Have you thought about putting the sample onto a vacuum line, freezing the sample, evacuating the sample, Warming, freezing, etc.? I used to do this for my viscous samples many years ago. If I remember we did about 5-6 cycles. Hope this helps. ************************************************************************ gfn@lilly.com All opinions are my own and do not represent my company ************************************************************************ From owner-structural-nmr@net.bio.net Sun May 07 23:00:00 1995 Path: biosci!BCVMS.BC.EDU!MARKMANO From: MARKMANO@BCVMS.BC.EDU Newsgroups: bionet.structural-nmr Subject: Charybdatoxin Date: 8 May 1995 15:45:20 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HQ9QTWC6FM8ZGXI7@bcvms.bc.edu> Reply-To: markmano@bcvms.bc.edu NNTP-Posting-Host: net.bio.net If anybody knows how I can get in tauch with any of the following: F. TOMA A. MENEZ B. GILQUIN F. BONTEMS Or if any of these is reading, I'd be happy to get an E-mail from them. It is regarding charybdotoxin's structure. Ofer Markman. Markman@bcchem markman@bcchem.bc.edu markman@bcvms.bc.edu markman@bcchme.bc.edu Tel: 617 - 552 3905 Fax: 617 - 552 2705 From owner-structural-nmr@net.bio.net Sun May 07 23:00:00 1995 Path: biosci!WWITCH.UNL.EDU!rshoe From: rshoe@WWITCH.UNL.EDU (Richard Shoemaker) Newsgroups: bionet.structural-nmr Subject: Re: looking for non-magnetic chairs Date: 8 May 1995 07:05:43 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 29 Sender: daemon@net.bio.net Distribution: world Message-ID: <9505081402.AA27076@wwitch.unl.edu.unl.edu> NNTP-Posting-Host: net.bio.net >>We would like to find where to buy office chairs made of >>non-magnetic material to use in our 300 mhz NMR room. >>The NMR field is affected by movement of steel chairs. >> >>Please respond to above address. >> >>Thanks >> >>Don Whyte > At most lawn/garden centers, plastic lawn chairs are available. >They work extremely well, are totally plastic, and typically cost >about $10. >Gary Turner I have tried a few varieties of these, but BEWARE of STATIC...BZZzzzt! Many of these chairs can build-up a huge static charge just by the sliding of one's hindquarters which occurs in the process of getting in and out of the chair... Just something to think about....I generally shop for 100%, old-fashioned, wood furniture...not very sexy looking, but functional and without the annoying static problem. Richard Shoemaker, Ph.D. Phone--(402) 472-6255 Instrumentation Director, Chemistry FAX---- -9402 Research Associate Professor, Chemistry University of Nebraska-Lincoln URL: http://wwitch.unl.edu/nmrlab.html From owner-structural-nmr@net.bio.net Mon May 08 23:00:00 1995 Path: biosci!sb.com!Lesley_K_Maclachlan%notes From: Lesley_K_Maclachlan%notes@sb.com (Lesley K Maclachlan) Newsgroups: bionet.structural-nmr Subject: Compatibility of Varian and Bruker probes. Date: 9 May 1995 04:18:28 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: <9505091418.AA1096@pho018.sb.com> NNTP-Posting-Host: net.bio.net Hello fellow NMR spectroscopists: Does any one have any experiences or knowledge of the possibility of using a Varian Probe on a Bruker AMX spectrometer? My particular interest would be using a Varian NanoProbe on a Bruker AMX spectrometer. Are there physical limitation with respect to the relative sizes of the probes, and/or are there electronic limitations? Could these be rectified by a competent electronics workshop? I would be very grateful to receive all opinions and suggestions. Best wishes, Lesley MacLachlan. Dr Lesley K MacLachlan Tel: +44-1438-78-2007 Analytical Sciences Fax: +44 -1438-78-2570 SmithKline Beecham Pharmaceuticals e-mail: Lesley_K_Maclachlan%notes@sb.com The Frythe Welwyn Hertfordshire AL6 9AR United Kingdom. From owner-structural-nmr@net.bio.net Mon May 08 23:00:00 1995 Path: biosci!SNEEZY.FHIS.NET!barry From: barry@SNEEZY.FHIS.NET ("Barry Schweitzer") Newsgroups: bionet.structural-nmr Subject: SDS/micelles & peptide NMR Date: 9 May 1995 15:27:44 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: <9505091827.ZM2058@sneezy.fhis.net> NNTP-Posting-Host: net.bio.net Hi Netters: I have a peptide that I would like to look at in the presence of SDS or in micelles (deuterated of course). Can anyone point me to a good reference that would give conditions such as SDS concentration, micelle preparation, etc.? 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 May 08 23:00:00 1995 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: Bioreactors for NMR Date: 9 May 1995 12:02:50 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 30 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net On Tue, 9 May 1995, Krzysztof Wroblewski wrote: > I am looking for a manufacturer of NMR bioreactors. There was such a company > presenting this kind of reactors last year in San Francisco (MRM Meeting) but > I lost all information I had. > > Krzysztof Wroblewski > I have no address for a manufacturer, but if you'd consider to build your own, then I'd recommend to contact Hadassa Degani (cidegani@weizmann.weizmann.ac.il). I have heard an impressive presentation of her about their own bioreactor for NMR studies using beads. Hope it is something you can use. 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 May 08 23:00:00 1995 Path: biosci!rutgers!gatech!newsfeed.pitt.edu!dsinc!netnews.upenn.edu!NMRPC1.BIOPHYS.upenn.edu!chris From: chris@highresnmr.biophys.upenn.edu (Krzysztof Wroblewski) Newsgroups: bionet.structural-nmr Subject: Bioreactors for NMR Date: Tue, 9 May 1995 14:00:12 Organization: University of Pennsylvania Lines: 5 Message-ID: NNTP-Posting-Host: nmrpc1.biophys.upenn.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] I am looking for a manufacturer of NMR bioreactors. There was such a company presenting this kind of reactors last year in San Francisco (MRM Meeting) but I lost all information I had. Krzysztof Wroblewski From owner-structural-nmr@net.bio.net Mon May 08 23:00:00 1995 Path: biosci!BIOC01.UTHSCSA.EDU!raman From: raman@BIOC01.UTHSCSA.EDU (C.S.RAMAN) Newsgroups: bionet.structural-nmr Subject: Re: SDS/micelles & peptide NMR Date: 9 May 1995 16:13:37 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 90 Sender: daemon@net.bio.net Distribution: world Message-ID: <9505092313.AA19699@bioc01.uthscsa.edu> References: <9505091827.ZM2058@sneezy.fhis.net> NNTP-Posting-Host: net.bio.net Hi Barry: > I have a peptide that I would like to look at in the presence of > SDS or in micelles (deuterated of course). Can anyone point me > to a good reference that would give conditions such as SDS > concentration, micelle preparation, etc.? Here are some citations that you might find useful. Stan Opella's group at Penn State has done a significant amount of work on this subject. In one of their papers which appeared in Science (vide infra), increasing the [SDS] much beyond the cmc resulted in excellent dispersion of peaks. I would also recommend a follow-up on the works from Brian Sykes' group. Opella SJ; Kim Y; McDonnell P. Experimental nuclear magnetic resonance studies of membrane proteins. Methods in Enzymology, 1994, 239:536-60. MCDONNELL PA; OPELLA SJ. EFFECT OF DETERGENT CONCENTRATION ON MULTIDIMENSIONAL SOLUTION NMR SPECTRA OF MEMBRANE PROTEINS IN MICELLES. JOURNAL OF MAGNETIC RESONANCE SERIES B, 1993 AUG, V102 N1:120-125. SHON KJ; KIM YG; COLNAGO LA; OPELLA SJ. NMR STUDIES OF THE STRUCTURE AND DYNAMICS OF MEMBRANE-BOUND BACTERIOPHAGE-PFL COAT PROTEIN. SCIENCE, 1991 MAY 31, V252 N5010:1303-1304. Henry GD; Sykes BD. Methods to study membrane protein structure in solution. Methods in Enzymology, 1994, 239:515-35. Other related references: ^^^^^^^^^^^^^^^^^^^^^^^^ Gilbert GE; Baleja JD. Membrane-binding peptide from the C2 domain of factor VIII forms an amphipathic structure as determined by NMR spectroscopy. Biochemistry, 1995 Mar 7, 34(9):3022-31. van de Ven FJ; van Os JW; Aelen JM; Wymenga SS; Remerowski ML; Konings RN; Hilbers CW. Assignment of 1H, 15N, and backbone 13C resonances in detergent-solubilized M13 coat protein via multinuclear multidimensional NMR: a model for the coat protein monomer. Biochemistry, 1993 Aug 17, 32(32):8322-8. Papavoine CH; Konings RN; Hilbers CW; van de Ven FJ. Location of M13 coat protein in sodium dodecyl sulfate micelles as determined by NMR. Biochemistry, 1994 Nov 8, 33(44):12990-7. Young JK; Anklin C; Hicks RP. NMR and molecular modeling investigations of the neuropeptide substance P in the presence of 15 mM sodium dodecyl sulfate micelles. Biopolymers, 1994 Nov, 34(11):1449-62. PERVUSHIN KV; OREKHOV VY; POPOV AI; MUSINA LY; and others. THREE-DIMENSIONAL STRUCTURE OF (1-71)BACTERIOOPSIN SOLUBILIZED IN METHANOL/CHLOROFORM AND SDS MICELLES DETERMINED BY N-15-H-1 HETERONUCLEAR NMR SPECTROSCOPY. EUROPEAN JOURNAL OF BIOCHEMISTRY, 1994 JAN 15, V219 N1-2:571-583. Graham WH; Carter ES 2d; Hicks RP. Conformational analysis of Met-enkephalin in both aqueous solution and in the presence of sodium dodecyl sulfate micelles using multidimensional NMR and molecular modeling. Biopolymers, 1992 Dec, 32(12):1755-64. Hope this helps. -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 _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From owner-structural-nmr@net.bio.net Mon May 08 23:00:00 1995 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: Compatibility of Varian and Bruker probes. Date: 9 May 1995 07:31:32 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <9505091418.AA1096@pho018.sb.com> NNTP-Posting-Host: net.bio.net Dear Lesley, I suppose you already have the Varian probe, if so, then my advise is not very helpful. However, if you don't, and wanted to acquire a probe, then Nalorac's microprobe seems to be pretty good (this is not personal experience, but I've seen presentations at ENC), and you'd have no compatibility problem either. Their pricing is quite competitive, too (I asked for quotes recently -- although European prices could be different). Good luck, with my best regards, 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 May 09 23:00:00 1995 Path: biosci!rutgers!gatech!usenet.eel.ufl.edu!noc.netcom.net!news.sprintlink.net!pipex!sunic!sunic.sunet.se!umdac!news From: jbhauk@alchemy.chem.umu.se (Jon B. Hauksson) Newsgroups: bionet.structural-nmr Subject: Homonuclear 3D NMR Date: 10 May 1995 07:50:13 GMT Organization: Phys Chem, University of Umea, Sweden Lines: 11 Sender: -Not-Authenticated-[8620] Message-ID: <3opr7l$fn5@studium.student.umu.se> NNTP-Posting-Host: plgmac.chem.umu.se X-Posted-From: InterNews 1.0.6@plgmac.chem.umu.se Xdisclaimer: No attempt was made to authenticate the sender's name. Dear NMR colleagues. Does anyone out there have any good advice on setting up 3D TOCSY-NOESY experiments on peptides (ca 30 aa residues) in SDS micelles, in 90 % H2O/10% D2O. Suggestions concerning processing and analyzing such a data set would also be appreciated. Regards, Jon B. Hauksson E-mail: jbhauk@alchemy.che.umu.se From owner-structural-nmr@net.bio.net Wed May 10 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!pipex!sunic!sunic.sunet.se!news.funet.fi!news.csc.fi!news.helsinki.fi!kruuna!paakkone From: paakkone@cc.Helsinki.FI (Kimmo Paakkonen) Newsgroups: bionet.structural-nmr Subject: Water suppression in SDS Date: 11 May 1995 10:51:31 GMT Organization: University of Helsinki Lines: 19 Message-ID: <3osq7j$eia@oravannahka.Helsinki.FI> NNTP-Posting-Host: kruuna.helsinki.fi Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: TIN [version 1.2 PL0] We have started working with peptides in SDS-micelles, and becouse this is new to us, of course we ran into some problems. We have measured ordinary 2D NOESY spectrum of a peptide in SDS-micelles at 40 C. The concentration of the peptide was 1mM, and the concentration of the SDS was 200 mM. SDS was deuterated. Water was suppressed by transmitter presaturation, and also during the mixing time. However, water signal was still too big. The gain was 20 out of 60, but we would like to get bigger gain. Higher temperature is a problem, as the peptide seems to aggregate at 50 C. Have any of you had problems with water signals when using SDS-micelles? What could be the reason for it? Is there a good pulse sequence for the water suppression, or some other method to better water saturation? -- Kimmo Paakkonen Email: paakkone@cc.helsinki.fi From owner-structural-nmr@net.bio.net Wed May 10 23:00:00 1995 Path: biosci!HX2.MED.UPENN.EDU!yawen From: yawen@HX2.MED.UPENN.EDU (Yawen Bai) Newsgroups: bionet.structural-nmr Subject: (none) Date: 10 May 1995 18:07:10 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: <9505110107.AA09994@hx2.med.upenn.edu> NNTP-Posting-Host: net.bio.net unsubscribe From owner-structural-nmr@net.bio.net Wed May 10 23:00:00 1995 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: Water suppression in SDS Date: 11 May 1995 07:36:59 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 64 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <3osq7j$eia@oravannahka.Helsinki.FI> NNTP-Posting-Host: net.bio.net On 11 May 1995, Kimmo Paakkonen wrote: > We have started working with peptides in SDS-micelles, and becouse this is > new to us, of course we ran into some problems. > We have measured ordinary 2D NOESY spectrum of a peptide in > SDS-micelles at 40 C. The concentration of the peptide was 1mM, and the > concentration of the SDS was 200 mM. SDS was deuterated. Water was suppressed > by transmitter presaturation, and also during the mixing time. However, water > signal was still too big. The gain was 20 out of 60, but we would like to > get bigger gain. Higher temperature is a problem, as the peptide seems to > aggregate at 50 C. > > Have any of you had problems with water signals when using > SDS-micelles? What could be the reason for it? Is there a good pulse > sequence for the water suppression, or some other method to better > water saturation? > > -- > Kimmo Paakkonen > Email: paakkone@cc.helsinki.fi There are certainly better methods than saturation of the water signal, which has been proven to degrade the overall sensitivity of the experiment through saturation transfer (which may be not uniform either). Hard pulse combinations which have no excitation at the water frequency (the jump-and-return [JR] pulse-pair is one of the most simple and yet quite efficient) are one family of methods (a good review can be found in Progress in NMR Spectroscopy from '92 or '93). Soft pulses are alternatives, such as NODE-1 published from Tom James' laboratory at UCSF in JMR in '94 (I guess -- sorry not having the full references for this quick response; I can find them if necessary) or shifted soft pulses (Steve Smallcombe has a nice paper in JACS in '94 about such applications). Should you have gradients in your hardware WATERGATE is probably the best method to date (Vladimir Sklenar published it with others in JMR, also in one of the recent Bruker Reports). Data processing is an additional tool for cleaning the spectrum from the residual signal and to avoid baseline problems -- time domain filtering is the most efficient approach, however, there are other alternatives, too. (We, Brian Carter from the UK and myself have a review on nD NMR data processing submitted for publication, which has a section about this -- I'll be happy to send you the relevant part with references listed if you wish.) This is intended to be a quick and brief reflection to your question for now -- I guess others will have more comments, too. Good luck, Best regards, 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 Thu May 11 23:00:00 1995 Path: biosci!cc.uoi.gr!astavrak From: astavrak@cc.uoi.gr (Athanasios Stavrakoudis) Newsgroups: bionet.structural-nmr Subject: mardigras-corma Date: 12 May 1995 07:20:43 -0700 Organization: University of Ioannina Computer Center Dourouti, Ioannina, Greece 451 10 tel: +30-651-45298, fax: +30-651-45298 Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: <9505121714.AA02553@solon.cc.uoi.gr> NNTP-Posting-Host: net.bio.net Hello everybody, does anyone know if the programs MARDIGRAS and CORMA are available at any ftp site ?? May l have the address ?? bye,bye Ath. Stavrakoudis Univ. IOannina GREECE From owner-structural-nmr@net.bio.net Thu May 11 23:00:00 1995 Path: biosci!rutgers!uwm.edu!spool.mu.edu!bloom-beacon.mit.edu!news.bu.edu!news3.near.net!yale!usenet From: abonvin@volta.csb.yale.edu ("Alexandre Bonvin") Newsgroups: bionet.structural-nmr Subject: Re: mardigras-corma Date: 12 May 1995 19:46:38 GMT Organization: Yale University, Department of Computer Science, New Haven, CT Lines: 18 Distribution: world Message-ID: <3p0duu$2rh@babyblue.cs.yale.edu> References: <9505121714.AA02553@solon.cc.uoi.gr> NNTP-Posting-Host: volta.csb.yale.edu In article <9505121714.AA02553@solon.cc.uoi.gr> astavrak@cc.uoi.gr (Athanasios Stavrakoudis) writes: > does anyone know if the programs MARDIGRAS and CORMA > are available at any ftp site ?? > There is a web page that should give you information. Check http://picasso.ucsf.edu/software.html Alexandre ========================================================================== | Alexandre Bonvin PhD | Phone: (203) 432-5066 | | Mol. Biophys. & Biochemistry | Fax: (203) 432-6946 | | Yale University | Email: abonvin@laplace.csb.yale.edu | | New Haven CT 06520-8114, USA | | ========================================================================== From owner-structural-nmr@net.bio.net Fri May 12 23:00:00 1995 Path: biosci!MED.UNC.EDU!sheng From: sheng@MED.UNC.EDU (Sheng Zhong) Newsgroups: bionet.structural-nmr Subject: chemical shift data base Date: 13 May 1995 06:03:31 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 27 Sender: daemon@net.bio.net Distribution: world Message-ID: <9505131303.AA17993@hasty.med.unc.edu> NNTP-Posting-Host: net.bio.net Dear netters, To assist study NMR solution structure of the protein I am currently working on I have been writing an interactive auto assignment program using both C-shield and Felix macro. I am using chemical shift data provided by Felix for the spin system pattern recognition right now. What I have found is that some chemical shift ranges for individual peak is not wide enough. Although my program is not much depended on the this data the better chemical shift data will still make things better. My question is that is anybody knows where I can find better chemical shift data (base) or who should I contact to get this kind of data? BTW, spin system assignment in this program is based on the fact that the best pattern recognition tool up to date is human eyes (correct me if I'm wrong). I let machine provide suggestions and human eyes make the choice. Everything is visualized at pattern recognition step. Thanks in advance. Dr. Sheng Zhong Dept of Biochem & Biophys UNC at Chapel Hill sheng@med.unc.edu From owner-structural-nmr@net.bio.net Fri May 12 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!msunews!netnews.upenn.edu!walnut!klassen From: klassen@walnut (Bryan Klassen) Newsgroups: bionet.structural-nmr Subject: SDS/micelles & peptide NMR Date: 13 May 1995 20:54:28 GMT Organization: Department of Chemistry, University of Pennsylvania Lines: 18 Message-ID: <3p36a4$uf@netnews.upenn.edu> NNTP-Posting-Host: walnut.chem.upenn.edu X-Newsreader: TIN [version 1.2 PL2] Barry-- Raman's refs are on the money. I work in Stan Opella's lab. I am not one of those who do much solution NMR (I'm a solids guy), but I can pass on your inquiries if the refs are insufficient for you. It's better to email me directly, since I don't check this newsgroup more than once weekly. I am at klassen@walnut.chem.upenn.edu. Other people in my group who could be helpful: Ruth Steele, at steele@chestnut.chem.upenn.edu; and Jennifer Gesell, gesell@chestnut.chem.upenn.edu. I typically prepared my samples by taking 5 mg protein, adding 80 mg of deuterated SDS, 450 uL of 40 mM NaCl, and adjusted the pH to 4.0. I then lyophilized the sample and redissolved the residue in 400uL H2O + 50 uL D2O. You want to keep the SDS concentration high to make sure you have protein monomers. See J. Mol. Biol. 1993 233 447-463. This corrects an error from the results reported in Biochem 1992 31 5284-5297. Cheers, Bryan Klassen From owner-structural-nmr@net.bio.net Sat May 13 23:00:00 1995 Path: biosci!BIOC01.UTHSCSA.EDU!raman From: raman@BIOC01.UTHSCSA.EDU (C.S.RAMAN) Newsgroups: bionet.structural-nmr Subject: Re: chemical shift data base Date: 13 May 1995 19:48:49 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 46 Sender: daemon@net.bio.net Distribution: world Message-ID: <9505140248.AA22826@bioc01.uthscsa.edu> References: <9505131303.AA17993@hasty.med.unc.edu> NNTP-Posting-Host: net.bio.net Sheng: > My question is that is anybody knows where I can find > better chemical shift data (base) or who should I contact to > get this kind of data? The chemical shift data used by Felix is from Gross and Kalbitzer [1988] J. Magn. Reson. 76, 87. In a recent review (see Methods in Enzymology [1994] 239, 363-392), Wishart and Sykes discuss in detail about using chemical shifts in structure determination. One nice thing about this review is that it describes the pitfalls and underscores the importance of establishing a consistency in the chemical shift data reported by different labs. This review also contains a table of Random coil chemical shifts for backbone atoms in proteins and includes corrections to an appropriate reference. NMR-TRIAD from Tripos utilizes the chemical shift data base from Sykes' group. For additional information you can reach Prof. Sykes at the following address: bds@polaris.biochem.ualberta.ca Cheers -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 _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From owner-structural-nmr@net.bio.net Sat May 13 23:00:00 1995 Path: biosci!BIOC01.UTHSCSA.EDU!raman From: raman@BIOC01.UTHSCSA.EDU (C.S.RAMAN) Newsgroups: bionet.structural-nmr Subject: EduNMRSoft version 1.1.1 (fwd) Date: 13 May 1995 19:54:42 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 45 Sender: daemon@net.bio.net Distribution: world Message-ID: <9505140254.AA22835@bioc01.uthscsa.edu> NNTP-Posting-Host: net.bio.net I guess Peter forgot Str-NMR and hence I am forwarding his message to the net. Cheers -raman > From: "Peter LUNDBERG" > Dear Spectroscopists, > > I have updated the Educational NMR Software list a little to version 1.1.1. > > If anyone is interested you can probably pick up a fresh copy soon from some of > the following sites: > > http://www.york.ac.uk/depts/chem/nmr/edusoft.html > http://tutor.oc.chemie.th-darmstadt.de/nmrsoft.html > ftp.bruker.de (149.236.1.1):/pub/nmr/processing > http://www.NMR.EMBL-Heidelberg.DE/NMR/PUBSoftware.html > ftp://tesla.york.ac.uk/pub/edusoft > ftp://alchemy.chem.umu.se/incoming (or /chemistry) > http://atlas.chemistry.uakron.edu:8080/cdept.docs/NMRsware.html > > Please contact me by email if you have any suggestions, or comments. >Email: PeterL@umdix.umdc.umu.se -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ C.S.RAMAN _/ _/ Department of Biochemistry _/ _/ University of Texas Health Science Center _/ _/ 7703 Floyd Curl Drive _/ _/ San Antonio, TX 78284-7760 _/ _/ USA _/ _/ _/ _/ Tel: (210) 567-6623 _/ _/ Fax: (210) 567-6595 _/ _/ E-mail: raman@bioc01.uthscsa.edu _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ How can it be that mathematics, a product of human thought _/ _/ independent of experience, is so admirably adapted to the _/ _/ objects of reality? -Albert Einstein _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From owner-structural-nmr@net.bio.net Sun May 14 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!news.sprintlink.net!demon!doc.news.pipex.net!pipex!sunic!sunic.sunet.se!umdac!news From: peterl@umdix.umdc.umu.se (Peter Lundberg) Newsgroups: bionet.structural-nmr Subject: EduNMRSoft 1.1.1 Date: 12 May 1995 07:34:33 GMT Organization: Phys Chem, University of Umea, Sweden Lines: 26 Sender: -Not-Authenticated-[8620] Message-ID: <3ov329$ki2@studium.student.umu.se> NNTP-Posting-Host: plgmac.chem.umu.se X-Posted-From: InterNews 1.0.6@plgmac.chem.umu.se Xdisclaimer: No attempt was made to authenticate the sender's name. Dear Spectroscopists, I have updated the Educational NMR Software list a little to version 1.1.1. If anyone is interested you can probably pick up a fresh copy soon from some of the following sites: http://www.york.ac.uk/depts/chem/nmr/edusoft.html http://tutor.oc.chemie.th-darmstadt.de/nmrsoft.html ftp.bruker.de (149.236.1.1):/pub/nmr/processing http://www.NMR.EMBL-Heidelberg.DE/NMR/PUBSoftware.html ftp://tesla.york.ac.uk/pub/edusoft ftp://alchemy.chem.umu.se/incoming (or /chemistry) http://atlas.chemistry.uakron.edu:8080/cdept.docs/NMRsware.html Please contact me by email if you have any suggestions, or comments. Sorry about the cross-posting. 73, Peter O==O ================================== O==O O==O Peter Lundberg O==O O==O Email: peterl@umdix.umdc.umu.se O==O O==O ============761.91141============= O==O From owner-structural-nmr@net.bio.net Sun May 14 23:00:00 1995 Path: biosci!rigel.tripos.com!weber From: weber@rigel.tripos.com ("Paul Weber") Newsgroups: bionet.structural-nmr Subject: Re: chemical shift data base Date: 15 May 1995 07:13:13 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 35 Sender: daemon@net.bio.net Distribution: world Message-ID: <9505150907.ZM5189@rigel> NNTP-Posting-Host: net.bio.net Hi Dr Zhong, > What I have found is that some chemical shift ranges for individual peak > is not wide enough. Although my program is not much depended on the this > data the better chemical shift data will still make things better. I can send you a database of chemical shifts that was originally compiled by Dr David Wishart; it is a few more years' recent than what you have with Felix. Nonetheless, you will probably find the chemical shift ranges do not change that much. Instead I would suggest that you re-evaluate the criterion/criteria that your program uses for determining if a peak is within the accepted range. I suggest you look at the article by Jun Xu et al., J. Biol. NMR 5 (1995) 183-192. > BTW, spin system assignment in this program is based on > the fact that the best pattern recognition tool up to date is > human eyes (correct me if I'm wrong). You are both wrong and right! The human eye (really, the human brain) is excelled at pattern recognition. However it can be easily fooled when performing assignments, by (1) ignoring patterns that are "not expected" but are quite correct (for example, the BPTI amide proton at 4.53ppm, or geminal protons with chemical shift deviations of >2 ppm, etc.); or (2) by "recognizing" the obvious pattern, but missing the less obvious one. Jun Xu shows a good example of this with one of those childrens' drawings where when the picture is viewed "right-side up", you see a princess, but rotate the page 180 degrees and you see the "beast." Hence there is a real need for software tools that assist or automate assignments that will be as perceptive as the human brain, but avoid the biases that we learn. From owner-structural-nmr@net.bio.net Sun May 14 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!swrinde!cs.utexas.edu!news.sprintlink.net!demon!uknet!daresbury!not-for-mail From: Graham Barlow Newsgroups: bionet.structural-nmr Subject: EduNMRSoft 1.1.1 - html version Date: 15 May 1995 12:49:43 +0100 Lines: 26 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3p7f4n$g7n@mserv1.dl.ac.uk> Reply-To: gkb1 X-Sender: Original-To: AMMRL , "bionet.structural-nmr mail newsgroup" , BUM Dear all, I have updated my html version of Peter Lundeberg's EduNMRSoft list. You can browse it on the net at: http://www.york.ac.uk/depts/chem/nmr/edusoft.html or obtain a copy from: ftp://tesla.york.ac.uk/pub/edusoft/ Many thanks to Peter for an invaluable document. Graham +----------------------==============================================+ | Dr. Graham Barlow | | | NMR Service Manager | e-mail: gkb1@york.ac.uk | | Dept. of Chemistry | Telephone: +44 (0)1904 432506 DDI | | University of York | Fax: +44 (0)1904 432516 | | Heslington, YORK, UK | WWW: http://www.york.ac.uk/depts/chem/nmr | +----------------------+=Mime OK ====================================+ From owner-structural-nmr@net.bio.net Sun May 14 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!cs.utexas.edu!news.sprintlink.net!pipex!sunic!sunic.sunet.se!trane.uninett.no!daresbury!hgmp.mrc.ac.uk!nimr.mrc.ac.uk!m-gradwe From: m-gradwe@nimr.mrc.ac.uk (Mike Gradwell) Newsgroups: bionet.structural-nmr Subject: XPLOR calculations on Heme Proteins Date: 15 May 1995 08:46:13 GMT Organization: National-Institute-for-Medical-Research Lines: 9 Distribution: world Message-ID: <3p74cl$31m@mercury.hgmp.mrc.ac.uk> NNTP-Posting-Host: nimsb42.nimr.mrc.ac.uk Dear Colleagues, We are attempting to devise a topology for a heme protein in Xplor for an NMR structure determination, and are experiencing problems. This lies in correctly defining Heme ligation to the histidines on the protein. We have followed examples in Xplor and used the PATCH statement, but the histidines always move to the same side of the heme!!! Has anyone had any succes with calculations of this type? Mike Gradwell, National Institute for Medical Research Fred Muskett, Queen Mary and Westfield College From owner-structural-nmr@net.bio.net Sun May 14 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!news.sprintlink.net!demon!doc.news.pipex.net!pipex!sunic!sunic.sunet.se!umdac!news From: Jon Hauksson Newsgroups: bionet.structural-nmr Subject: (no subject) Date: 12 May 1995 12:54:13 GMT Organization: University of Umea, Sweden Lines: 16 Message-ID: <3ovlpl$o1o@studium.student.umu.se> NNTP-Posting-Host: alchemy.chem.umu.se Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1b3 (X11; I; SunOS 5.3 sun4m) X-URL: news:bionet.structural-nmr Dear Colleagues. Is there anyone out there who has experirence in running heteronuclear 3D NMR on peptides of proteins that do not contain any isotopically enriched labels. I am working on a difficult assignment problem with a 28 amino acids long peptide in SDS micelles, wher spectral overlap between hydrophobic residues is a serious problem. Tips on minimum sample concentrations, sutiable pulse sequences, approximate measuring times, etc. would be greatly appreciated. Sincerely Jon B. Hauksson Department of Physical Chemistry, Umea University S-901 87 Umea SWEDEN E-mail: jbhauk@alchemy.chem.umu.se From owner-structural-nmr@net.bio.net Mon May 15 23:00:00 1995 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: D-amino acids in chemical shift index calculations. Date: 16 May 1995 06:08:10 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 27 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <9505161423.AA1462@pho018.sb.com> NNTP-Posting-Host: net.bio.net Dear Lesley, (and those interested in chemical shifts for amino acids) I have run across two papers recently, which could be interesting for you I guess: Wishart, D. S., et al.; 1H, 13C and 15N random coil NMR chemical shifts of the common amino acids. I. Investigations of nearest-neighbor effects J. Biomol. NMR 5(1995)67-81 (I have a feeling that Alexandre has mentioned this earlier) and Merutka, G., Dyson, H. J., and Wright, P. E.; 'Random coil' 1H chemical shifts obtained as a function of temperature and trifluoroethanol concentration for the peptide series GGXGG J. Biomol. NMR 5(1995)14-24 All the best, 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 May 15 23:00:00 1995 Path: biosci!MUWAYF.UNIMELB.EDU.AU!kinetics_group From: kinetics_group@MUWAYF.UNIMELB.EDU.AU (Kinetics Group) Newsgroups: bionet.structural-nmr Subject: 13-C shift prediction Date: 16 May 1995 05:44:16 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HQL5Q06N0200BVH9@muwayb.ucs.unimelb.edu.au> NNTP-Posting-Host: net.bio.net Subject: Time: 10:35 PM OFFICE MEMO 13-C shift prediction Date: 16/5/95 I am interested in predicting resonance shifts of some short chain hydroxy acids upon complexation with main group metals eg. Al(III) in aqueous and non-aqueous media. Does anyone know of any lit. reports, and how usable they might be ? Thanks Julian Salerno Chemistry Melbourne University Australia From owner-structural-nmr@net.bio.net Mon May 15 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!news.sprintlink.net!uunet!newsfeed.ACO.net!news.univie.ac.at!helix.mdy.univie.ac.at!hs From: hs@helix.mdy.univie.ac.at (Hellfried Schreiber) Newsgroups: bionet.structural-nmr Subject: Conference Announcement Date: 16 May 1995 12:30:10 GMT Organization: Inst. for Theoretical Chemistry / Univ. of Vienna Lines: 166 Distribution: world Message-ID: <3pa5si$19ce@ftp.univie.ac.at> NNTP-Posting-Host: helix.mdy.univie.ac.at >> INTERNATIONAL CONFERENCE ON MOLECULAR STRUCTURAL BIOLOGY << Organized by the Austrian Chemical Society Vienna (Austria), September 17-20, 1995 TOPICS: 1) The Impact of Molecular Biology on Structural Biology 2) Biomolecular Structure Determination a) X-Ray Diffraction b) NMR Spectroscopy 3) Dynamics and Function of Biomolecules 4) Computational Methods 5) Protein Engineering and Design The scientific programme is designed to cover a broad range of disciplines in molecular structural biology. Topics will be presented in the form of plenary lectures, posters, discussions and exhibitions. Sunday, (17.9) ----------------------------------------------------------------------------- Registration Welcome Cocktail Honory Lecture by H.Neurath Monday, (18.9) ----------------------------------------------------------------------------- 1. The impact of Molecular Biology on Structural Biology C.Cantor (USA) "Application of Streptavidin and Genetically Engineered Variants" T.Blundell (GB) "Protein Super Families: Genome Analyses and Drug Discovery" 2. Biomolecular Structure Determination a) X-Ray Crystallography R.Huber (D) "Proteolytic Enzymes and Their Natural Inhibitors - New Functions and New Structures and No End in Sight" M.Walkinshaw (CH) "Structures and Biological Implications of Series of Cyclophilin-Cyclosporin Crystal Complexes" I.Schlichting (D) "Ligand Binding in Heme Proteins Studied by Kinetic X-Ray Crystallography" Tuesday (19.9.) ----------------------------------------------------------------------------- b) NMR Spectroscopy O.Jardetzky (USA) "Flexibility and Function in a DNA Binding Protein - the Trp-Repressor of E.Coli" P.Roesch (D) "The Structure of Iron-Sulfur Proteins in Solution" C.Dobson (GB) "The Structural Basis of Protein Folding" 3. Dynamics and Function of Biomolecules J.Lakowicz (USA) "Fluorescence Spectroscopic Studies of the Structure and Dynamics of Biomolecules" W.Kuehlbrandt (D) "Structure Determination of Membrane Proteins by High-Resolution Electron Microscopy" H.Frauenfelder (USA) "Dynamics and Function of Biomolecules" Wednesday (20.9.) ----------------------------------------------------------------------------- 4. Computational Methods M.Karplus (USA) "Simulations of Protein Folding From the Native to the Denatured State and Back Again" J.Skolnick (USA) "A Hierarchial Approach to the Prediction of Protein Structures" H.-J.Boehm (D) "New Computational Tools for Structure Based Drug Design" 5. Protein Engineering and Design A.Fersht (GB) "Pathways of Protein Folding" L.Presta (USA) "Protein Engineering of Immunoglobulins and Immunoglobulin-Like Domains" M.Mutter (CH) "De Novo Protein Design" CALL FOR POSTERS ----------------- All those intending to participate in the conference are invited to submit posters presenting original work. Abstracts prepared according to the instructions given below should arrive NOT LATER THAN JUNE 30th, 1995. The authors will be informed about the provisional acceptance in July, 1995. The presentation of the posters will be finally approved and thus the contribution included in the Book of Abstracts when at least one of the registers before August 1st, 1995. Contributors of outstanding posters will be chosen by the scientific committee to give a 20 minute lecture. Head of Scientific Committee: P.Schuster EXHIBITON: --------- An exhibition of instruments, accessories, software, literature and other items is planned. Companies interested in displaying their products are kindly requested to contact the conference secretariat. INDUSTRIAL SATELLITE MEETING: ----------------------------- A half day industrial symposium is planned. Those companies who are interested in presenting up-to-date results obtained on their products in the form of 20 minute lectures are kindly requested to contact the conference secretariat. Registration Fees (before August 1): Regular Participant 4000 ATS GOeCH Member 3500 ATS Student 2000 ATS The registration fee includes the Book of Abstracts, the welcome cocktail and buffet, the invitation to the Viennese Rathaus, a ticket for the piano concert, coffee breaks and tram tickets. If your are interested in a folder of the second announcement including a registration form and the social program, please contact: A.Kungl Gesellschaft Oesterreichischer Chemiker AG Biophysikalische Chemie Nibelungengasse 11 A-1010 Wien, Austria Tel.: (43) 1 587249 FAX.: (43) 1 587966 e-mail: msb95@helix.mdy.univie.ac.at -- +-----------------------------------------------------------------------------+ | | | Hellfried Schreiber, Ph.D. | | | +---------------------------------------+-------------------------------------+ | | | | Institute for Theoretical Chemistry | | | Theoretical Biochemistry Group | Mail: hs@helix.mdy.univie.ac.at | | Waehrigerstrasse 17 | Voice: +43 1 40480 - 618 | | A-1090 Wien, Austria, Europe | FAX: +43 1 4028525 | | | | +-----------------------------------------------------------------------------+ From owner-structural-nmr@net.bio.net Mon May 15 23:00:00 1995 Path: biosci!sb.com!Lesley_K_Maclachlan%notes From: Lesley_K_Maclachlan%notes@sb.com (Lesley K Maclachlan) Newsgroups: bionet.structural-nmr Subject: D-amino acids in chemical shift index calculations. Date: 16 May 1995 04:24:02 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 34 Sender: daemon@net.bio.net Distribution: world Message-ID: <9505161423.AA1462@pho018.sb.com> NNTP-Posting-Host: net.bio.net Dear fellow NMR spectroscopists, I'd like to pick up on the recent discussions on the use of chemical shift databases and the chemical shift index with reference to a particular problem we have in house. We are looking at a pair of peptides which differ only by a point mutation, Thr to d-Trp, and we'd like to use the chemical shift index to characterise any changes in secondary structure as a result of the mutation. The Wishart-Sykes tables for calculating the CSI don't refer to d-amino acids - does anyone have any information on how to manage these in CSI calculations, or the applicability of the original chemical shift tables? I'd be very pleased to hear any comments on this subject. On a related subject, we are using the CSI to characterise the conformations of peptides in trifluoroethanol solution. Using the above-mentioned tables, we get pretty good results overall, except that Leu and Ile residues give results that we would not expect (eg. in a stretch of alpha-helix, -1 index, these residues score 0). I was wondering if this was a sheer coincidence or if this is as a result of applying the analysis to a TFE solution. Any ideas? Yours, Lesley MacLachlan Dr L K MacLachlan Analytical Science SmithKline Beecham Pharmaceuticals The Frythe Welwyn Herts. AL6 9AR United Kingdom. Tel.: +44-1438-78-2007 Fax: +44-1438-78-2570 E-mail: Lesley_K_Maclachlan%notes@sb.com From owner-structural-nmr@net.bio.net Mon May 15 23:00:00 1995 Path: biosci!MED.UNC.EDU!sheng From: sheng@MED.UNC.EDU (Sheng Zhong) Newsgroups: bionet.structural-nmr Subject: chemical shift Date: 16 May 1995 07:32:26 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 30 Sender: daemon@net.bio.net Distribution: world Message-ID: <9505161432.AA09516@hasty.med.unc.edu> NNTP-Posting-Host: net.bio.net Hi, Thanks very much everyone for providing me the address and references regarding to chemical shift data. I wish I had known the address of this database earlier. Dr. Paul Weber raised a very interesting question regarding pattern recognition. He is 100% right that human will be fooled sometime. I also want to add a point to his argument that the degrees of successfully recognizing certain patterns will vary from person to person. One of the best pattern recognition tool that I know of is neural network. I am not sure if it can beat human or not. I am willing to learn more about the this matter and will appreciate any advice regarding to it. I just wrote a match maker to match my protein against sequences of database. This is just a curiosity. I cannot match more than 4 residues of my protein against database. I don't know if anyone have ever done the similar match study and what is the result. Ragards, Dr. Sheng Zhong Dept of Biochem & Biophys UNC at Chapel Hill sheng@med.unc.edu From owner-structural-nmr@net.bio.net Tue May 16 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!news.sprintlink.net!news.ICSI.Net!news From: "William A. Daunch" Newsgroups: bionet.structural-nmr Subject: Re: Conference Announcement Date: 17 May 1995 07:28:27 GMT Organization: Department of Chemistry, U of A Lines: 12 Message-ID: <3pc8ir$k5h@degas.ICSI.Net> References: <3pa5si$19ce@ftp.univie.ac.at> NNTP-Posting-Host: atlas.chemistry.uakron.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; SunOS 4.1.3 sun4m) X-URL: news:3pa5si$19ce@ftp.univie.ac.at You can find a WWW version of this conference announcement at the following URL: http://atlas.chemistry.uakron.edu:8080/cdept.docs/MAGNET/confnmr.html Compliments of MAG-NET: Your Magnetic Resonance Internet Resource Guide http://atlas.chemistry.uakron.edu:8080/cdept.docs/nmrsites.html - Bill Daunch MAG-NET Webmaster From owner-structural-nmr@net.bio.net Wed May 17 23:00:00 1995 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: (no subject) Date: 18 May 1995 10:56:50 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 39 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <3ovlpl$o1o@studium.student.umu.se> NNTP-Posting-Host: net.bio.net As I recall, Horst Kessler's lab has published papers on such experiments -- there were few in JACS and JBN, possibly in JMR, too. Sorry not having full reference handy. Should not you find them I'll dig them up. 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) On 12 May 1995, Jon Hauksson wrote: > Dear Colleagues. > Is there anyone out there who has experirence in running heteronuclear 3D NMR > on peptides of proteins that do not contain any isotopically enriched labels. I > am working on a difficult assignment problem with a 28 amino acids long peptide > in SDS micelles, wher spectral overlap between hydrophobic residues is a > serious problem. Tips on minimum sample concentrations, sutiable pulse > sequences, approximate measuring times, etc. would be greatly appreciated. > > Sincerely > Jon B. Hauksson > Department of Physical Chemistry, > Umea University > S-901 87 Umea > SWEDEN > E-mail: jbhauk@alchemy.chem.umu.se > > > From owner-structural-nmr@net.bio.net Wed May 17 23:00:00 1995 Path: biosci!CCS1.CC.MONASH.EDU.AU!KHIGGINS From: KHIGGINS@CCS1.CC.MONASH.EDU.AU ("MS K HIGGINS [BIC]") Newsgroups: bionet.structural-nmr Subject: resin bound peptides Date: 17 May 1995 22:30:43 -0700 Organization: Monash University Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: <20FF92F4C55@ccs1.cc.monash.edu.au> NNTP-Posting-Host: net.bio.net Hi I have had a query concerning NMR studies of resin bound peptides from solid phase synthesis and was wondering if there is anyone out who has had some experience undertaking such studies. Thanks in advance, Kerry From owner-structural-nmr@net.bio.net Thu May 18 23:00:00 1995 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!news.sprintlink.net!demon!doc.news.pipex.net!pipex!uknet!daresbury!not-for-mail From: "D.GUTHRIE" Newsgroups: bionet.structural-nmr Subject: NMR and resin bound peptides Date: 19 May 1995 12:30:43 +0100 Lines: 135 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3phvh3$o2@mserv1.dl.ac.uk> Original-To: str-nmr@dl.ac.uk Hi Netters The following request appeared recently from Kerry Higgins >Hi >I have had a query concerning NMR studies of resin bound peptides >from solid phase synthesis and was wondering if there is anyone out >who has had some experience undertaking such studies. >Thanks in advance, > I have no hands on experience, but have collected the following references which may be of some help. Record - 1 TI- HIGH-RESOLUTION H-1-NMR IN SOLID-PHASE ORGANIC-SYNTHESIS AU- FITCH, WL;DETRE, G;HOLMES, CP;SHOOLERY, JN;KEIFER, PA JN- JOURNAL OF ORGANIC CHEMISTRY PY- 1994 VO- 59 NO- 26 PG- 7955-7956 Record - 2 TI- APPLICATION OF 1D AND 2D GEL-PHASE C-13 NMR TO SOLID-PHASE SYNTHESIS AU- JOHN, V;ROBINSON, CY;SHETTY, HU;BRYANT, K;DAVIS, D JN- ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY PY- 1991 VO- 201 NO- APR PG- 148-ANYL Record - 3 TI- ANALYSIS OF THE STRUCTURE OF SYNTHETIC AND NATURAL MELANINS BY SOLID-PHASE NMR AU- DUFF, GA;ROBERTS, JE;FOSTER, N JN- BIOCHEMISTRY PY- 1988 VO- 27 NO- 18 PG- 7112-7116 Record - 4 TI- SOLID-PHASE HIGH-RESOLUTION NUCLEAR MAGNETIC-RESONANCE AU- FOLTZ, MB JN- BOLETIN DE LA SOCIEDAD CHILENA DE QUIMICA PY- 1988 VO- 33 NO- 3 PG- A 17-A 20 Record - 5 TI- NEW ANCHORS USEFUL IN SOLID-PHASE PEPTIDE-SYNTHESIS, EVIDENCE OF AN UNEXPECTED POLYACRYLIC SUPPORTED REACTION BY NON DESTRUCTIVE C-13 NMR-SPECTROSCOPY AND TANDEM MASS-SPECTROMETRY AU- ALFRED, JC;AUBAGNAC, JL;CALMES, M;DAUNIS, J;ELAMRANI, B;JACQUIER, R;NKUSI, G JN- TETRAHEDRON PY- 1988 VO- 44 NO- 14 PG- 4407-4413 Record - 6 TI- SOLID-PHASE PEPTIDE-SYNTHESIS AND SOLID-STATE NMR-SPECTROSCOPY OF [ALA3-N-15][VAL1]GRAMICIDIN-A AU- FIELDS, GB;FIELDS, CG;PETEFISH, J;VANWART, HE;CROSS, TA JN- PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA PY- 1988 VO- 85 NO- 5 PG- 1384-1388 Record - 7 TI- SOLID-PHASE SYNTHESIS AND SOLID-STATE N-15 NMR-SPECTROSCOPY OF GRAMICIDIN-A, GRAMICIDIN-B, AND GRAMICIDIN-C AU- FIELDS, CG;LOGRASSO, PV;CROSS, TA JN- FASEB JOURNAL PY- 1988 VO- 2 NO- 4 PG- A 320-A 320 Record - 8 TI- GEL PHASE C-13 NMR-SPECTROSCOPY AS AN INVESTIGATIVE TOOL IN ULTRAHIGH LOAD SOLID (GEL) PHASE PEPTIDE-SYNTHESIS AU- EPTON, R;WELLINGS, DA JN- REACTIVE POLYMERS ION EXCHANGERS SORBENTS PY- 1987 VO- 6 NO- 2-3 PG- 333-333 Record - 9 TI- SOLID-PHASE PEPTIDE-SYNTHESIS - STRUCTURAL CHARACTERIZATION BY H-1-NMR OF A PEPTIDE IMMOBILIZED ON A POLYACRYLIC RESIN AU- MAZURE, M;CALAS, B;CAVE, A;PARELLO, J JN- COMPTES RENDUS DE L ACADEMIE DES SCIENCES SERIE II-MECANIQUE PHYSIQUE CHIMIE SCIENCES DE L UNIVERS SCIENCES DE LA TERRE PY- 1986 VO- 303 NO- 7 PG- 553-556 Record - 10 TI- APPLICATION OF GEL-PHASE C-13-NMR TO MONITOR SOLID-PHASE PEPTIDE-SYNTHESIS AU- GIRALT, E;RIZO, J;PEDROSO, E JN- TETRAHEDRON PY- 1984 VO- 40 NO- 20 PG- 4141-4152 Record - 11 TI- APPLICATION OF NMR C-13 SPECTROSCOPY TO CONTROL OVER THE PEPTIDE-SYNTHESIS OF FRAGMENT 20-24 OF THE ACTH AMINO-ACID-SEQUENCE AU- SVERGUN, VI;SMIRNOV, MB;ANTONOV, AA;KRYSIN, EP;PANOV, VP;NIKITINA, TK JN- KHIMIKO-FARMATSEVTICHESKII ZHURNAL PY- 1981 VO- 15 NO- 5 PG- 92-97 Make the beads spin! David Guthrie From owner-structural-nmr@net.bio.net Sat May 20 23:00:00 1995 Newsgroups: bionet.structural-nmr Path: biosci!bloom-beacon.mit.edu!gatech!news.sprintlink.net!pipex!lyra.csx.cam.ac.uk!warwick!bsmail!zeus!bijt From: bijt@zeus.bris.ac.uk (J. Takei) Subject: Seeking an NMR post Message-ID: Sender: usenet@info.bris.ac.uk (Usenet news owner) Nntp-Posting-Host: zeus.bris.ac.uk Organization: University of Bristol, England X-Newsreader: TIN [version 1.2 PL2] Date: Sat, 20 May 1995 22:00:03 GMT Lines: 24 Dear Netters, I'm looking for a graduate assistantship in the field of biomolecular NMR and other spectroscopic studies in biochemistry. I'm extensively experienced in NMR together with CD and Raman. Fluent in Unix, Vax, Windows, Macintosh. Very good knowledge in Felix and X-plor. Techniques used: amide exchange, reconstitution of peptide into vesicles, HPLC. Hoping to hear from you. Regards, Jiro Takei Dept. of Biochemistry University of Bristol UK *44-117-928-9000 x.4971 *44-117-928-8274 (fax) *44-117-927-3890 (home) j.takei@bris.ac.uk From owner-structural-nmr@net.bio.net Sun May 21 23:00:00 1995 Path: biosci!cnrs-orleans.fr!sodano From: sodano@cnrs-orleans.fr ("patrick Sodano") Newsgroups: bionet.structural-nmr Subject: seeking a software for image manipulation Date: 22 May 1995 06:44:05 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: <9505221331.AA18667@admin.cnrs-orleans.fr> NNTP-Posting-Host: net.bio.net Dear netters, we are seeking a software for image manipulation that works on PCs. The goal is to integrate NMR spectra in a text and to include text in the spectra too. This is mainly for publication purposes. Any suggestions will be wellcome. Thanks P. Sodano Centre de Biophysique Moleculaire Rue Charles Sadron 45 000 Orleans Cedex 02 France From owner-structural-nmr@net.bio.net Mon May 22 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!news.sprintlink.net!demon!doc.news.pipex.net!pipex!sunic!sunic.sunet.se!news.funet.fi!luotsi.uku.fi!usenet From: Matthias Niemitz Newsgroups: bionet.structural-nmr Subject: Re: seeking a software for image manipulation Date: 23 May 1995 06:42:45 GMT Organization: University of Kuopio Lines: 30 Message-ID: <3ps055$jeb@luotsi.uku.fi> References: <9505221331.AA18667@admin.cnrs-orleans.fr> NNTP-Posting-Host: s3038.uku.fi Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Windows; I; 16bit) To: sodano@cnrs-orleans.fr sodano@cnrs-orleans.fr ("patrick Sodano") wrote: >Dear netters, >we are seeking a software for image manipulation that works on PCs. The >goal is to integrate NMR spectra in a text and to include text in the >spectra too. This is mainly for publication purposes. Any suggestions >will be wellcome. > >Thanks > >P. Sodano >Centre de Biophysique Moleculaire >Rue Charles Sadron >45 000 Orleans Cedex 02 >France Most commercial NMR software packages (e.g. WinNMR, Nuts, Felix, PERCH) provide copying of spectra via Windows clipboard in high resolution metafile format. A simple screen dump is also possible but quality is rather poor. Adding text directly is available only in WinNMR and PERCH (http://www.uku.fi/perch.html) but you can do that later within a text processor as well. Regards, Matthias Niemitz Department of Chemistry phone: + 358 71 163241 University of Kuopio fax: + 358 71 163259 P.O.B. 1627 e-mail: Matthias.Niemitz@uku.fi FIN-70211 Kuopio, FINLAND WWW: http://www.uku.fi/perch.html From owner-structural-nmr@net.bio.net Mon May 22 23:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!ix.netcom.com!netcomsv!uu3news.netcom.com!netcomsv!uucp3.netcom.com!woody!uwoody Newsgroups: bionet.structural-nmr Message-ID: <742@woody.acornnmr.com> References: Reply-To: uwoody@woody.acornnmr.com (Acorn NMR) From: uwoody@woody.acornnmr.com (Acorn NMR) Date: Tue, 23 May 1995 16:51:48 GMT Subject: Re: Magnitude-mode Macro for Felix Lines: 91 In article , Klaus Zangger (zangger@email.kfunigraz.ac.at) writes: >I am looking for a Macro to transform 2D magnitude-mode spectra in Bruker >format (acquired on a Bruker AM360). The Macro provided by our Felix version >(2.05) is damaged and all attempts to write a magnitude-mode Macro worked >only with data in complex format. >Simply exchanging "ft" by "bft" (for D1 transform) wasn't successfull. In the early days of Acorn NMR, we used DOS Felix for processing, and I wrote macros for 2D processing, because it is definitely not obvious. The DOS version was very similar to the UNIX version, so I hope this macro will translate. The confusing part has to do with how the data are stored. Felix stored complex data as alternating real and imaginary points. Even though you keep the imaginary part til the end, you lie to Felix and define the matrix type as Real. The real and imaginary data are written to the matrix after the first FT as separate real and imaginary halves, with odd numbered rows being real and even numbered rows being imaginary. This also gets confusing because you lie to Felix about the data size. So after the D1 FT, there is the command "sep" which separates the real and imaginary, so that the first half of the data points are real and the second half are imaginary. Then you tell it the data is real and set size. Write one row to the matrix. Then you increment the row counter, set the size to twice what it was, left shift to throw away the real part. So now you have the imaginary half. Reset the size and store. We have now saved the real and imaginary halves so that when read in the 2nd dimension they are alternating real and imaginary points and you will do a complex FT. Got all that?! Note that this was *not* written for Bruker data, so you need to make the D1 ft into a bft. cl get 'Enter data file name:' name get 'No. of t1 slices?' nrow get 'Size of each?' ncol get 'Enter name for matrix file:' mname eva double (2*&nrow) eva twice (&ncol*2) bld &mname 2 &ncol &double 0 mat &mname w def rrow 1 def datype 1 def datsiz &ncol for row 1 &nrow rn &name def datype 1 qss &ncol 0 .5 ft rev sep ; separate real & imag parts def datype 0 ; data type = real def datsiz &ncol ; set size sto 0 &rrow ; write real half eva rrow (&rrow+1) ; increment counter def datsiz &twice ; double data size shl &ncol ; left shift to throw away 1st half (reals) def datsiz &ncol ; reset size sto 0 &rrow ; write imag half eva rrow (&rrow+1) ; increment counter ty row=&row $ next ; end of loop for D1 processing for col 1 &ncol loa &col 0 def datype 1 ; data type = complex def datsiz &nrow zf &double qss &nrow 0 .5 ft ms ; magnitude spectrum red ; reduce to real sto &col 0 ty col=&col $ next end I hadn't looked at this in a couple of years, since our NUTS program started doing 2D, and I had forgotten how convoluted it all was! Good luck, hope this helps. ==================================================================== Virginia W. Miner Voice (510) 683-8595 Acorn NMR Inc. FAX (510) 683-6784 46560 Fremont Blvd., #418 Email gina@acornnmr.com Fremont, CA 94538-6491 From owner-structural-nmr@net.bio.net Mon May 22 23:00:00 1995 Path: biosci!CONVEX.OX.AC.UK!bhardy From: bhardy@CONVEX.OX.AC.UK (Barry Hardy) Newsgroups: bionet.structural-nmr Subject: NMR Poster95 - First Electronic NMR Poster Session Date: 23 May 1995 07:46:08 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 93 Sender: daemon@net.bio.net Distribution: world Message-ID: <199505231443.PAA15199@convex.ox.ac.uk> NNTP-Posting-Host: net.bio.net NMR Poster95 - First Electronic NMR Poster Session ************************************************** The NMR Poster95 sites are up and running in preliminary format. The actual session with discussion will run from June 12-16 '95. If you are interested in participating please send in a URL and email address. The European site URL is: http://bellatrix.pcl.ox.ac.uk/nmr/poster.html The U.S. Site URL is: http://zinc.csb.yale.edu/nmr/poster.html The event is now on the front cover of the June edition of Magnetic Resonance (The Internet Edition) at: http://micro.ifas.ufl.edu/ Barry J. Hardy ALSO: **** BRYAN FINN wrote up a little piece to attempt to answer questions he was getting over the event. Enclosed is what he wrote: What is NMR POSTER95? 1. Are we affiliated with the Gordon Conf. or other conferences or organizations? Answer: No. 2. Is anyone allowed to contribute a poster? Answer: Yes, just so it's NMR related. 3. Is the electronic poster session "registered" and is the data presented count in any way as an offical abstract? Answer: Since we're not associated with any organization (at least not yet), the abstract won't be published anywhere that can be checked later to see if it actually existed. However, publication of abstracts is not universally done at regular meetings either. 4. Is the data protected from "poaching" from competitors who might look at the poster and then rush a similar study to press? Answer: The data presented is entirely at the risk and responsibility of the presentor, just like any poster session or if you hung the poster in the hall outside of your office. 5. Is there a possibility of conflict when it comes to data later (or simultaneously) being published in a journal (i.e. copyright, etc.)? Answer: Same as for question 4, it is entirely between the presenter and the publisher of the article. However, I don't know of publishers ever having a problem with posters and articles conflicting. If there is a concern, use original figures. 6. Is there a fee? Answer: No, our direct costs are low, it only costs us the time to set up and organize the thing. 7. What is this anyway? (My personal favorite question) Answer: Essentially, this is an experiment. The history of this Net NMR Poster session is basically that Barry Hardy contacted some people before last years Gordon conf on Bio-NMR in NH to see if we were interested in taking advantage of the WWW for fostering intercommunication in the NMR community. We (Barry, Kevin, myself, and some others) just took the opportunity of our all being at the GC to discuss what we could do in this regard. The most promising idea seemed to be a net poster session since, just like a regular poster session, the participants each prepare their own work for presentation. The Gordon conference is not associated with the poster session in any official sponsoring way, it was just a convenient forum to get together and get the "ball rolling". Therefore, the session is rather informal and I'm sure will be a learning experience for us all both scientifically and organizationally. The session is open to anyone with an NMR related poster. We are the organizers and at least two of us will run the main relay servers with links to the poster presenters' URLs. For those who do not have their own server, we are willing to mount their poster directly on one of our servers. If you think you can get a poster ready by June 12th, send us the URL address on your server where it is located (e.g. my poster is at http://www.fkem2.lth.se/personnel/bryan/poster/poster.html). Please let us know by June 1 if possible. If you absolutely can't get a poster ready by then but want to check out the session, just connect to one of the poster sites during June 12-16. Although we'd prefer participants to contribute a poster, everyone is welcome to look in. From owner-structural-nmr@net.bio.net Mon May 22 23:00:00 1995 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: seeking a software for image manipulation Date: 23 May 1995 06:14:19 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 37 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <9505221331.AA18667@admin.cnrs-orleans.fr> NNTP-Posting-Host: net.bio.net There are probably several good alternatives; Adobe Illustrator works very well for us. An address in Europe: Adobe Sysytems Europe B.V., Europlaza, Hoogoorddreef 54a, 1101 BE Amsterdam Z.O., The Netherlands. All the best, 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 22 May 1995, patrick Sodano wrote: > Dear netters, > we are seeking a software for image manipulation that works on PCs. The > goal is to integrate NMR spectra in a text and to include text in the > spectra too. This is mainly for publication purposes. Any suggestions > will be wellcome. > > Thanks > > P. Sodano > Centre de Biophysique Moleculaire > Rue Charles Sadron > 45 000 Orleans Cedex 02 > France > > From owner-structural-nmr@net.bio.net Mon May 22 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!news.sprintlink.net!demon!doc.news.pipex.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!newsfeed.ACO.net!fstgds15.tu-graz.ac.at!balu.kfunigraz.ac.at!email.kfunigraz.ac.at!zangger From: zangger@email.kfunigraz.ac.at (Klaus Zangger) Newsgroups: bionet.structural-nmr Subject: Magnitude-mode Macro for Felix Date: Tue, 23 May 1995 11:23:59 Organization: Institut für organische Chemie Lines: 10 Distribution: world Message-ID: NNTP-Posting-Host: boch04.kfunigraz.ac.at X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Dear Netters, I am looking for a Macro to transform 2D magnitude-mode spectra in Bruker format (acquired on a Bruker AM360). The Macro provided by our Felix version (2.05) is damaged and all attempts to write a magnitude-mode Macro worked only with data in complex format. Simply exchanging "ft" by "bft" (for D1 transform) wasn't successfull. Help would be appreciated. Klaus From owner-structural-nmr@net.bio.net Tue May 23 23:00:00 1995 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: TH Date: 24 May 1995 06:09:55 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Would anyone know a working email address for Tad Holak? I'd very much appreciate to know it. Thanks, 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 May 23 23:00:00 1995 Path: biosci!CURLY.BIOP.UMICH.EDU!lzeng From: lzeng@CURLY.BIOP.UMICH.EDU (Lei Zeng) Newsgroups: bionet.structural-nmr Subject: (none) Date: 24 May 1995 12:48:17 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: <9505241949.AA14470@curly.biop.umich.edu> Reply-To: lzeng@curly.biop.umich.edu NNTP-Posting-Host: net.bio.net I want to subscribe the str-nmr net. Thanks Lei Zeng Biophysics Research Division The University of Michigan From owner-structural-nmr@net.bio.net Tue May 23 23:00:00 1995 Path: biosci!MED.UNC.EDU!sheng From: sheng@MED.UNC.EDU (Sheng Zhong) Newsgroups: bionet.structural-nmr Subject: (none) Date: 23 May 1995 20:29:21 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: <9505240328.AA26886@hasty.med.unc.edu> NNTP-Posting-Host: net.bio.net Dear netters, If anyone knows the e-mail address of Dr. Ulrich Hommel from SANDOZ Switzerland please let me know. Dr. Sheng Zhong Dept of Biochem & Biophys UNC at Chapel Hill sheng@med.unc.edu From owner-structural-nmr@net.bio.net Thu May 25 23:00:00 1995 Path: biosci!MAILBOX.SYR.EDU!lpappala From: lpappala@MAILBOX.SYR.EDU (Lucia Pappalardo) Newsgroups: bionet.structural-nmr Subject: subscribe Date: 25 May 1995 19:37:52 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 3 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net subscribe From owner-structural-nmr@net.bio.net Thu May 25 23:00:00 1995 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.structural-nmr Subject: UNSUBSCRIBING, BIOSCI ARCHIVES, ADDRESS DATABASE & BIOSCI FAQ Date: 26 May 1995 02:00:28 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 347 Sender: daemon@net.bio.net Distribution: world Message-ID: <199505260900.CAA26136@net.bio.net> NNTP-Posting-Host: net.bio.net Four important items follow: How to cancel e-mail subscriptions to BIOSCI newsgroups, BIOSCI archive searching, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our BIOSCI user directory, please take a few minutes to complete and return the form below. If your personal information has changed since you listed yourself, please send us a complete new updated form. We can not make manual revisions to existing entries. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net **** How to cancel a BIOSCI e-mail subscription **** If you want to cancel your e-mail subscription to this group, PLEASE DO NOT POST YOUR UNSUBSCRIBE REQUEST TO THE NEWSGROUP ADDRESS (NOR REPLY TO A MESSAGE POSTED TO THE NEWSGROUP)!!! This would send your request to all of the readers of the newsgroup, but it might still not be seen by the BIOSCI staff - thus you would annoy many people and possibly not accomplish your goal anyway. IF YOU ARE LOCATED IN THE AMERICAS OR PACIFIC RIM COUNTRIES, please send a message to biosci@net.bio.net Instructions on how to subscribe/unsubscribe will be returned automatically, so the contents of your message do not matter. IF YOU ARE LOCATED IN EUROPE, AFRICA OR CENTRAL ASIA, please send a message to MXT@dl.ac.uk containing the word help in the body of the message to retrieve e-mail server instructions. Any text placed on the Subject: line of your message will be ignored, so be sure to put the "help" command in the body of the message. If you need personal assistance, a BIOSCI staff member can be contacted at either of the following addresses. Please contact the address designated for your location. Support Address Location --------------- -------- biosci@daresbury.ac.uk Europe, Africa, and Central Asia biosci-help@net.bio.net Americas and the Pacific Rim **** SEARCHING BIOSCI ARCHIVES **** The easiest way to search the BIOSCI archives is to use Mosaic or another World Wide Web browser and connect to the BIOSCI WWW home page at URL http://www.bio.net/. Select the hypertext link to the BIOSCI archives. This gives you read access to all newsgroup messages and the ability to search the indexes described below. You can also use gopher software and connect over the Internet to net.bio.net, the U.S. BIOSCI computer. We maintain three indexes which are searchable from the main gopher menu on net.bio.net: (1) an index of all BIOSCI postings; (2) an index of individual journal article references from the Table of Contents postings on the BIO-JOURNALS newsgroup; and (3) an index of BIOSCI users including regular mail and e-mail addresses, phone/FAX numbers, research interests, and newsgroup participation. E-mail users can search the BIOSCI archives by using our waismail e-mail server. For instructions send the message help to waismail@net.bio.net. Leave the Subject: line blank (anything entered on the Subject: line is ignored). WAIS software can also be used to search the archives as described in the BIOSCI FAQ (see below). Finally, the BIOSCI archive files are accessible by anonymous FTP to net.bio.net [134.172.2.69] in the directory pub/BIOSCI. **** BIOSCI FREQUENTLY ASKED QUESTIONS (FAQ) SHEET **** New users of BIOSCI/bionet may want to read the "Frequently Asked Questions" or "FAQ" sheet for BIOSCI. The FAQ provides details on how to participate in these forums and fix problems that you might encounter in using the newsgroups. The FAQ and other BIOSCI documentation is available through our WWW home page at URL http://www.bio.net/. It is also available for anonymous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/doc/biosci.FAQ or for retrieval by gopher to net.bio.net, port 70. It may also be requested by sending the command info faq in the body of an e-mail message to the Internet address biosci-server@net.bio.net. Please do not enter the info faq command on the Subject: line of your message since the e-mail server ignores text on the Subject: line. The FAQ is also posted on the first of each month to the newsgroup BIONEWS/bionet.announce immediately following the posting of the BIOSCI information sheet. **** BIOSCI USER ADDRESS DIRECTORY **** Please take this opportunity to add your name and address information to the BIOSCI User Address Database if you have not already done so. Below is the address form that we would like each reader of the BIOSCI/bionet newsgroups to complete and return if you would like to be listed in our database. The database serves as a directory that enables biologists, who are currently using (or even just reading) the BIOSCI newsgroups, to look up e-mail addresses and other information about our users. The address database is reindexed nightly for WAIS, waismail, gopher, and WWW access (the URL is http://www.bio.net). If you have access to gopher, connect to net.bio.net to search the database. If you have access to WAIS, please use our WAIS source biologists-addresses.src. If you are not on the Internet, please use our waismail server (send the word "help" to waismail@net.bio.net to get instructions; any text on the Subject: line of your message will be ignored, so put the help command in the body of the mail message.). Please carefully follow the instructions for completing the form below and return it to either of the following two addresses (whichever is more convenient for you). Thanks in advance for taking the time to complete and return the form. Addresses for returning forms Location Network ----------------------------- -------- ------- biovote@net.bio.net U.S.A. Internet/BITNET biovote@daresbury.ac.uk U.K. JANET MAKING SURE THAT YOUR INFORMATION IS CURRENT This notice will be mailed bimonthly to each newsgroup. You should check your database entry from time-to-time to see if your address information is still up-to-date. Using Gopher to complete the form --------------------------------- If you don't want to use a text editor, you can also use Dan Jacobson's gopher site to fill out the address database form as follows. Otherwise skip this section on gopher and proceed to the instructions for filling out the form below. > To add yourself to the database just point your > gopher client at merlot.gdb.org and select the following: > > --> 14. Searching For Biologists/ > > --> 9. E-mail Addresses of Biosci-Bionet Users/ > > --> 1. Add (or Correct) Your Address to the BIOSCI User Address > Data.. > > > And fill out the form. or Rob Harper's gopher site in Europe as follows: > Europeans can point their gopher client at gopher.csc.fi and add their > information to the database. All entries will be mailed directly to > Dave for incorporation in a wais source. > > The path to the questionare is as follows. > > > 6. Information in English/ > > 5. Scientific and other topics/ > > 1. Finnish EMBnet BioBox/ > > 9. FAQ Files/ > > 5. Bionauts Address Database (questionaire) > IMPORTANT INSTRUCTIONS - PLEASE READ CAREFULLY Please enter all responses after the : on each line, leaving one (1) blank space after the : (i.e., before the start of your text). Please do NOT extend your responses past the end of each line (80 characters). PLEASE DO NOT alter any of the field identifiers such as "first name: ". If you have nothing to enter after a field identifier, PLEASE LEAVE IT - do not delete it even if there is no data on the line in question. Several lines are provided at the end of the form for comments, but, please adhere to the line length restriction. On the date: line, please enter the date in the DD-MM-YY format, e.g., 15-05-93 for 15 May 1993. This line will tell others when the information was last updated. Please be sure to include the 0's for single digit days or months, e.g., 15-05-93, not 15-5-93. Note that the "e-mail network: " line below is for specifying, e.g., "Internet," "BITNET," "EARN," "JANET," or whatever other network that your computer may be on. If you are uncertain about any field, please feel free to leave it blank, but please DO NOT DELETE the field identifier from the form! In the first field below, "New information or Update ...", please enter "N" if this is the first time that you have registered in the directory or "U" if you are correcting a listing that you sent to us previously. The comment: lines may be used for anything that you like but PLEASE DO NOT DELETE THEM FROM THE FORM OR ALTER THEM. One suggested use is to list the names of the newsgroups in which you participate. Please use the MAILING LIST name (see below - the latest version of the list can be requested from biosci@net.bio.net) instead of the USENET name even if you don't participate by e-mail. WAIS might get confused by the periods in the USENET names. This allows one to retrieve via WAIS or waismail the list of participants in a particular group. For example: comment: ARABIDOPSIS PLANT-BIOLOGY BIONEWS On the comment: lines use these names below ---- NOT the USENET names below MAILING LIST NAME USENET Newsgroup Name ----------------- --------------------- ACEDB-SOFT bionet.software.acedb AGEING bionet.molbio.ageing AGROFORESTRY bionet.agroforestry ARABIDOPSIS bionet.genome.arabidopsis ASCB bionet.prof-society.ascb BIOCAN bionet.prof-society.cfbs BIOFORUM bionet.general BIO-INFORMATION-THEORY bionet.info-theory BIONAUTS bionet.users.addresses BIONEWS bionet.announce BIO-JOURNALS bionet.journals.contents BIO-MATRIX bionet.molbio.bio-matrix BIOPHYSICAL-SOCIETY bionet.prof-society.biophysics BIOPHYSICS bionet.biophysics BIO-SOFTWARE bionet.software BIOTHERMOKINETICS bionet.metabolic-reg BIO-WWW bionet.software.www CARDIOVASCULAR-RESEARCH bionet.biology.cardiovascular CELEGANS bionet.celegans CELL-BIOLOGY bionet.cellbiol CHLAMYDOMONAS bionet.chlamydomonas CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY bionet.biology.computational CSM bionet.prof-society.csm CYTONET bionet.cellbiol.cytonet DROSOPHILA bionet.drosophila EMBL-DATABANK bionet.molbio.embldatabank EMF-BIO bionet.emf-bio EMPLOYMENT bionet.jobs EMPLOYMENT-WANTED bionet.jobs.wanted FASEB bionet.prof-society.faseb GDB bionet.molbio.gdb GENBANK-BB bionet.molbio.genbank GENETIC-LINKAGE bionet.molbio.gene-linkage GRASSES-SCIENCE bionet.biology.grasses HIV-MOLECULAR-BIOLOGY bionet.molbio.hiv HUMAN-GENOME-PROGRAM bionet.molbio.genome-program IMMUNOLOGY bionet.immunology INFO-GCG bionet.software.gcg JOURNAL-NOTES bionet.journals.note METHODS-AND-REAGENTS bionet.molbio.methds-reagnts MICROBIOLOGY bionet.microbiology MOLECULAR-EVOLUTION bionet.molbio.evolution MOLECULAR-MODELLING bionet.molec-model MOLLUSC-MOLECULAR-NEWS bionet.molbio.molluscs MYCOLOGY bionet.mycology NEUROSCIENCE bionet.neuroscience N2-FIXATION bionet.biology.n2-fixation PARASITOLOGY bionet.parasitology PHOTOSYNTHESIS bionet.photosynthesis PLANT-BIOLOGY bionet.plants POPULATION-BIOLOGY bionet.population-bio PROTEIN-ANALYSIS bionet.molbio.proteins PROTEIN-CRYSTALLOGRAPHY bionet.xtallography PROTISTA bionet.protista RAPD bionet.molbio.rapd SCIENCE-RESOURCES bionet.sci-resources STADEN bionet.software.staden STRUCTURAL-NMR bionet.structural-nmr TROPICAL-BIOLOGY bionet.biology.tropical URODELES bionet.organisms.urodeles VIROLOGY bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio YEAST bionet.molbio.yeast ZBRAFISH bionet.organisms.zebrafish Listing newsgroups on the comment: line is optional, of course. Thanks again for your cooperation! --------------- please cut here and return portion below --------------- New information or Update to old record (enter N or U): date (DD-MM-YY): first name: middle initial: family name: job title: e-mail address: e-mail network: phone number: FAX number: institution: address1: address2: address3: city: state/province: country: postal code: research interest: research interest: comment: comment: comment: comment: comment: From owner-structural-nmr@net.bio.net Thu May 25 23:00:00 1995 Path: biosci!fcu.um.es!boullon From: boullon@fcu.um.es (Jose Villalain Boullon) Newsgroups: bionet.structural-nmr Subject: Help: conversion from ascii to FELIX binary format Date: 26 May 1995 07:28:48 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 32 Sender: daemon@net.bio.net Distribution: world Message-ID: <9505261429.AA25231@afrodita> NNTP-Posting-Host: net.bio.net Dear netters: I have been trying for several days to convert an 2H-NMR spectrum saved either as an ascii file (ascii y data without header) or saved in WIN-NMR binary file format to the FELIX binary file format (Biosym Technologies). I have compiled the programs toasci.for and frasci.for which came with the FELIX package, as well as I have tried to use the filter programs which came with FELIX. However, no one of these compiled programs could read my data. I have converted the FELIX binary sample files *.dat into ascii with the FELIX command wa, and then I tried to write my data into this ascii format, however without success. Is anybody there which has had the same problem and resolved it ?. Any help will be much appreciated. ***************************************************** Dr. Jose Villalain Dpto. Bioquimica (A) Edf. Veterinaria Universidad de Murcia Apdo. 4021 E-30080 MURCIA (Spain) Tel. 34-68-307100 (Ext.2921) Fax 34-68-364147 ***************************************************** From owner-structural-nmr@net.bio.net Fri May 26 23:00:00 1995 Path: biosci!SUNCHEM.CHEM.UGA.EDU!bphart From: bphart@SUNCHEM.CHEM.UGA.EDU ("B. P. Hart") Newsgroups: bionet.structural-nmr Subject: info on fixed evolution hetcor sequence Date: 27 May 1995 08:12:27 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <199505271512.LAA24112@sunchem.chem.uga.edu> NNTP-Posting-Host: net.bio.net To whom it may concern, I am interesting in hearing from anyone who has in the past or is presently running a HETCOR pulse sequence known as Fixed Evolution Hetcor. The reference for this pulse sequence is as follows Magnetic Resonance In Chemistry, Vol 26, 358-361, 1988. The authors are M. P. Dumont, W. R. Reynoldsand R. G. Enriquez. I am especially interested in getting in touch with anyone who might be able to mail me a printout of the pulse sequence that could run on a Bruker AC spectrometer. B. Hart From owner-structural-nmr@net.bio.net Sun May 28 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!news.sprintlink.net!demon!doc.news.pipex.net!pipex!sunsite.doc.ic.ac.uk!susx.ac.uk!kapk4 From: kapk4@central.susx.ac.uk (Chris Carpenter) Newsgroups: bionet.structural-nmr Subject: Deconvolution of NMR spectra Date: 29 May 1995 14:54:03 GMT Organization: University of Sussex Lines: 7 Message-ID: <3qcn6b$ndh@infa.central.susx.ac.uk> NNTP-Posting-Host: solx1.central.susx.ac.uk X-Newsreader: TIN [version 1.2 PL2] Hi NMR NETTERS, does anyone know of a deconvolution program that is availble on the net. I have a series of solid state NMR spectra to investigate, the spectrometer doesn't have any program to do this (Bruker ACP 250). Cheers in advance. Mail me if you can. Chris Carpenter From owner-structural-nmr@net.bio.net Tue May 30 23:00:00 1995 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!swrinde!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: th@mrc-cpe.cam.ac.uk (Tim Hubbard) Newsgroups: bionet.structural-nmr Subject: ANNOUNCEMENT: IRBM practical course: frontiers of protein structure prediction Date: 31 May 1995 18:57:26 +0100 Lines: 62 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3qiam6$1j3@mserv1.dl.ac.uk> X-Sender: th@ind1.mrc-lmb.cam.ac.uk Original-To: pdb-l@pdb.pdb.bnl.gov, bioforum@dl.ac.uk, bionews@dl.ac.uk, biophys@dl.ac.uk, bio-soft@dl.ac.uk, comp-bio@dl.ac.uk, methods@dl.ac.uk, molmodel@dl.ac.uk, proteins@dl.ac.uk, xtal-log@dl.ac.uk, str-nmr@dl.ac.uk Announcement: Call for applications =================================== IRBM practical course: frontiers of protein structure prediction The course is directed at young scientists with some experience and a strong interest in protein structure and structure prediction who wish to learn about the latest developments in the field. The aim of the workshop is to predict as much as possible about the structure of a number of proteins of biological interest, taking advantage of the most recent methodologies for fold recognition and ab initio prediction. The participants will be divided into working groups assisted by an instructor. Each group will be equipped with state of the art software and hardware (kindly provided by Silicon Graphics) and assigned the sequences of proteins whose structure has to be predicted. The predictions will be made public as a technical document and also available via World Wide Web. Suggestions for target proteins can also be submitted by non-participants via WWW (see accompanying email) Organizers: Tim Hubbard (CPE, MRC), Anna Tramontano (IRBM) Instructors: G. Barton (Oxford), T. Hubbard (Cambridge), D. Jones (London), M. Sippl (Salzburg), A.