From owner-structural-nmr@net.bio.net Wed May 01 23:00:00 1996 Path: biosci!sfu.ca!dnaugler From: dnaugler@sfu.ca (David Naugler) Newsgroups: bionet.structural-nmr Subject: Heteronuclear 3D NMR simulator Date: 1 May 1996 17:01:51 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: <199605012358.XAA27152@beaufort.sfu.ca> NNTP-Posting-Host: net.bio.net Heteronuclear 3D NMR experiments take a long time to set up and run. Consequently, it takes a long time to surmount the learning curve. Has anyone developed a software simulator for heteronuclear 3D that can do the job of illustrating the principles involved and which would permit the user to experiment with different pulse sequences? Can anyone suggest any other types of learning resources which would be useful? Thank you. David Naugler Institute of Molecular Biology and Biochemistry Simon Fraser University From owner-structural-nmr@net.bio.net Thu May 02 23:00:00 1996 Newsgroups: bionet.structural-nmr Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!sangam!iitb!powai!sasidhar From: sasidhar@powai.cc.iitb.ernet.in (dr y u sasidhar) Subject: deuterated TFE Message-ID: Date: Fri, 3 May 1996 05:15:32 GMT Organization: Computer Centre, Indian Institute of Technology, Bombay X-Newsreader: TIN [version 1.2 PL2] Lines: 5 dear netters, could you please let me know where i can obtain a vial of deuterated TFE (1ml-5ml). From owner-structural-nmr@net.bio.net Thu May 02 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!EU.net!news.eunet.fi!newsmaster From: piero pollesello Newsgroups: bionet.structural-nmr Subject: ASN:HD* and GLN:HE* Date: 3 May 1996 05:19:22 GMT Organization: POLYbios, Area Science Park, Trieste, Italy Lines: 13 Message-ID: <4mc50q$kme@idefix.eunet.fi> NNTP-Posting-Host: protein.orion.fi Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12(Macintosh; I; 68K) X-URL: news:bionet.structural-nmr I have a question: which is the chemical shifts (randon conformation) of the 2 -NH protons (cys and trans relatively to the =CO) on the residues of Asn and Gln? In the book of Wuetrich they are listed with 2 different chemical shifts, but which is which? Thanks Piero Pollesello fax:int-358-0-429-2924 From owner-structural-nmr@net.bio.net Thu May 02 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!EU.net!news.eunet.fi!newsmaster From: piero pollesello Newsgroups: bionet.structural-nmr Subject: ASN:HD* and GLN:HE* Date: 3 May 1996 05:27:51 GMT Organization: POLYbios, Area Science Park, Trieste, Italy Lines: 13 Message-ID: <4mc5gn$kme@idefix.eunet.fi> NNTP-Posting-Host: protein.orion.fi Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12(Macintosh; I; 68K) X-URL: news:bionet.structural-nmr I have a question: In the ASN and GLN side chain there is an amido group with two protons, one in position trans and one in position cis. Wuetrich reports two different chemical shifts for those protons in the amino acids are in random conformation. But which is which? Is the trans amidic proton at lower field? Thanks for answers or comments Piero Pollesello Fax:int-358-0-429-2924 From owner-structural-nmr@net.bio.net Thu May 02 23:00:00 1996 Path: biosci!galaxy.ucr.edu!library.ucla.edu!csulb.edu!newshub.csu.net!imci3!imci4!newsfeed.internetmci.com!news.kei.com!nntp.coast.net!news00.sunet.se!sunic!news99.sunet.se!news.uni-c.dk!news From: Mogens Kjaer Newsgroups: bionet.structural-nmr,sci.techniques.mag-resonance Subject: Pronto 3D available Date: Wed, 01 May 1996 11:21:34 +0200 Organization: Carlsberg Laboratory Lines: 43 Message-ID: <31872D1E.41C6@unidhp.uni-c.dk> NNTP-Posting-Host: lgb268.ppp.uni-c.dk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) Xref: biosci bionet.structural-nmr:1245 sci.techniques.mag-resonance:1619 Announcement: New version of Pronto/3D available: =================================== The latest version of Pronto/3D is available at: http://unidhp.uni-c.dk/~carlmk What is Pronto/3D? ================== Pronto is a tool for analysis of 2D, 3D, and 4D NMR spectra of proteins. You can contour spectra, locate cross peaks, build spin systems, assign NOEs, prepare distance restraint files and analyse calculated structures. What does it require? ===================== Two binary distributions are available, one for Silicon Graphics and one for Sun SPARC stations, running SunOS. Follow the installation procedures listed on the home page mentioned above! You'll have to mail me for a license code. License codes are distributes both to non-profit and profit institutions. The program reads spectra processed by Bruker's UXNMR, Felix, VNMR, and by MNMR, a processing package available separately from Carlsberg Laboratory. If you have any questions, please contact me at the address below. Mogens -- Mogens Kjaer, Carlsberg Laboratory, Dept. of Chemistry Gamle Carlsberg Vej 10, DK-2500 Valby, Denmark Phone: +45 33 27 53 25, Fax: +45 33 27 47 08 Email: carlmk@unidhp.uni-c.dk From owner-structural-nmr@net.bio.net Thu May 02 23:00:00 1996 Path: biosci!Merck.Com!yves_aubin From: yves_aubin@Merck.Com (Yves Aubin) Newsgroups: bionet.structural-nmr Subject: Re: ASN:HD* and GLN:HE* Date: 3 May 1996 06:58:31 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 49 Sender: daemon@net.bio.net Distribution: world Message-ID: <199605031352.JAA19429@igw2> NNTP-Posting-Host: net.bio.net Piero Pollesello wrote: >I have a question: > >In the ASN and GLN side chain there is an amido group with two protons, >one in position trans and one in position cis. Wuetrich reports two >different chemical shifts for those protons in the amino acids are in >random conformation. But which is which? Is the trans amidic proton at >lower field? >Thanks for answers or comments > >Piero Pollesello >Fax:int-358-0-429-2924 Dear Piero, I would think that the major contribution to the chemical shift of the NH2 protons of ASN and GLN side chain will come from the anisotric cone of the carbonyl. The proton the most shielded (lower ppm) would be nearby the cone and therefore would be the TRANS while the CIS being more deshielded (higher ppm). Unless the CIS proton is strongly influenced by a neighbor, the carbonyl anisotropy should be the strongest contribution. O | C H (~6.90 ppm) \ / \ / N | | H (~7.59 ppm ) Hope this helps! Yves Yves Aubin Ph.D. Merck Frosst Canada Inc. P.O. Box1005 Pointe-Claire--Dorval QC, H9R 4P8 tel: (514) 428-3931 fax: (514) 428-8615 From owner-structural-nmr@net.bio.net Thu May 02 23:00:00 1996 Path: biosci!PHOENIX.PRINCETON.EDU!ipelczer From: ipelczer@PHOENIX.PRINCETON.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: deuterated TFE Date: 3 May 1996 06:25:20 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 26 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net Cambridge Isotope Laboratories, or Isotec, or probably Aldrich would be good companies to ask. I am sure that there are others, too, sorry for the incomplete list. Good luck, Istvan wwww,wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww Istvan Pelczer, Ph.D. Email: ipelczer@princeton.edu Senior NMR Spectroscopist Princeton University Department of Chemistry ph# (609) 258 2342 Frick Laboratory fax# (609) 258 6746 Washington Road Princeton, NJ 08544 On Fri, 3 May 1996, dr y u sasidhar wrote: > dear netters, > could you please let me know where i can obtain a vial of deuterated TFE > (1ml-5ml). > > > > From owner-structural-nmr@net.bio.net Thu May 02 23:00:00 1996 Path: biosci!NMRWORK1!wwang From: wwang@NMRWORK1 (Wei Wang) Newsgroups: bionet.structural-nmr Subject: (none) Date: 3 May 1996 13:07:16 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <199605032002.NAA11324@NMRWORK1> NNTP-Posting-Host: net.bio.net please add my name to your discussion group. Wei Wang NMR Spectroscopist Department of Chemistry Princeton University Princeton, NJ 08544 (609) 258-1633 Voice (609) 258-6746 Fax From owner-structural-nmr@net.bio.net Thu May 02 23:00:00 1996 Path: biosci!PHOENIX.PRINCETON.EDU!ipelczer From: ipelczer@PHOENIX.PRINCETON.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: ASN:HD* and GLN:HE* Date: 3 May 1996 04:19:20 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 35 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <4mc5gn$kme@idefix.eunet.fi> NNTP-Posting-Host: net.bio.net In proteins (or smaller molecules with non-random structure) assignment of these protons is not obvious. Guy Montelione had a couple of papers (I believe in JACS in early 90es) where stereospecific assignment for such protons were given, based on NOE effects. Greetings, Istvan wwww,wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww Istvan Pelczer, Ph.D. Email: ipelczer@princeton.edu Senior NMR Spectroscopist Princeton University Department of Chemistry ph# (609) 258 2342 Frick Laboratory fax# (609) 258 6746 Washington Road Princeton, NJ 08544 On 3 May 1996, piero pollesello wrote: > I have a question: > > In the ASN and GLN side chain there is an amido group with two protons, > one in position trans and one in position cis. Wuetrich reports two > different chemical shifts for those protons in the amino acids are in > random conformation. But which is which? Is the trans amidic proton at > lower field? > Thanks for answers or comments > > Piero Pollesello > Fax:int-358-0-429-2924 > > > > From owner-structural-nmr@net.bio.net Fri May 03 23:00:00 1996 Path: biosci!cc.uoi.gr!astavrak From: astavrak@cc.uoi.gr (Athanasios Stavrakoudis) Newsgroups: bionet.structural-nmr Subject: Re: Pronto 3D available Date: 4 May 1996 07:34:23 -0700 Organization: University of Ioannina Computer Center Ioannina, Greece 451 10 tel: +30-651-45298, fax: +30-651-45298 Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <9605041731.AA00432@solon.cc.uoi.gr> NNTP-Posting-Host: net.bio.net Dear Dr Kjaer, l am interested to try Pronto 3D , but it is very difficult to get through netscape or lynx . So l ask if there is another way of transfer , like e-mail or ftp . Please inform about this . Thank you , Athanassios Stavrakoudis University of Ioannina Department of Chemistry GR-451 10, Ioannina GREECE e-mail : astavrak@cc.uoi.gr From owner-structural-nmr@net.bio.net Fri May 03 23:00:00 1996 Path: biosci!NMR1.IOC.AC.RU!zatonsk From: zatonsk@NMR1.IOC.AC.RU ("Zatonskiy George V.") Newsgroups: bionet.structural-nmr Subject: subscribe Date: 4 May 1996 10:41:12 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <77845.zatonsk@nmr1.ioc.ac.ru> NNTP-Posting-Host: net.bio.net Subscribe Zatonskiy George, please. Zatonskiy George, zatonsk@nmr1.ioc.ac.ru George V.Zatonskiy NMR laboratory, N.D. Zeliskii Institute of Organic Chemistry, Russian Academy of Science (RAS). e-mail: zatonsk@nmr1.ioc.ac.ru tel.: (7-095) 135-9094 fax : (7-095) 135-5328 From owner-structural-nmr@net.bio.net Sat May 04 23:00:00 1996 Newsgroups: bionet.structural-nmr Path: biosci!news.Stanford.EDU!nntp-hub2.barrnet.net!sgigate.sgi.com!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!sangam!iitb!powai!sasidhar From: sasidhar@powai.cc.iitb.ernet.in (dr y u sasidhar) Subject: pdb input for peptides Message-ID: Date: Sun, 5 May 1996 05:48:52 GMT Organization: Computer Centre, Indian Institute of Technology, Bombay X-Newsreader: TIN [version 1.2 PL2] Lines: 16 dear netters, is there a program which takes the amino acide sequence of a peptide (about 15-20 residues) with backbone and side chain dihedral angles as input and generate a coordinate file in PDB format, which can directly be used as input for RASMOL or KINEMAGES. Thanks in advance -Sasidhar _________________________________________________ Dr. Y.U. Sasidhar Assistant Professor Dept. of Chemistry Indian Institute of Technology Bombay 400 076 India From owner-structural-nmr@net.bio.net Sun May 05 23:00:00 1996 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!howland.reston.ans.net!EU.net!news.eunet.fi!newsmaster From: piero pollesello Newsgroups: bionet.structural-nmr Subject: Re: ASN:HD* and GLN:HE* Date: 6 May 1996 13:43:49 GMT Organization: POLYbios, Area Science Park, Trieste, Italy Lines: 9 Message-ID: <4mkvml$gls@idefix.eunet.fi> References: <4mc5gn$kme@idefix.eunet.fi> NNTP-Posting-Host: protein.orion.fi Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12(Macintosh; I; 68K) To: ipelczer@PHOENIX.PRINCETON.EDU X-URL: news:Pine.SUN.3.91.960503070531.2697B-100000@phoenix.princeton.edu Thanks for the answer! Together with a collegue of mine we end up with this conclusion: the amido proton which show the stronger NOESY cross peak with beta proton (in ASN) or gamma (in GLN) is the trans. In our case they were all at lower field than the cis. Piero From owner-structural-nmr@net.bio.net Sun May 05 23:00:00 1996 Path: biosci!rutgers!gatech!news.jsums.edu!neonlights.uoregon.edu!news.uoregon.edu!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!indyvax.iupui.edu!physics.nmr.iupui.edu!user Newsgroups: bionet.structural-nmr Subject: Re: deuterated TFE Message-ID: From: bray@indyvax.iupui.edu (Bruce D. Ray) Date: Mon, 06 May 1996 12:20:15 +0000 References: Organization: IUPUI Physics Dept. Nntp-Posting-Host: physics.nmr.iupui.edu Lines: 24 In article , sasidhar@powai.cc.iitb.ernet.in (dr y u sasidhar) wrote: > dear netters, > could you please let me know where i can obtain a vial of deuterated TFE > (1ml-5ml). Contact Cambridge Isotope Labs about their catalog number DMM-27, Trifluoroethanol (D-3, 98%) address is 50 Frontage Rd., Andover, MA 01810, USA. I do not know if they have a distributor in India. Their phone no. is (508) 749-8000. On the net, you can reach either Lynne Batchelder or John Aberhart by e-mail as lynneb@isotope.com and as aberhart@isotope.com respectively. HTH -- The first five letters of laboratory are labor. In this lab, it's all manual. In the well-run synthetic organic lab, nothing sits. Even the reaction has to stand. So, lets stand up and get to work. From owner-structural-nmr@net.bio.net Sun May 05 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!scripps.edu!obelix!weber From: weber@obelix.scripps (Christoph Weber) Newsgroups: bionet.structural-nmr Subject: Re: ASN:HD* and GLN:HE* Date: 6 May 1996 19:20:57 GMT Organization: The Scripps Research Institute Lines: 21 Message-ID: <4mljep$9i5@riscsm.scripps.edu> References: <4mc5gn$kme@idefix.eunet.fi> <4mkvml$gls@idefix.eunet.fi> NNTP-Posting-Host: obelix.scripps.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit In article <4mkvml$gls@idefix.eunet.fi>, piero pollesello writes: > Thanks for the answer! > Together with a collegue of mine we end up with this conclusion: > the amido proton which show the stronger NOESY cross peak with beta > proton (in ASN) or gamma (in GLN) is the trans. In our case they were > all at lower field than the cis. Just be careful with the chemical shift argument. We found in the NPNA-motif that the case was reversed for one of the Asn residues. And that was in a linear peptide! See Bisang et al., JACS 117, 7904-7915 (1995) for details. I would expect that all bets are off in a protein. The NOE method is easy and reliable in most cases, though. | Christoph Weber Sen. Research Associate | Dept.of Molecular Biology, MB2 619-554-7283 or -8754 (phone) | The Scripps Research Institute 619-554-3757 (FAX) | La Jolla CA 92037 weber@scripps.edu | http://www.scripps.edu/~chazin/people/cw.html From owner-structural-nmr@net.bio.net Mon May 06 23:00:00 1996 Path: biosci!ns1.faseb.org!lamarck.sura.net!newsfeed.internetmci.com!in2.uu.net!newsfeed.pitt.edu!bb3.andrew.cmu.edu!andrew.cmu.edu!mm6n+ From: Marcella Madrid Newsgroups: bionet.structural-nmr Subject: Sequence Analysis workshops offered at the PSC Date: Tue, 7 May 1996 15:16:43 -0400 Organization: Pittsburgh Supercomputing Center, Carnegie Mellon, Pittsburgh, PA Lines: 122 Message-ID: NNTP-Posting-Host: po8.andrew.cmu.edu NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS WORKSHOPS FOR BIOMEDICAL RESEARCHERS PITTSBURGH SUPERCOMPUTING CENTER Biomedical Workshops offered by the Pittsburgh Supercomputing Center typically consist of theoretical lectures taught by leaders in the respective scientific discipline, and extensive hands-on computer sessions. During the computer sessions, participants are able to work on the examples provided or on their own experimental data. Attendance is limited to 20 participants to allow one-on-one instruction and encourage scientific interactions and discussions. Researchers nationwide are invited to apply. For additional information, please refer to http://www.psc.edu/biomed/workshops.html CONTACT INFORMATION: Nancy Blankenstein, Biomedical Program Assistant, (412)268-4960, blankens@psc.edu The following two Sequence Analysis workshops will be offered this summer: *********NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS: June 9-14.************** Emphasis will be on alignment of and pattern extraction from multiple sequences. Topics to be discussed include Comparing and aligning sequences Identifying informative patterns in a set of sequences Using extracted informative patterns to identify related sequences. Leaders are: Dr. Gary Churchill, Cornell University; Dr. Michael Gribskov, San Diego Supercomputer Center and Dr. Hugh B. Nicholas Jr., Pittsburgh Supercomputing Center. Financial Information: A limited number of grants to cover travel and/or hotel accommodations are available for U.S. academic participants. ALL PARTICIPANTS ARE REQUIRED TO PAY A $135 REGISTRATION FEE UPON ACCEPTANCE INTO THE WORKSHOP. Complimentary breakfast and lunches will be provided. APPLICATION DEADLINE: May 17, 1996. *****ADVANCED NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS: August 25-28.****** Open to researchers who have previously attended one of the PSC's annual "Nucleic Acid and Protein Sequence Analysis" workshops or who have appreciable experience with computerized sequence analysis. The workshop will build on previous experience to teach techniques for analyzing families and superfamilies of genes and proteins. Leaders are: Dr Stephen H. Bryant, National Center for Biotechnology Information, National Library of Medicine Dr. Michael Gribskov, San Diego Supercomputer Center and Dr. Hugh B. Nicholas Jr., Pittsburgh Supercomputing Center. Financial Information : Hotel accommodations during the workshop for researchers affiliated with U.S. academic institutions will be paid by our NIH grant. Complimentary breakfast and lunches will also be provided. There is NO REGISTRATION FEE for this workshop. All other costs incurred in attending (travel, other meals, etc.) are the responsibility of the individual participant. APPLICATION DEADLINE: July 10, 1996. ********** PITTSBURGH SUPERCOMPUTING CENTER WORKSHOPS FOR BIOMEDICAL RESEARCHERS APPLICATION Workshop I am interested in attending:_______________________________________ Name: ______________________________________________________________ Affiliation: ______________________________________________________________ Address: ______________________________________________________________ (Business) ______________________________________________________________ ______________________________________________________________ (Home) ______________________________________________________________ Telephone: ____________________________ ____________________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship:_________________ Electronic Mail Address:_____________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) Please indicate specifically any special housing, transportation or dietary arrangements you will need: __________________________________________ How did you learn about this workshop:_______________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, the sequence analysis problems encountered in your research, and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vitae. Graduate students must have a letter of recommendation from a faculty member. Please return all application materials to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960. *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From owner-structural-nmr@net.bio.net Mon May 06 23:00:00 1996 Path: biosci!PHOENIX.PRINCETON.EDU!ipelczer From: ipelczer@PHOENIX.PRINCETON.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: c Date: 7 May 1996 09:47:06 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Netters, I am looking for information on structural studies on apo-cytochrome c, both by NMR and X-ray. I'll appreciate info on references as well as personal info (if someone would be working on it right now). Thanks, Istvan wwww,wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww Istvan Pelczer, Ph.D. Email: ipelczer@princeton.edu Senior NMR Spectroscopist Princeton University Department of Chemistry ph# (609) 258 2342 Frick Laboratory fax# (609) 258 6746 Washington Road Princeton, NJ 08544 From owner-structural-nmr@net.bio.net Mon May 06 23:00:00 1996 Path: biosci!ANDREW.CMU.EDU!mm6n+ From: mm6n+@ANDREW.CMU.EDU (Marcella Madrid) Newsgroups: bionet.structural-nmr Subject: Sequence Analysis workshops offered at the PSC Date: 7 May 1996 12:22:00 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 122 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS WORKSHOPS FOR BIOMEDICAL RESEARCHERS PITTSBURGH SUPERCOMPUTING CENTER Biomedical Workshops offered by the Pittsburgh Supercomputing Center typically consist of theoretical lectures taught by leaders in the respective scientific discipline, and extensive hands-on computer sessions. During the computer sessions, participants are able to work on the examples provided or on their own experimental data. Attendance is limited to 20 participants to allow one-on-one instruction and encourage scientific interactions and discussions. Researchers nationwide are invited to apply. For additional information, please refer to http://www.psc.edu/biomed/workshops.html CONTACT INFORMATION: Nancy Blankenstein, Biomedical Program Assistant, (412)268-4960, blankens@psc.edu The following two Sequence Analysis workshops will be offered this summer: *********NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS: June 9-14.************** Emphasis will be on alignment of and pattern extraction from multiple sequences. Topics to be discussed include Comparing and aligning sequences Identifying informative patterns in a set of sequences Using extracted informative patterns to identify related sequences. Leaders are: Dr. Gary Churchill, Cornell University; Dr. Michael Gribskov, San Diego Supercomputer Center and Dr. Hugh B. Nicholas Jr., Pittsburgh Supercomputing Center. Financial Information: A limited number of grants to cover travel and/or hotel accommodations are available for U.S. academic participants. ALL PARTICIPANTS ARE REQUIRED TO PAY A $135 REGISTRATION FEE UPON ACCEPTANCE INTO THE WORKSHOP. Complimentary breakfast and lunches will be provided. APPLICATION DEADLINE: May 17, 1996. *****ADVANCED NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS: August 25-28.****** Open to researchers who have previously attended one of the PSC's annual "Nucleic Acid and Protein Sequence Analysis" workshops or who have appreciable experience with computerized sequence analysis. The workshop will build on previous experience to teach techniques for analyzing families and superfamilies of genes and proteins. Leaders are: Dr Stephen H. Bryant, National Center for Biotechnology Information, National Library of Medicine Dr. Michael Gribskov, San Diego Supercomputer Center and Dr. Hugh B. Nicholas Jr., Pittsburgh Supercomputing Center. Financial Information : Hotel accommodations during the workshop for researchers affiliated with U.S. academic institutions will be paid by our NIH grant. Complimentary breakfast and lunches will also be provided. There is NO REGISTRATION FEE for this workshop. All other costs incurred in attending (travel, other meals, etc.) are the responsibility of the individual participant. APPLICATION DEADLINE: July 10, 1996. ********** PITTSBURGH SUPERCOMPUTING CENTER WORKSHOPS FOR BIOMEDICAL RESEARCHERS APPLICATION Workshop I am interested in attending:_______________________________________ Name: ______________________________________________________________ Affiliation: ______________________________________________________________ Address: ______________________________________________________________ (Business) ______________________________________________________________ ______________________________________________________________ (Home) ______________________________________________________________ Telephone: ____________________________ ____________________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship:_________________ Electronic Mail Address:_____________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) Please indicate specifically any special housing, transportation or dietary arrangements you will need: __________________________________________ How did you learn about this workshop:_______________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, the sequence analysis problems encountered in your research, and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vitae. Graduate students must have a letter of recommendation from a faculty member. Please return all application materials to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960. *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From owner-structural-nmr@net.bio.net Mon May 06 23:00:00 1996 Path: biosci!fmp.fta-berlin.de!rappsilber From: rappsilber@fmp.fta-berlin.de (Juri Rappsilber) Newsgroups: bionet.structural-nmr Subject: (none) Date: 7 May 1996 03:11:47 -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 Mon May 06 23:00:00 1996 Path: biosci!GATE.SINICA.EDU.TW!ccchuang From: ccchuang@GATE.SINICA.EDU.TW (Chyh-chong Chuang) Newsgroups: bionet.structural-nmr Subject: How to set 3J-dihedral restrain in Biosym's NMR-refine? Date: 7 May 1996 01:06:17 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 27 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <199604010638.IAA04757@hydrant.icm.edu.pl> NNTP-Posting-Host: net.bio.net Dear NMR experts: Does any one had the experience to use 3J-dihedral restrain in Biosym's NMR-refine modual? I am curios how to define the 4 atoms for a protein's backbone phi angle? From paper, it is said to give a dihedral constant restrain for a residue, say, -140 to -100 for a 3JNH of >9Hz. My qestion is how to define the 4 atoms for a phi angle restrain of -140 to -100. I used Biosym's 3J_to_dihed funtion to calculate the phi angle restrain and was given a value 151.2 to -151.2 for a 3J=9.3+/-1 for the 4 atoms assigned to residue's HN, N, CA, HA atom (I give 3 constant as 6.7, -1.3, 1.5). The range did not match, so I suggest that it is not the same for these two case to assign 4 atoms for the phi angle. How to deal with this? Any comment/suggestion will be great appreciated. ccchuang ============================================ Chyh-Chong Chuang Institude of Biological Chemistry, Academia Sinica,Taipei, Taiwan -------------------------------------------- Phone: 886-2-7858981 ext 7091 Fax: 886-2-7883473 E-Mail: ccchuang@gate.sinica.edu.tw ============================================ From owner-structural-nmr@net.bio.net Mon May 06 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!torn!nott!crc-news.doc.ca!news.drenet.dnd.ca!ub!newserve!schulte From: schulte@bingsuns.cc.binghamton.edu () Newsgroups: bionet.structural-nmr Subject: Roommate for EENC in Paris Date: 7 May 1996 03:09:43 GMT Organization: Binghamton University, Binghamton, NY Lines: 17 Message-ID: <4mmetn$32l@bingnet1.cc.binghamton.edu> NNTP-Posting-Host: 128.226.1.20 X-Newsreader: TIN [version 1.2 PL2] Who (male, preferredly non-smoker) would be willing to share a hotel room at the European Experimental NMR Conference from May 19 to 24 in Paris with me. Please answer by e-mail. -- ---------------------------------------------------------------------- Juergen Schulte ! ! NMR Specialist U SUNY Binghamton ~ Department of Chemistry Phone: (607) 777-4405 Binghamton, NY 13902-6016 Fax: (607) 777-4478 ---------------------------------------------------------------------- schulte@bingsuns.cc.binghamton.edu, schulte@binghamton.edu ---------------------------------------------------------------------- From owner-structural-nmr@net.bio.net Mon May 06 23:00:00 1996 Path: biosci!rutgers!uwm.edu!lll-winken.llnl.gov!nntp.coast.net!news00.sunet.se!sunic!news99.sunet.se!news.uni-c.dk!unidhp!carlmk From: carlmk@unidhp (Mogens Kjaer) Newsgroups: bionet.structural-nmr Subject: Re: Pronto 3D available Date: 5 May 1996 09:39:55 GMT Organization: News Server at UNI-C, Danish Computing Centre for Research and Education. Lines: 31 Distribution: world Message-ID: <4mht1b$l8i@news.uni-c.dk> References: <9605041731.AA00432@solon.cc.uoi.gr> NNTP-Posting-Host: unidhp.uni-c.dk X-Newsreader: TIN [version 1.2 PL1] Athanasios Stavrakoudis (astavrak@cc.uoi.gr) wrote: : Dear Dr Kjaer, : l am interested to try Pronto 3D , : but it is very difficult to get through netscape : or lynx . So l ask if there is another way : of transfer , like e-mail or ftp . : Please inform about this . : Thank you , Currently, this is the only way I have of distributing Pronto. Hopefully, we will have our own internet connection set up in half a year, this should make things a bit easier. If someone wants to mirror Pronto on a ftp site, please do this. Mogens -- Mogens Kjaer Carlsberg Laboratory, Dept. of Chemistry Gamle Carlsberg Vej 10 DK-2500 Valby Denmark Phone: + 45 33 27 53 25 Fax: + 45 33 27 47 08 Email: carlmk@unidhp.uni-c.dk From owner-structural-nmr@net.bio.net Tue May 07 23:00:00 1996 Path: biosci!rutgers!uwm.edu!lll-winken.llnl.gov!nntp.coast.net!swidir.switch.ch!serra.unipi.it!ictpsp10.ictp.trieste.it!polbpc From: radoico@poly01.tbs.trieste.it Newsgroups: bionet.structural-nmr Subject: NMR software Date: Wed, 08 May 96 16:00:52 GMT Organization: ICTP-Trieste-Italy Lines: 15 Message-ID: <4mqgfk$ctk_003@tbs.trieste.it> NNTP-Posting-Host: polbpc.tbs.trieste.it Keywords: NMR, software X-Newsreader: News Xpress Version 1.0 Beta #4 We are interested in software for 1D-2D NMR processing Bruker files (AC200 and AM300), working on PC with O.S. Windows or Solaris or Linux. Has someone any suggestion and experience on it? Thanks Our address is mailbox@poly01.tbs.trieste.it NMR and MRI Laboratory POLY-bios Research Center Area Science Park Padriciano 99 34012 Trieste Italy Tel.+39-40-3756606 Fax +39-40-7797091 From owner-structural-nmr@net.bio.net Tue May 07 23:00:00 1996 Path: biosci!galaxy.ucr.edu!library.ucla.edu!csulb.edu!newshub.csu.net!imci3!imci4!newsfeed.internetmci.com!news.kei.com!nntp.coast.net!news00.sunet.se!sunic!news99.sunet.se!news.uni-c.dk!news From: Mogens Kjaer Newsgroups: bionet.structural-nmr,sci.techniques.mag-resonance Subject: Re: Pronto 3D available Date: Mon, 06 May 1996 14:29:03 +0200 Organization: Carlsberg Laboratory Lines: 18 Message-ID: <318DF08F.41C6@unidhp.uni-c.dk> References: <31872D1E.41C6@unidhp.uni-c.dk> NNTP-Posting-Host: lgb277.ppp.uni-c.dk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) Xref: biosci bionet.structural-nmr:1263 sci.techniques.mag-resonance:1633 I wrote: > > Announcement: > ........ > Two binary distributions are available, one for Silicon > Graphics and one for Sun SPARC stations, running SunOS. A version for Solaris has been added. Mogens -- Mogens Kjaer, Carlsberg Laboratory, Dept. of Chemistry Gamle Carlsberg Vej 10, DK-2500 Valby, Denmark Phone: +45 33 27 53 25, Fax: +45 33 27 47 08 Email: carlmk@unidhp.uni-c.dk From owner-structural-nmr@net.bio.net Tue May 07 23:00:00 1996 Path: biosci!BIOC01.UTHSCSA.EDU!raman From: raman@BIOC01.UTHSCSA.EDU (C.S.RAMAN) Newsgroups: bionet.structural-nmr Subject: Re: apo-cytochrome c Date: 7 May 1996 18:36:05 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 93 Sender: daemon@net.bio.net Distribution: world Message-ID: <9605080131.AA16516@bioc01.uthscsa.edu> References: NNTP-Posting-Host: net.bio.net Dear Istvan: How is Princeton? :-> > I am looking for information on structural studies on apo-cytochrome c, > both by NMR and X-ray. I'll appreciate info on references as well as > personal info (if someone would be working on it right now). First, there are NO X-ray or NMR structures for apo-cytochrome c (apo-cytc). Reason: unlike apo-myoglobin which retains most of its structure in the absence of the heme moiety, apo-cytc is devoid of any structure. It can be considered a "random" coil. It appears that the covalently bound heme is absolutely necessary for the folding of cytochrome c. Evidence: CD, FTIR studies both indicate that apo-cytc lacks structure and is completely unfolded. Differential Scanning Calorimetry studies show that no energy is cosumed towards melting the protein and one can overlay the thermogram quite well with the baseline (after appropriate corrections for partial specific volume & the associated heat capacity change). Here are some of the references to get you started: I. Most of the structural work on apo-cytc has been done by Ben de Kruijff's group in collaboration with Derek Marsh and Rob Kaptein (Rijksuniversiteit, Utrecht). A tremendous amount of effort has gone into characterizing the interaction of apo-cytc with membranes and is quite thorough. I would strongly recommend obtaining a copy of the doctoral dissertation of: MARGOT SNEL which is an excellent resource for studies on Apo-cytc. If you need further details let me know. II. Biochim. Biophys. Acta 1078, 289-295 (1991) "Acid denatured apo-cytc is a random coil: evidence from small angle X-ray scattering and dynamic light scattering" is a very nice study by Damaschun et al., Berlin Buch. III. Potekin and Pfeil (1989) Biophysical Chemistry 34, 55-62 "Microcalorimetric studies of conformational transitions of ferricytochrome c in acidic solution" - see Fig. 4 on p.59. IV. Monoclonal antibodies elicited to apo-cytc by Hans Bosshard's group (Universit"at Z"urich) do show the presence of discontiguous epitopes indicative of fine structure undetectable via electronic CD or FTIR. See Eur. J. Biochem., 178, 219-224 (1988). V. Two independent studies have shown that both N and C terminal helices of cytochrome c when isolated in solution as free peptides, assume helical conformation in the presence of 2M Sodium sulphate. See Kuroda (1993) 32, 1219-1224 "Residual helical structure in the C-terminal fragment of cytochrome c"; and Wu et al., (1993) 32, 10271 "A non-covalent peptide complex as a model for an early folding intermediate of cytochrome c" The latter study was a collaboration between Heiner Roder (Fox Chase, Phila) and Janette Carey (Princeton - just down your alley!!). VI. An elegant study from Ben de Kruijff's group also provides the far-UV CD spectrum of apo-cytc and can be found in: Biochemistry, 31, 1636-1643 [1992] "A water-lipid interface induces a highly dynamic folded state in apocytochrome c and cytochrome c, which may prepresent a common folding intermediate" - see Fig 1. VII. Tony Fink (U. Cal., Santa Cruz) and Yuji Goto (Osaka U.,) have published some nice results on the folding properties of apo-cytochrome c under various conditions - salt, pH etc., ; see Hamada et al., (1993) Biochemistry 32, 10351-358 " Intermediate conformational states of apo-cytc". VIII. The preparation of large NMR quantities of apo-cytc can be tricky and if you are interested can contact me for hints on purification and storage. Since the apoprotein is very hydrophobic, aggregates if improperly handled. Best regards -raman -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ C.S.RAMAN _/ _/ Department of Biochemistry _/ _/ University of Texas Health Science Center _/ _/ 7703 Floyd Curl Drive _/ _/ San Antonio, TX 78284-7760 _/ _/ USA _/ _/ _/ _/ Tel: (210) 567-6623 _/ _/ Fax: (210) 567-6595 _/ _/ E-mail: raman@bioc01.uthscsa.edu _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ "The real problem in speech is not precise language. _/ _/ The problem is clear language." --Richard Feynman _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From owner-structural-nmr@net.bio.net Wed May 08 23:00:00 1996 Path: biosci!GATE.SINICA.EDU.TW!ccchuang From: ccchuang@GATE.SINICA.EDU.TW (Chyh-chong Chuang) Newsgroups: bionet.structural-nmr Subject: Access of The Complex Carbohydrate Structure Database at U. of Georgia Date: 8 May 1996 19:23:36 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <199603200122.LAA24367@pulse.health.adelaide.edu.au> NNTP-Posting-Host: net.bio.net Drear Netters: Could anyone tell me how to access the Complex Carbohydrate Structure Database (CCSD) at University of Georgia by internet (WWW, E-mail,..). I had done a search at yahoo but conld not find any server related with the Complex Carbohydrate Structure Database. Thank you for any help/suggestion. ccchuang ============================================ Chyh-Chong Chuang Institude of Biological Chemistry, Academia Sinica,Taipei, Taiwan -------------------------------------------- Phone: 886-2-7858981 ext 7091 Fax: 886-2-7883473 E-Mail: ccchuang@gate.sinica.edu.tw ============================================ From owner-structural-nmr@net.bio.net Wed May 08 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: Graham Barlow Newsgroups: bionet.structural-nmr Subject: Re: Pronto 3D available Date: 9 May 1996 17:34:47 +0100 Lines: 50 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4mt6r7$e1b@mserv1.dl.ac.uk> References: <9657192430.~INN-ILBa14669.bionet-news@dl.ac.uk> Reply-To: gkb1@unix.york.ac.uk Original-To: carlmk@unidhp.uni-c.dk (Mogens Kjaer), strnmr@bohr.york.ac.uk On May 7, 7:24pm, Mogens Kjaer wrote: > : l am interested to try Pronto 3D , > : but it is very difficult to get through netscape > : or lynx . So l ask if there is another way > : of transfer , like e-mail or ftp . > > : Please inform about this . > > : Thank you , > > Currently, this is the only way I have of distributing Pronto. > Hopefully, we will have our own internet connection set up in > half a year, this should make things a bit easier. > > If someone wants to mirror Pronto on a ftp site, please do this. > > Mogens Kjaer > Carlsberg Laboratory, Dept. of Chemistry >-- End of excerpt from Mogens Kjaer Pronto is now available by FTP from tesla.york.ac.uk in pub/pronto3d (URL is ftp://tesla.york.ac.uk/pub/pronto). All three binaries, the manual in html and the FAQ are there, here are the details: /pub/pronto3d 26 # ls -l total 9134 -r--r--r-- 1 ftp other 19773 May 9 16:16 faq960315.html -r--r--r-- 1 ftp other 2021 May 9 16:16 pronto3d.html -r--r--r-- 1 ftp other 3511 May 9 16:16 readme.html -r--r--r-- 1 ftp other 2385 May 9 16:16 readme.txt -r--r--r-- 1 ftp other 1993672 May 9 16:16 sgi.tar.gz -r--r--r-- 1 ftp other 1140910 May 9 16:16 solaris.tar.gz -r--r--r-- 1 ftp other 1513440 May 9 16:16 sunos.tar.gz These files are also available from my WWW pages at http://www.york.ac.uk/depts/chem/nmr/NMR_Links.html#specific Graham -- / Dr. Graham Barlow, NMR Service Manager \ / gkb1@york.ac.uk \ [ Dept. of Chemistry, Univ. of York, York, UK ][ Tel: 01904 432506 ] [ http://www.york.ac.uk/depts/chem/nmr ][ Mobile: 0402 181253 ] \ http://www.york.ac.uk/~gkb1/ / \ Fax: 01904 432516 / From owner-structural-nmr@net.bio.net Wed May 08 23:00:00 1996 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!scripps.edu!obelix!weber From: weber@obelix.scripps (Christoph Weber) Newsgroups: bionet.structural-nmr Subject: Re: Felix question Date: 9 May 1996 17:19:27 GMT Organization: The Scripps Research Institute Lines: 17 Message-ID: <4mt9ev$5s0@riscsm.scripps.edu> References: NNTP-Posting-Host: obelix.scripps.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Currently, there is no way to distinguish two chains in Felix, even though one uses Insight nomenclature like 1:arg_22:hb* as you indicated. A name like 2:arg_22:hb* would have no meaning to Felix, unfortunately. The workaround is to make a single virtual chain from 1 to 52 in your case. I'm not sure how you would treat the nonexistant bond between residues 26 and 27 during structure calculations. You will want to get in touch with support people at MSI for that. Hope that helps, Christoph | Christoph Weber Sen. Research Associate | Dept.of Molecular Biology, MB2 619-554-7283 or -8754 (phone) | The Scripps Research Institute 619-554-3757 (FAX) | La Jolla CA 92037 weber@scripps.edu | http://www.scripps.edu/~chazin/people/cw.html From owner-structural-nmr@net.bio.net Wed May 08 23:00:00 1996 Newsgroups: bionet.structural-nmr Path: biosci!daresbury!yama.mcc.ac.uk!bignews.shef.ac.uk!warwick!bsmail!zeus!bijt From: bijt@zeus.bris.ac.uk (J. Takei) Subject: Felix question Message-ID: Sender: usenet@uns.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: Thu, 9 May 1996 09:18:27 GMT Lines: 24 Hello all, I have a question and am hoping that somebody out there can help me. We are working on a synthetic peptide homo-dimer, 26 a.a. residue each. A monomer contains Cys at the position 23, and crosslinked to each other (am I clear?). My question is, how do you name different chains within Felix? Somehow I managed not to understand the Felix manual. The only thing I know is to name one like "1:arg_22:hb*" and that's it. We are hoping to get the structure of the peptide out of our NMR data. One interesting thing is whether we can make a coiled-coil 100% from NMR distance constraints or not. CD data of the crosslinke dimer looks it's a coiled-coil alpha helix. Hum..., we will see. Thanks in advance. Jiro Takei Department of Biochemistry University of Bristol j.takei@bris.ac.uk From owner-structural-nmr@net.bio.net Thu May 09 23:00:00 1996 Path: biosci!PHOENIX.PRINCETON.EDU!ipelczer From: ipelczer@PHOENIX.PRINCETON.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: NMR software Date: 9 May 1996 20:57:03 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 39 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <4mqgfk$ctk_003@tbs.trieste.it> NNTP-Posting-Host: net.bio.net There are a few options, but have you tried NUTS from Acorn NMR? I have no personal hands-on experience but I believe it is neat for most routine applications. Info and demo copies can be accessed by ftp (ftp.acornnmr.com) or on the Web (http://www.acornnmr.com) -- as I read their ad from "The NMR Newsletter" of Barry Shapiro [..."this is the place of the commercial"... :)] All the best, Istvan wwww,wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww Istvan Pelczer, Ph.D. Email: ipelczer@princeton.edu Senior NMR Spectroscopist Princeton University Department of Chemistry ph# (609) 258 2342 Frick Laboratory fax# (609) 258 6746 Washington Road Princeton, NJ 08544 On Wed, 8 May 1996 radoico@poly01.tbs.trieste.it wrote: > > We are interested in software for 1D-2D NMR processing Bruker files (AC200 > and AM300), working on PC with O.S. Windows or Solaris or Linux. > Has someone any suggestion and experience on it? > Thanks > > Our address is mailbox@poly01.tbs.trieste.it > > NMR and MRI Laboratory > POLY-bios Research Center > Area Science Park > Padriciano 99 > 34012 Trieste Italy > Tel.+39-40-3756606 > Fax +39-40-7797091 > > From owner-structural-nmr@net.bio.net Thu May 09 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!news.kth.se!news From: Arne Elofsson Newsgroups: bionet.structural-nmr Subject: Professorship in Structural Biology Date: 10 May 1996 16:37:01 +0200 Lines: 75 Message-ID: NNTP-Posting-Host: rune.biokemi.su.se Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: September Gnus v0.77/XEmacs 19.13 STOCKHOLM UNIVERSITY FACULTY OF NATURAL SCIENCES PROFESSOR OF STRUCTURAL BIOCHEMISTRY Stockholm University invites applications for a position as Professor of Structural Biochemistry at the Faculty of Natural Sciences. The successful applicant will be a member of the Department of Biochemistry, one of the largest within the Faculty of Natural Sciences. The Department is involved in undergraduate teaching at all levels and has an extensive graduate program, at present involving 55 students. The research projects include Molecular Bioenergetics especially Photosynthesis (B. Andersson), Membrane Protein Insertion & Folding (G. von Heijne), Structure & Function of Proteins (M. Saraste), Biochemical Toxicology (J. DePierre), Protein Trafficing, Mitochondrial Biogenesis, Genetic Modification of Starch Biosynthesis and Nitrogen Fixation. The Department is well equipped and located with the other departments of chemistry and Life Sciences in the Arrhenius Laboratories for Natural Sciences. The Arrhenius Laboratories are situated in the northern part of the University Campus at Frescati, close to the centre of Stockholm. When appointing a professor at public universities in Sweden, emphasis is given to excellence in both research and teaching. Consideration is also given to administrative skills, in particular management. Proficiency in Swedish (Scandinavian) or English is necessary. The appointee will be expected to contribute to teaching at the undergraduate level as well as to the supervision of doctoral students. Salary is negotiable. The University is an Equal Opportunities employer, and since most professors at the Faculty of Natural Sciences are men, applications from female candidates are particularly welcome. Residence in the Stockholm area will be expected, at least after an initial start-up period. Informal inquiries may be made to professor Bertil Andersson, phone +46 8 16 29 10, e-mail bertil@biokemi.su.se or to the Head of the Department professor Stefan Nordlund, phone +46 8 16 29 32, e-mail stefan@biokemi.su.se Applications, quoting reference no 611-0000/96, should be sent to the Registrar, Staff Management Division, Stockholm University, S-106 91 Stockholm, Sweden. They must reach the Registrar's Office no later than 31 May 1996. The following items, all in four copies, should be included: 1. Curriculum vitae 2. Bibliography (numbered) 3. Description of the candidate's research achievements, teaching experience and management (5-10 pages). A guidance regarding the presentation of teaching qualifications may be obtained from Ulf Lindgren of the Staff Management Division, phone +46 8 16 33 22, fax +46 8 612 59 60. 4. Photocopies of relevant graduation diplomas. 5. Research publications of the candidate's own choice, numbered according to the bibliography. Items 1 and 2 should research the University before the application period expires. Items 3 and 4, and one copy of each item 5 should arrive no later than June 21, 1996. The three additional copies of item 5 are to be sent later, upon notification from the University, to the three Expert Members of the Appointment Board. -- ----------------------------------------------------------------- From: Arne Elofsson Email: arne@rune.biokemi.su.se Tel:+46(0)8-161553 WWW: http://www.biokemi.su.se/~arne/ From owner-structural-nmr@net.bio.net Sun May 12 23:00:00 1996 Path: biosci!MAIL.UNMC.EDU!BGMEINER From: BGMEINER@MAIL.UNMC.EDU (Bill Gmeiner) Newsgroups: bionet.structural-nmr Subject: pH electrode to fit 5mm NMR tube -Reply Date: 13 May 1996 06:06:59 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net >>> Kristy Downing 05/13/96 05:21am >>> I would be very appreciative if anyone who has bought a pH electrode with diameter small enough to fit into a 5mm NMR tube could let me know their supplier. Cole-Parmer is one source of pH electrodes for 5 mm NMR tubes. I am searching for a pH electrode for a 3 mm NMR tube if anyone knows of their availability. Bill Gmeiner From owner-structural-nmr@net.bio.net Sun May 12 23:00:00 1996 Path: biosci!rutgers!uwm.edu!lll-winken.llnl.gov!nntp.coast.net!howland.reston.ans.net!swrinde!newsfeed.internetmci.com!in2.uu.net!fdn.fr!jussieu.fr!Newsmaster From: Michel SEIGNEURET Newsgroups: bionet.structural-nmr Subject: Re: pH electrode to fit 5mm NMR tube Date: 13 May 1996 15:51:02 GMT Organization: Universites Paris VI/Paris VII - France Lines: 12 Message-ID: <4n7lp6$45o@vishnu.jussieu.fr> References: <4n72fn$n4o@news.ox.ac.uk> NNTP-Posting-Host: mood.biophy.jussieu.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; IRIX 5.3 IP20) To: kristy@bioch.ox.ac.uk X-URL: news:4n72fn$n4o@news.ox.ac.uk We have used 5mm diameter electrodes for NMR tubes from Wilmad and from Aldrich. I would recommend the former: it is more fragile and more expensive but lasts longer if treated with care. Several types of connectors are available. Good luck. Michel Michel Seigneuret Lab. de Biophysique Cellulaire et RMN Universite Paris 7 France From owner-structural-nmr@net.bio.net Sun May 12 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: Marc-Andre.Delsuc@tome.cbs.univ-montp1.fr (Marc-Andre Delsuc) Newsgroups: bionet.structural-nmr Subject: Re : NMR software Date: 13 May 1996 13:43:50 +0100 Lines: 32 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4n7aq6$aa5@mserv1.dl.ac.uk> X-Sender: mad@tome.cbs.univ-montp1.fr Original-To: str-nmr@dl.ac.uk, mailbox@poly01.tbs.trieste.it Recently you wrote : >We are interested in software for 1D-2D NMR processing Bruker files (AC200 >and AM300), working on PC with O.S. Windows or Solaris or Linux. >Has someone any suggestion and experience on it? >Thanks >Our address is mailbox@poly01.tbs.trieste.it > >NMR and MRI Laboratory >POLY-bios Research Center >Area Science Park Padriciano 99 >34012 Trieste Italy >Tel.+39-40-3756606 >Fax +39-40-7797091 You may also try our NMR-processing software called Gifa that works under Linux (among other Unix platforms). It is free of charge for academic laboratories and available at : ftp://tome.cbs.univ-montp1.fr check also : http://tome.cbs.univ-montp1.fr/Posters/jluc_post/general.html for a general presentation of the software. _________________________________________________________________________ Marc-Andre' Delsuc Centre de Biochimie Structurale Marc-Andre.Delsuc@cbs.univ-montp1.fr Faculte de Pharmacie tel : (33) 67 04 34 36 15 av, Charles Flahault fax : (33) 67 52 96 23 34060 Montpellier cedex www : http://tome.cbs.univ-montp1.fr FRANCE From owner-structural-nmr@net.bio.net Sun May 12 23:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news.ox.ac.uk!nmrl.ocms!kristy From: kristy@bioch.ox.ac.uk (Kristy Downing) Newsgroups: bionet.structural-nmr Subject: pH electrode to fit 5mm NMR tube Date: 13 May 1996 10:21:43 GMT Organization: Oxford University Lines: 15 Message-ID: <4n72fn$n4o@news.ox.ac.uk> NNTP-Posting-Host: nmrl.ocms.ox.ac.uk Keywords: pH, electrode, NMR I would be very appreciative if anyone who has bought a pH electrode with diameter small enough to fit into a 5mm NMR tube could let me know their supplier. Thank you, Kristy Downing -- Dr. A. Kristina Downing e-mail: kristy@bioch.ox.ac.uk University of Oxford Oxford Centre for Molecular Sciences fax. +44 (0) 1865-275253 New Chemistry Laboratory tel. +44 (0) 1865-275956 South Parks Road, Oxford OX1 3QT ENGLAND From owner-structural-nmr@net.bio.net Sun May 12 23:00:00 1996 Path: biosci!PHOENIX.PRINCETON.EDU!ipelczer From: ipelczer@PHOENIX.PRINCETON.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: pH electrode to fit 5mm NMR tube Date: 13 May 1996 08:17:53 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <4n72fn$n4o@news.ox.ac.uk> NNTP-Posting-Host: net.bio.net I have seen pH electrode which fits a 5mm NMR tube in Wilmad's catalogue (now they have a www site, too, an interactive catalogue: www.wilmad.com). Good luck, Istvan wwww,wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww Istvan Pelczer, Ph.D. Email: ipelczer@princeton.edu Senior NMR Spectroscopist Princeton University Department of Chemistry ph# (609) 258 2342 Frick Laboratory fax# (609) 258 6746 Washington Road Princeton, NJ 08544 From owner-structural-nmr@net.bio.net Mon May 13 23:00:00 1996 Path: biosci!INTREPID.CHM.JHU.EDU!rlk From: rlk@INTREPID.CHM.JHU.EDU (rlk) Newsgroups: bionet.structural-nmr Subject: Re:pH electrode to fit 5mm NMR tube Date: 14 May 1996 14:05:55 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: <9605142129.AA23356@intrepid.chm.jhu.edu> NNTP-Posting-Host: net.bio.net Microelectrodes, Inc. phone 601.668.0690 fax 603.668.7926 40 Harvey Rd. Bedford, NH 0311-6805 USA hope that helps -ron From owner-structural-nmr@net.bio.net Mon May 13 23:00:00 1996 Path: biosci!biosci!not-for-mail From: torda@rsc.anu.edu.au (Andrew Torda) Newsgroups: bionet.molec-model,bionet.molecules.peptides,bionet.info-theory,bionet.molbio.proteins,sci.chem,bionet.structural-nmr Subject: Post-doc in computational chemistry, Canberra, Australia Date: 13 May 1996 22:07:01 -0700 Organization: Research School of Chemistry, Australian National University Lines: 69 Sender: daemon@net.bio.net Distribution: world Message-ID: <4n24rj$8v6@manuel.anu.edu.au> Reply-To: Andrew.Torda@anu.edu.au NNTP-Posting-Host: net.bio.net Xref: biosci bionet.molec-model:925 bionet.molecules.peptides:314 bionet.info-theory:4122 bionet.molbio.proteins:7885 sci.chem:56139 bionet.structural-nmr:1276 POST DOCTORAL POSITION in Canberra, Australia with Andrew Torda Each year, the Research School of Chemistry at the Australian National University has a series of post-doctoral fellowships awarded on a competitive basis. Applications for the current round will be taken until about June 1, 1996. There are positions in several groups. The research group of Andrew Torda is oriented towards biomolecular calculation and simulation. We are working in areas such as low-resolution (protein fold recognition) force fields, refinement of experimental structures using MD simulation and lattice models of protein-lipid interactions. All the projects in the group involve coding - not just applications. It would be an advantage to have a reasonable knowledge of data structures and algorithms and programming experience in a civilized language (not fortran). Currently, possible projects would be centred around some new algorithms for aligning amino acid sequences to structures, based on the force fields we have developed. We are also looking at protein fold classification using topological and graph theory methods. Projects are negotiable. Salary is about A$38 000/year, initially for two years with a possible extension to a third year. The university will provide return air-fares to successful candidates and family. There is a housing office to help find accommodation. The Research School of Chemistry is part of the Institute of Advanced Studies which runs special research schools, in parallel to the normal teaching schools, and without any undergraduate teaching duties. The university is in the centre of Canberra (the nation's capital). Given the research orientation of the school, there is a lively academic environment. We have close contacts with the school's other theoretical groups in statistical mechanics, quantum chemistry and chemical physics. From the point of view of experimental groups, we maintain close ties to the school's NMR, X-ray crystallography and molecular biology groups. For further information about the possible projects of interest to the Torda group, contact Andrew Torda directly (Andrew.Torda@anu.edu.au) or slow mail: Andrew Torda, Research School of Chemistry Australian National University ACT, 0200 Australia or even fax: +61-6-249 0750 For information about the other groups and application forms, email the school secretary directly at schlsec@rsc.anu.edu.au and ask for a post-doctoral application pack to be mailed to you. To have a look at an uninformative home page with a low-resolution and uninteresting (but obligatory) photo, point your browser at http://rsc.anu.edu.au/~torda For the school's home page: http://rsc.anu.edu.au/Home.html From owner-structural-nmr@net.bio.net Mon May 13 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: nmrorg@bellatrix.pcl.ox.ac.uk (nmrorg) Newsgroups: bionet.structural-nmr Subject: OPEN: SECOND ELECTRONIC NMR POSTER SESSION Date: 14 May 1996 23:13:47 +0100 Lines: 33 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4nb0ir$1b5@mserv1.dl.ac.uk> Original-To: str-nmr@dl.ac.uk NMR EPS-2: SECOND ELECTRONIC NMR POSTER SESSION Following up on last year's First Electronic NMR Poster session (see http://bellatrix.pcl.ox.ac.uk/nmr/poster.html or mirror sites listed there) a Second Electronic Poster Session on NMR is being held from June 17 to June 21. Participants can mount an NMR-related poster on the World Wide Web and engage in interactive discussions on the poster material and current NMR technology during the week. The registration facility for NMR EPS-2 is now open at: http://bellatrix.pcl.ox.ac.uk/nmr96/ If you fill out the registration form located there you will receive a userid and password which you may use to access the event. Potential commercial exhibitors or sponsors should contact us directly over arrangements for their displays. To present a poster you need to send the following pieces of information by June 1 to nmrorg@bellatrix.pcl.ox.ac.uk: 1) The Web site location (URL) where you will serve your poster. 2) Your email address for correspondence. 3) Your abstract stating title, list of authors, institutions, and mailing address. If you do not have the ability to mount a poster on the Web yourself please email nmrorg@bellatrix.pcl.ox.ac.uk. We should be able to aid you in loading a poster. From owner-structural-nmr@net.bio.net Mon May 13 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!newsfeed.sunet.se!news01.sunet.se!sunic!news99.sunet.se!umdac!news From: peterl@chem.umu.se (Peter Lundberg) Newsgroups: bionet.structural-nmr Subject: Re: pH electrode to fit 5mm NMR tube Date: 14 May 1996 14:40:38 GMT Organization: Phys Chem, University of Umea, Sweden Lines: 29 Sender: -Not-Authenticated-[5799] Message-ID: <4na616$4lo@studium.student.umu.se> References: <4n72fn$n4o@news.ox.ac.uk> 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. In article <4n72fn$n4o@news.ox.ac.uk> kristy@bioch.ox.ac.uk (Kristy Downing) writes: > I would be very appreciative if anyone who has bought a pH electrode with > diameter small enough to fit into a 5mm NMR tube could let me know their supplier. The ones we use here (the length of the narrow section is 176 mm) are made by Ingold (Ingold Messtechnik Gmbh, D-6374 Steinbach/Ts, Germany. They are labeled 6030-112(?)-BNC, Cat no 414023002 1. The electrodes are filled with 3 M KCl saturated with AgCl. 2. I have also 'Electrode cleaner' (protein contaminations) containing 'pepsin/HCl', 3. and 'Diaphragm cleaner' (sulfide contaminations - black diaphragms) containing thiourea/HCl. The latter works well with my samples (when the electrode 'efficiency' drops too much. I don't know if this is the one sold by Wilmad or Aldrich. We got it from the local Ingold source. Just my 2 oere. 73, Peter O==O ================================== O==O O==O Peter Lundberg O==O O==O Email: peterl@chem.umu.se O==O O==O ============761.91141============= O==O From owner-structural-nmr@net.bio.net Mon May 13 23:00:00 1996 Path: biosci!agate!cocoa.brown.edu!news From: Pascal_Bochet@brown.edu (Pascal_Bochet) Newsgroups: bionet.structural-nmr Subject: rasmol and NMR structures Date: 14 May 1996 21:21:37 GMT Organization: Brown University, Providence, RI -- USA Lines: 7 Message-ID: <4nath1$i8t@cocoa.brown.edu> Reply-To: Pascal_Bochet@brown.edu NNTP-Posting-Host: 128.148.53.52 Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.7 Hello Does anybody here know how to view PDB structures from files containing several NMR structures? Rasmol which I use on a PC only shows me the first one. Thank you for your help. Pascal_Bochet@brown.edu From owner-structural-nmr@net.bio.net Tue May 14 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!news.kth.se!news From: Arne Elofsson Newsgroups: bionet.structural-nmr Subject: Winterschool in biophysical aspects of protein folding Date: 15 May 1996 20:08:32 +0200 Lines: 42 Message-ID: NNTP-Posting-Host: assar.biokemi.su.se Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: September Gnus v0.84/XEmacs 19.13 1997 WINTER SCHOOL IN BIOPHYSICS BIOPHYSICAL ASPECTS OF PROTEIN FOLDING. APRIL 1- 4 1997 ------------------------------------------------------------------------ See http://www.biokemi.su.se/~arne/kurser/winterschool.html for more info As a part of the Stockholm Biophysics Graduate School program we will organize a "Winter School in Biophysics" in the Swedish mountain regions (Storlien). The theme for the 1997 winter school will be "Biophysical Aspects of Protein Folding". The 1997 Stockholm Biophysics will be held in the Swedish mountain regions during week 14 (April 1-4). There will be time for scientific discussions as well as for relaxing activities. INVITED LECTURERS ----------------- Alexei Finkelstein, P. Privalov Alan R. Fersht Ken Dill Sheena Radford. Nalle Jonsson PRICE ------ 2500:- SEK (for late applications (after 1/10 3500:- SEK) (1SEK=$6.70 1 May 1996) Including registration, accommodation in double room (Tuesday-Saturday/Sunday) and meals (Monday dinner until Sunday breakfast). The number of participants will be limited to approximately 50 participants. Extra nights are available for approximately 300:- SEK per night. (accomodation only) An unknown number of traveling grants will be available for graduate students (and postdocs) that apply early. -- ----------------------------------------------------------------- From: Arne Elofsson Email: arne@rune.biokemi.su.se Tel:+46(0)8-161553 WWW: http://www.biokemi.su.se/~arne/ From owner-structural-nmr@net.bio.net Tue May 14 23:00:00 1996 Path: biosci!rutgers!csn!nntp-xfer-1.csn.net!imci3!imci2!news.internetMCI.com!newsfeed.internetmci.com!uuneo.neosoft.com!news.uh.edu!news.uth.tmc.edu!bmb155.med.uth.tmc.edu!user From: tliang@utmmg.med.uth.tmc.edu (T. Chyau Liang) Newsgroups: bionet.structural-nmr Subject: Re: rasmol and NMR structures Date: Wed, 15 May 1996 09:00:54 +0100 Organization: U. Texas-Houston Lines: 19 Message-ID: References: <4nath1$i8t@cocoa.brown.edu> NNTP-Posting-Host: bmb155.med.uth.tmc.edu Mime-Version: 1.0 Content-Type: text/plain;charset=US-ASCII Content-Transfer-Encoding: 7bit Try PDB_Viewer, which can display multiple structures but doesn't give you nice displays as RasMol does. You can get it at: http://expasy.hcuge.ch/swissmod/Swiss-PdbViewer/mainpage.html Hope this helps. T. Chyau Liang U. Texas-Houston In article <4nath1$i8t@cocoa.brown.edu>, Pascal_Bochet@brown.edu wrote: > Hello > Does anybody here know how to view PDB structures from files containing > several NMR structures? Rasmol which I use on a PC only shows me the first > one. > Thank you for your help. > Pascal_Bochet@brown.edu From owner-structural-nmr@net.bio.net Wed May 15 23:00:00 1996 Newsgroups: bionet.structural-nmr Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!newsflash.concordia.ca!utcsri!utgpu!utinfo!bloch.med.utoronto.ca!gardner From: gardner@bloch.med.utoronto.ca (Kevin Gardner) Subject: Re: rasmol and NMR structures X-Nntp-Posting-Host: bloch.med.utoronto.ca Message-ID: Sender: news@utcc.utoronto.ca (News) Organization: UTCC Campus Access X-Newsreader: TIN [version 1.2 PL2] References: <4nath1$i8t@cocoa.brown.edu> Date: Thu, 16 May 1996 00:45:38 GMT Lines: 29 In article <4nath1$i8t@cocoa.brown.edu>, Pascal_Bochet@brown.edu wrote: > Does anybody here know how to view PDB structures from files containing > several NMR structures? Rasmol which I use on a PC only shows me the first > one. Beginning with Rasmol 2.6, the ability to read and analyze NMR models from a single PDB file was built in. The command is: load nmrpdb The selection facility has been refined as well to let the user pick atoms/residues, etc from specific models. There are several other nice changes as well (cartoon diagrams; interactive determination of distances, angles, etc). For more details check out the Rasmol WWW page @ UMass, in particular the page describing the changes to RasMol 2.6: http://www.umass.edu/microbio/rasmol/getras.htm Kevin -- ************************************************************************* Kevin Gardner gardner@redfield.med.utoronto.ca University of Toronto http://abragam.med.utoronto.ca/~gardner Dept. of Medical Genetics phone: 416-978-0642/FAX: -6885 --> NMR Electronic Poster Session 2: June 17-21, 1996 <-- --> http://bellatrix.pcl.ox.ac.uk/nmr96/Welcome.html <-- From owner-structural-nmr@net.bio.net Wed May 15 23:00:00 1996 Path: biosci!daresbury!hgmp.mrc.ac.uk!sunsite.doc.ic.ac.uk!qmw!alpha!ugca501 From: ugca501@alpha.qmw.ac.uk (Nathalie Mahieu) Newsgroups: bionet.structural-nmr Subject: Re: pH electrode to fit 5mm NMR tube Date: 16 May 1996 08:05:35 GMT Organization: Chemistry Dpt, QMWC, London Lines: 15 Message-ID: <4nenkf$k6v@epsilon.qmw.ac.uk> References: <4n72fn$n4o@news.ox.ac.uk> Reply-To: n.mahieu@qmw.ac.uk NNTP-Posting-Host: alpha.qmw.ac.uk X-Newsreader: TIN [version 1.2 PL2] On 13 May 1996 10:21:43 GMT, Kristy Downing (kristy@bioch.ox.ac.uk) wrote: > I would be very appreciative if anyone who has bought a pH electrode with > diameter small enough to fit into a 5mm NMR tube could let me know their supplier. I have used one from Russel, Auchtermuchty, Fife, Scotland, ref. TRCMW757/ 3.7/180. It costs 100 UK pounds. Nathalie -- *************************************************************************** * Nathalie Mahieu * sicut erat in principio * * N.Mahieu@qmw.ac.uk * et nunc et in saecula saeculorum * *************************************************************************** Durga (Doudou): EU (B+O)t G 7 X L W+ I T++ E++ H++/+++ V+ Q- P+ B+ From owner-structural-nmr@net.bio.net Thu May 16 23:00:00 1996 Path: biosci!biosci!not-for-mail From: Reto Koradi Newsgroups: bionet.structural-nmr,bionet.biophysics,bionet.molbio.proteins,bionet.molec-model,bionet.software,comp.graphics.visualization Subject: ANNOUNCE: MOLMOL 2.2.0 Date: 16 May 1996 20:59:01 -0700 Organization: Molekularbiologie & Biophysik, ETH Zurich Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: <4ncvds$b84@elna.ethz.ch> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.structural-nmr:1287 bionet.biophysics:2021 bionet.molbio.proteins:7920 bionet.molec-model:930 bionet.software:15517 comp.graphics.visualization:7630 Release 2.2.0 of MOLMOL is now available. Check the web pages at: http://www.mol.biol.ethz.ch/wuthrich/software/molmol/ for detailed information, a list of changes, and instructions about downloading. Precompiled versions are available for SGI (IRIX 4.0.5 and 5.3), AIX, Digital UNIX, Solaris 2.4 and Linux. Source code is also available. MOLMOL is a program for display and analysis of macromolecular structures. It was developed as a joint project between BRUKER/Spectrospin and the group of Prof. Wuthrich at the Institut fuer Molekularbiologie und Biophysik, ETH Zurich. From owner-structural-nmr@net.bio.net Thu May 16 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!vixen.cso.uiuc.edu!newsrelay.iastate.edu!news.iastate.edu!baker From: baker@iastate.edu (Wayne R. Baker) Newsgroups: bionet.molec-model,bionet.structural-nmr,bionet.biophysics,sci.techniques.mag-resonance Subject: NMR Spectroscopist Position Available Date: 17 May 1996 20:56:07 GMT Organization: Biochemistry & Biophysics, Iowa State University Lines: 32 Message-ID: <4nip57$jnf@news.iastate.edu> Reply-To: hjfromm@iastate.edu NNTP-Posting-Host: pv0a0b.vincent.iastate.edu Xref: biosci bionet.molec-model:932 bionet.structural-nmr:1289 bionet.biophysics:2026 sci.techniques.mag-resonance:1658 The Department of Biochemistry and Biophysics, Iowa State University, seeks an NMR specialist to perform routine maintenance and to train users, as well as to design, implement and analyze experiments on a Varian Unity 500 NMR. A Ph.D. or the equivalent is required. Experience in biophysics, biochemistry or physical chemistry, along with expertise in current application of NMR to biological molecules is essential. Collaborative research using NMR and other biophysical techniques is encouraged. Send C.V. and three letters of reference to: Dr. Herbert J. Fromm c/o Stacey Poling Department of Biochemistry & Biophysics 1210 Molecular Biology Building Iowa State University Ames IA 50011-3260 Phone 515 294 6116 Deadline for receiving applications is June 30, 1996. For additional information about the Department and Iowa State University, see http://molebio.iastate.edu/bbhtml/homepage.htm Iowa State University is an Affirmative Action/Equal Opportunity Employer. Applications from women and minority candidates are especially encouraged. -- Wayne Baker (baker@iastate.edu) He who has a why to live for 4288 Molecular Biology Building can bear almost any how. Iowa State University --Nietzsche From owner-structural-nmr@net.bio.net Thu May 16 23:00:00 1996 Path: biosci!RIGEL.BIOCHEM.UALBERTA.CA!kkr From: kkr@RIGEL.BIOCHEM.UALBERTA.CA (Krishna Rajarathnam) Newsgroups: bionet.structural-nmr Subject: (none) Date: 17 May 1996 16:53:30 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: <199605172352.RAA05631@rigel.biochem.ualberta.ca> NNTP-Posting-Host: net.bio.net subscribe ________________________________________________________________________ Krishna Rajarathnam PENCE 713 Heritage Building University of Alberta Edmonton, Alberta Canada T6G 2S2 Phone:(403) 492 7540 FAX:(403) 492 1473 From owner-structural-nmr@net.bio.net Thu May 16 23:00:00 1996 Path: biosci!RUTCHEM.RUTGERS.EDU!jwest From: jwest@RUTCHEM.RUTGERS.EDU (John Westbrook) Newsgroups: bionet.structural-nmr Subject: New WWW Interface to the Nucleic Acid Database Date: 17 May 1996 13:42:11 -0700 Organization: Rutgers University Department of Chemistry Lines: 37 Sender: daemon@net.bio.net Distribution: world Message-ID: <319CE20C.167E@rutchem.rutgers.edu> NNTP-Posting-Host: net.bio.net New WWW Interface to the Nucleic Acid Database (NDB) --------------------------------------------------- The Nucleic Acid Database (NDB) Project assembles and distributes structural information about nucleic acids. It is a repository for the coordinates of nucleic acid-containing crystal structures and provides information of interest to researchers in the field, including standard geometry files for use in refinement and molecular modeling programs. The NDB can be accessed on the World Wide Web at: http://ndbserver.rutgers.edu/ and http://www.ebi.ac.uk/NDB/ (NDB mirror site at the European Bioinformatics Institute) A query interface that allows users to search the NDB is available at these WWW sites. The latest version of this interface provides several new options for using the database, including a full structure selection and report generation interface, a simple structure selection form for making quick selections, and a forms interface for creating status reports on the NDB holdings. Tutorials for using this interface are also available at these sites. We are very interested in getting your feedback. If you have any questions about the NDB or the new interface, or if you uncover a bug, please let us know by sending mail to ndbadmin@ndbserver.rutgers.edu. -- ****************************************************************** * John Westbrook Ph: (908) 445-4290 * * Department of Chemistry Fax: (908) 445-4320 * * Rutgers University * * PO Box 939 e-mail: jwest@ndb.rutgers.edu * * Piscataway, NJ 08855-0939 * ****************************************************************** From owner-structural-nmr@net.bio.net Sat May 18 23:00:00 1996 Path: biosci!PHOENIX.PRINCETON.EDU!ipelczer From: ipelczer@PHOENIX.PRINCETON.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: used equipment (fwd) Date: 19 May 1996 16:21:39 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 83 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Netters, Let me forward to you a message from Phil Borer from SU about some used NMR equipment for sale. Istvan wwww,wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww Istvan Pelczer, Ph.D. Email: ipelczer@princeton.edu Senior NMR Spectroscopist Princeton University Department of Chemistry ph# (609) 258 2342 Frick Laboratory fax# (609) 258 6746 Washington Road Princeton, NJ 08544 ---------- Forwarded message ---------- Date: Thu, 16 May 1996 16:33:33 -0400 (EDT) From: Philip Borer For Sale: Used NMR Instruments and Related Items Reasonable offers considered for complete systems or individual components Availability ~ Sep - Nov 1996 Contact Phil Borer (315 443 5925; pnborer@mailbox.syr.edu) or Debbie Kerwood (315 443 5932; kerwood@odo.nsc.syr.edu) at Chemistry Department, Syracuse University, Syracuse, NY 13244-4100 1. 300 MHz NMR console & magnet GE QE-300, purchased new in 1985 Includes: 5 mm 1H/13C dual probe Variable temperature unit Electronic components Zeta plotter Fully operational $25,000/offer + shipping + de-energization cost 2. 250 MHz NMR console & magnet Cryomagnet Systems CM-250, purchased new in 1982 Includes: Bruker Aspect 3000 computer Bruker pulse programmer Two PTS-500 frequency synthesizers PTS-160 lock frequency synthesizer (needs ~$800 repair) 50W and 3W linear amplifiers 5 mm 1H/Broadband probe with quartz insert for observing 11B 10 mm 1H/Broadband probe Variable temperature unit Needs minor repair to make it fully operational $10,000/offer + shipping + de-energization cost 3. TecMag Scorpio S-16 upgrade for GE GN-500, purchased in 1993 for $40k Includes: Pulse programmer Dek-Kit proton and X-nucleus broadband decoupler Amplifiers PTS-500 frequency synthesizer Macintosh Centris 650 computer Fully operational with GN-500 components, item 4, below $10,000/offer + shipping 4. GE GN-500 console components, purchased new in 1985 Includes: Lock, transceiver, audio filter, decoupler modules Power amplifier Probe preamplifiers Variable temperature unit Seven GE and custom-built probeheads Nic 1280 mother board $10,000/offer + shipping 5. Frequency synthesizer (PTS 310) purchased in 1993 for $5k $3,000/offer 6. Power amplifier (Amer. Microwave Tech. M3206) purchased in 1993 for $5k $2,000/offer 7. He leak detector, forepump and diffusion pump (Alcatel ASM-10) rarely used $6,000/offer From owner-structural-nmr@net.bio.net Sun May 19 23:00:00 1996 Path: biosci!sfu.ca!dnaugler From: dnaugler@sfu.ca (David Naugler) Newsgroups: bionet.structural-nmr Subject: Unix pipes in multidimensional NMR data acquisition Date: 19 May 1996 20:38:09 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 44 Sender: daemon@net.bio.net Distribution: world Message-ID: <199605200334.DAA27454@beaufort.sfu.ca> NNTP-Posting-Host: net.bio.net Our Bruker AMX600 is set up to acquire data in only one way, with all multidimensional data stored in a serial file. This imposes severe restrictions when setting up an experiment. There must be a better way. I can imagine a setup that can be described using Unix pipes. I would like to know if anything like this has been implemented. I believe it can be shown that digital oversampling can somewhat improve the dynamic range, signal to noise and flatness of the baseline which is important in nD NMR. Providing permanent storage for all that data imposes an impossible limitation however. Unix pipes are a nice way of processing large amounts of data without requiring large amounts of temporary storage. It must be an important concept because one NMR processing package is called NMRpipe. While Bruker's method of storing large serial files works OK for 2D work, it can be argued that the method is fundamentally unsound for nD work. The correct way (possibly the DMX way) can be represented by pipes: PP | TD | t3FT | PK | ST > file for a 3D experiment, where, in the above: PP = nD Pulse program producing stream of FID's, with digital oversampling at ~ 100,000 complex samples per second. TD = time domain processing e.g. digital filtering for removal of solvent signal. t3FT = Fourier Transform in t3. PK = phase correction. ST = extraction of strip transform and other data compression. file = a smaller matrix (t2, t1) file of complex (compressed) spectra of the region of interest. Has anyone implemented a data acquisition scheme like this? Can this scheme be implemented on a Bruker AMX600? David Naugler Institute of Molecular Biology and Biochemistry Simon Fraser University From owner-structural-nmr@net.bio.net Mon May 20 23:00:00 1996 Path: biosci!rutgers!uwm.edu!newsfeed.internetmci.com!usenet.eel.ufl.edu!bofh.dot!warwick!qmw!news From: john white Newsgroups: bionet.structural-nmr Subject: Re:pH electrode to fit 5mm NMR tube Date: 20 May 1996 12:42:53 GMT Organization: The Royal London Hospitals Trust Lines: 5 Message-ID: <4nppcd$n6@epsilon.qmw.ac.uk> References: <9605142129.AA23356@intrepid.chm.jhu.edu> NNTP-Posting-Host: n97-12.lhmc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 16bit) aldrich do one 115.00 pounds sterling (cat .no. Z11,343-3 or Z11,344-1 depending on connections) From owner-structural-nmr@net.bio.net Mon May 20 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!newsfeed.sunet.se!news01.sunet.se!sunic!news99.sunet.se!columba.udac.uu.se!nostromo.bmc.uu.se!user From: gerard@xray.bmc.uu.se (Gerard Kleywegt) Newsgroups: bionet.software.x-plor,bionet.xtallography,bionet.structural-nmr,bionet.molec-model Subject: 8 Research Studentships (Structural Biology) available in Sweden Date: 20 May 1996 15:01:19 GMT Organization: Uppsala University Lines: 46 Message-ID: Reply-To: alwyn@xray.bmc.uu.se NNTP-Posting-Host: nostromo.bmc.uu.se X-Newsreader: Value-Added NewsWatcher 2.0d31h+ Xref: biosci bionet.software.x-plor:541 bionet.xtallography:2590 bionet.structural-nmr:1294 bionet.molec-model:935 SWEDISH STRUCTURAL BIOLOGY NETWORK ********************************** The Swedish Structural Biology Network is a five-year project funded by the Strategic Research Foundation with an annual budget of more than ten million Swedish Crowns. Its aim is to strengthen the strategic value of Structural Biology in Sweden. The Network consists of the Swedish academic centres involved in protein and DNA crystallography, NMR spectroscopy and modelling. The Network fosters collaboration in matters of research, education and knowledge transfer, and funds many new academic positions. At present, candidates are sought for 8 RESEARCH STUDENTSHIPS. Each position will be associated with a Swedish University, will be funded for a period of 4 years, and is expected to result in a doctoral dissertation. Candidates are required to have successfully completed undergraduate studies in a relevant area (e.g., molecular biology, biochemistry, biophysics). Studentships are available for the following research projects: (1) Structural studies on the Platelet-Derived Growth Factor Receptor and its complex with Platelet-Derived Growth Factor (X-ray) (2) Ribonucleotide Reductase holoenzyme complexes (X-ray) (3) Structure of viruses and viral components (X-ray) (4) Protein secretion (X-ray) (5) Ribosomal proteins and factors (X-ray) (6) Protein-protein interactions: structural studies of Bruton's Tyrosine Kinase(NMR) (7) Expression and NMR analysis of triply-labelled proteins (NMR) (8) Initiation of blood coagulation: interaction between Factor VII and Tissue Factor,and the role of non-catalytic domains (NMR) More information about these positions may be obtained from the Program Director: Prof. T.A. Jones, Department of Molecular Biology, Biomedical Centre, Uppsala University, Box 590, S-751 24 Uppsala (Fax: + 46 - 18 - 53 69 71, E-mail: alwyn@xray.bmc.uu.se). More information about the Structural Biology Network is availableon the World Wide Web, at URL: http://onyx.bmc.uu.se/~gerard/srf/srf.html Female candidates are expressly encouraged to apply. The closing date for applications is 15 June, 1996. -------------------------------------------------------------------- Gerard J. Kleywegt Department of Molecular Biology, Biomedical Centre Uppsala University, Uppsala, SWEDEN From owner-structural-nmr@net.bio.net Tue May 21 23:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.structural-nmr Subject: IMPORTANT - BIOSCI Fundraising Update! Date: 22 May 1996 02:00:50 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 154 Sender: daemon@net.bio.net Distribution: world Message-ID: <199605220900.CAA07412@net.bio.net> NNTP-Posting-Host: net.bio.net BIOSCI is about halfway to its funding goal!! I'm interrupting the usual monthly posting of the BIOSCI miniFAQ to bring you up to date on BIOSCI fundraising progress, a topic of concern to your future use of this resource. Thank you in advance for taking the time to read this message carefully. Last year we announced that BIOSCI was going to adopt the U.S. Public Broadcasting System model to fund its operations after our DOE/NSF grant runs out later this year. Unlike PBS, we are not soliciting contributions from users; we are only selling ads on our Web pages solely to cover our operating costs. Our goal is to seek sponsorships until we build up an operating reserve of about $100,000 and then cease further promotions until we need to build the reserve back up. (The accountants among our readership will be familiar with the problem of deferred revenue which we can not safely utilize until ads have been displayed for a period of time.) We are only about halfway to our funding goal and need to raise further funds to avoid having to curtail services at net.bio.net. Fundraising is time-consuming, however, and we need your help as explained further below. Our operating costs consist of our network connection, phone lines, hardware maintenance (we will be getting newer and faster hardware soon!), plus 0.7 FTE of salaries covering UNIX systems admin, technical support, quality assurance, i.e., testing, of our system, and administrative costs (such as the time it takes to actually find/write/call potential sponsors and raise money!). Although the BIOSCI staff does get compensated for a portion of the work that they do, this project has always received a lot of free after-hours and "vacation" time labor, so we hope that no one will begrudge the time that we do charge to the project to serve you. All of the three part-time staff members, Dave Mack, Julie Lawrence, and myself, have full time day jobs and families in addition to working hard to keep this service running for all of you. Julie and Dave Mack are subcontractors for BIOSCI; my time that is charged to the project defrays a portion of my regular salary instead of adding to my income. Besides having to relocate the project, we were very busy this last year building new infrastructure such as our WWW hypermail interface to the system. This was released last December along with scores of WAIS indices for the newsgroups. Virtually everything is complete, although we do continue to find and fix bugs (many through your helpful feedback!). We are still having some problems with our WAIS indexing. The archives continue to grow rapidly. We are running over 100 indexes now versus three previously and any systems crashes cause greater havoc with the indexing than before! We are still working to fix this as fast as our resources permit and appreciate your patience, but we have been able to automate a lot of the infrastructure to reduce labor as compared to past requirements. We have also implemented new software to make moderation of BIOSCI/bionet newsgroups much easier and combat the growing problem of Internet junk mail and USENET "spamming." About 20% of our groups are now moderated, many of them by the BIOSCI staff! This, for example, made a major difference last year in the quality of content in our EMPLOYMENT/bionet.jobs.offered newsgroup which many commercial concerns and recruiting firms are using **without charge** to recruit candidates for positions in the biological sciences. We are also now in a position to have sponsors for individual newsgroups as you will have noticed if you have visited http://www.bio.net/ and clicked on "Access the BIOSCI/bionet newsgroups" recently. So, how can you help?? ---------------------- As noted above it can take a lot of time to contact potential sponsors if I have to do it all myself. Our request is quite simple. You can do two important things which will take very little time for you individually. First, please use our WWW system at http://www.bio.net/ to access the archives. You can now post or reply to messages via your Web browser. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. Our hope is to quickly raise several large corporate/institutional sponsors on our heavily-used WWW locations (some stats appended below), and then end this sponsorship campaign so that our resources can continue to be used for service provision, not fundraising. Many of our specialty newsgroup WWW archives are still used by small communities of scientists (and they haven't been heavily promoted yet). While these may be valuable niche markets to some advertisers, it will generate more labor and overhead having to find these sponsors, fairly price the locations, and deal with lots of smaller sponsorships than fewer mid-to large sponsors. We are striving to keep our operation as lean and efficient as possible since we are not trying to make careers out of running BIOSCI. We are trying if at all possible to avoid the administrative overhead entailed with processing lots of small payments to reach our fundraising goals. I'd like to thank all of you for your help in advance. In helping us, you are also helping yourselves, not only in keeping this resource available for all of the both large and small research communities that we serve, but also by alleviating the need for us to go back and compete with researchers for tight grant dollars! We promised NSF when we were awarded the BIOSCI grant that we would carry out this mission to make the service self-supporting. With your help, we will succeed in continuing BIOSCI's work into its second decade. Thank you very much! Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net A list of our prime WWW sponsorship locations follow. Please contact us for further details. ---------------------------------------------------------------------- The overall BIOSCI WWW pages are currently visited by users from close to 5500 unique computer hosts per week. Web servers only log the Internet computer/host name and frequently more than one individual can connect to us from a particular host. Main home page, http://www.bio.net, visited recently by about 2100 unique hosts per week Main Newsgroups archives page, http://www.bio.net/archives.html, visited recently by about 1200 Unique hosts per week BIO-JOURNALS archive page, http://www.bio.net/BIO-JOURNALS.html, visited recently by about 1000 unique hosts per week. EMPLOYMENT archive pages: http://www.bio.net:80/hypermail/EMPLOYMENT/ and monthly header pages, visited recently by about 800 unique hosts per week. Address database search page, http://www.bio.net/addrsearch.html, visited recently by about 450 unique hosts per week. Methods newsgroup archive pages, http://www.bio.net:80/hypermail/METHDS- REAGNTS/ and monthly header pages, visited recently by about 350 unique hosts per week. Ads can also be displayed on various combinations of other BIOSCI/bionet newsgroups. Please contact us at biosci-help@net.bio.net for details. ---------------------------------------------------------------------- From owner-structural-nmr@net.bio.net Tue May 21 23:00:00 1996 Path: biosci!MRR.COM!jon From: jon@MRR.COM (Jon Webb) Newsgroups: bionet.structural-nmr Subject: Need Spectrometer Date: 22 May 1996 14:03:21 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: <2.2.32.19960522185658.0069f5a0@205.198.86.145> NNTP-Posting-Host: net.bio.net Dear Colleagues, M R Resources is currently in need of a Bruker AM-360 NMR spectrometer. System must be complete with magnet. If you are about to dispose of or trade in such a system, please contact us as we will pay top dollar for this equipment. Sorry for the cross posting. Best regards, Jon Webb, M R Resources, Inc Remanufactured NMR & MRI Systems, Parts and Services 158 R. Main Street P.O. Box 880 Gardner, MA 01440 Voice: 508-632-7000 Fax: 508-630-2509 Email: jon@mrr.com Web Site: http://www.mrr.com From owner-structural-nmr@net.bio.net Wed May 22 23:00:00 1996 Path: biosci!HELIX.NIH.GOV!huang From: huang@HELIX.NIH.GOV (Xialing Huang) Newsgroups: bionet.structural-nmr Subject: Meeting Date: 23 May 1996 07:20:27 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: <199605231417.KAA26554@helix.nih.gov> NNTP-Posting-Host: net.bio.net Hi, Dear netters I'll attend XVIIth International Conference on Magnetic Resonance in Biological Systems.(August 18-23, 1996---Keystone, Colorada). I try to find a female to share double room in Keystone Resort. If anyone is interested, please respond me by e-mail. Xiaolin Huang Bldg37, Rm5C02 LMC/NCI/NIH Bethesda, Maryland 20892 Tel: 301-402-3113 (w) e-mail: huang@helix.nih.gov From owner-structural-nmr@net.bio.net Sun May 26 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: nmrorg@bellatrix.pcl.ox.ac.uk (nmrorg) Newsgroups: bionet.structural-nmr Subject: NMR EPS-2: SECOND ELECTRONIC NMR POSTER SESSION Date: 27 May 1996 12:04:53 +0100 Lines: 34 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4oc28l$1dc@mserv1.dl.ac.uk> Original-To: str-nmr@dl.ac.uk (Please note upcoming dates & deadlines) NMR EPS-2: SECOND ELECTRONIC NMR POSTER SESSION Following up on last year's First Electronic NMR Poster session (see http://bellatrix.pcl.ox.ac.uk/nmr/poster.html or mirror sites listed there) a Second Electronic Poster Session on NMR is being held from June 17 to June 21. Participants can mount an NMR-related poster on the World Wide Web and engage in interactive discussions on the poster material and current NMR technology during the week. The registration facility for NMR EPS-2 is now open at: http://bellatrix.pcl.ox.ac.uk/nmr96/ If you fill out the registration form located there you will receive a userid and password which you may use to access the event. Potential commercial exhibitors or sponsors should contact us directly over arrangements for their displays. To present a poster you need to send the following pieces of information by June 1 to nmrorg@bellatrix.pcl.ox.ac.uk: 1) The Web site location (URL) where you will serve your poster. 2) Your email address for correspondence. 3) Your abstract stating title, list of authors, institutions, and mailing address. If you do not have the ability to mount a poster on the Web yourself please email nmrorg@bellatrix.pcl.ox.ac.uk. We should be able to aid you in loading a poster. From owner-structural-nmr@net.bio.net Tue May 28 23:00:00 1996 Path: biosci!BIOC01.UTHSCSA.EDU!sudha From: sudha@BIOC01.UTHSCSA.EDU (Sudha Veeraraghavan) Newsgroups: bionet.structural-nmr Subject: 15N-ammonium chloride Date: 29 May 1996 12:10:04 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 30 Sender: daemon@net.bio.net Distribution: world Message-ID: <9605291904.AA04701@bioc01.uthscsa.edu> NNTP-Posting-Host: net.bio.net Dear NMR friends, In our lab, we have run into a problem with a specific lot of 15N-ammonium chloride purchased from CIL in late 1994. This compound, bought to make labeled protein, turns out to be 14N-amm. chloride. The lot number is P-4478. We found the problem when our "labeled" protein turned out to be unlabeled. Also, we confirmed the lack of 15N in the ammonium chloride by running 1D spectra on this and another lot. While the other lot shows the ~90Hz splitting, P-4478 did not. My question to you is: Have any of you had a similar problem with compounds purchased from CIL or other companies? Did anyone have the same experience as us with lot P4478? If so, how did you deal with it? Can you also tell us how the company dealt with the issue? Thanks for your input in advance. Sincerely, Sudha V. -- !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Sudha Veeraraghavan sudha@bioc01.uthscsa.edu Department of Biochemistry sveerara@opal.med.tufts.edu Tufts University School of Medicine [Tel] (617) 636-6873 136 Harrison Ave. [Fax] (617) 636-6409 Boston, MA 02111 U.S.A. !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! From owner-structural-nmr@net.bio.net Tue May 28 23:00:00 1996 Path: biosci!NMRSGI2.NCIFCRF.GOV!rabyrd From: rabyrd@NMRSGI2.NCIFCRF.GOV (R. Andrew Byrd) Newsgroups: bionet.structural-nmr Subject: XVIIth ICMRBS Date: 29 May 1996 15:11:12 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: <199605292154.RAA13172@nmrsgi2.ncifcrf.gov> NNTP-Posting-Host: net.bio.net This is a reminder that abstracts are due on June 1st at the conference office in Santa Fe, NM, USA. Please refer to the web site for information: http://nmrsgi1.ncifcrf.gov/icmrbsxvii/ NOTE: In order to assist people to locate other people who may be interested in sharing accomodations and transportation arrangements, the web site has two bulletin boards. There was a problem with these features which has been found and corrected. If you have tried to use these facilities and had difficulties, please try again. Also, please let us know if you have any other problems with the features available at this site. A program update will be posted soon. ------------------ Dr. R. Andrew Byrd Macromolecular NMR/MSL/ABL TEL: 301-846-1407 FAX: 301-846-6195 From owner-structural-nmr@net.bio.net Wed May 29 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!sgigate.sgi.com!nntp.coast.net!lll-winken.llnl.gov!fnnews.fnal.gov!unixhub!news.Stanford.EDU!not-for-mail From: koehler@chem.Stanford.EDU (Michael Frederick Koehler) Newsgroups: bionet.structural-nmr Subject: Question: noise along D1? Date: 30 May 1996 14:22:05 -0700 Organization: Stanford University, CA 94305, USA Lines: 18 Message-ID: <4ol3ht$10k4@chem.Stanford.EDU> NNTP-Posting-Host: chem.stanford.edu Hello there. I am a graduate student working on 2D NMR structural studies of various organic molecules. I am doing my spectroscopy on a Varian UNITY 500, and working up the data in Felix 2.30. In my most recent spectra, I have ENORMOUS lines running along D1 in the tranformed spectra. 1D slices through D1 and D2 show normal looking spectra, but the baseline of the slices along D1 has a DC offset that varies, forming sharp peaks when viewed along D2. The only difference between these spectra and some that I have transformed successfully is that I turned on digital signal processing to eliminate a baseline roll produced by the large 1H-benzene peak (spectra were performed in D6-benzene). Is Felix somehow unequipped to handle this? I have read the Magnetic Moments article on digital filtering, which implies that using the digital filters can produce a DC offset. Is that what I'm seeing? Any suggestions are greatly appreciated. Michael Koehler From owner-structural-nmr@net.bio.net Thu May 30 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!newsfeed.internetmci.com!in2.uu.net!news.ner.bbnplanet.net!usenet.uchc.edu!usenet From: Walfrido Antuch Newsgroups: bionet.structural-nmr Subject: postdoctoral position Date: Fri, 31 May 1996 12:15:43 -0400 Organization: Univ. of Connecticut Health Center, Dept. Biochemistry Lines: 114 Message-ID: <31AF1B2F.167E@panda.uchc.edu> NNTP-Posting-Host: wilma.uchc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) To whom it may concern: Dr. Greg Mullen has an opening for a postdoctoral position in Biomolecular NMR at the Department of Biochemistry of the University of Connecticut Health Center. Would you please put the enclosed announcement in your "Employment Opportunity" section. Thank you very much and best Regards, Walfrido Antuch ____________________________________________________________________________ POSTDOCTORAL POSITION IN BIOMOLECULAR NMR A postdoctoral position is open in the area of multidimensional NMR studies of proteins. In one area, we are studying DNA polymerase beta as part of an NIH funded research grant. Plans for expansion of the research on this project will be in the resonance assignments, solution structure, subdomain dynamics, and substrate interactions with the catalytic domain (240 residues) of beta-Pol. Studies of catalytic groups and divalent metal coordination by the enzyme are anticipated. The protein is provided in a collaborative arrangement. Very high quality 3D NMR data have been recorded for the beta-Pol catalytic domain. The postdoctoral associate is encouraged to apply for a postdoctoral fellowship once on board. Studies of proteins involved in DNA recombination are a second focus of the laboratory. For this project applicants would be encouraged to develop a research problem and apply for postdoctoral funding. Present focus in the lab is on the site-specific DNA recombinase gamma, delta resolvase. NMR structure of DNA binding domains of related recombinases should be considered. Overlap between the B-Pol and recombinase projects is possible. For studies in either of these research areas initial salary support is available for 2 years. Applicants should have experience in multidimensional NMR techniques, preferably with large proteins, and a biochemical background. Dedicated resources include a biochemical laboratory, an NMR laboratory equipped with Varian Unity-plus 4-channel 600 MHz and 500 MHz NMR spectrometers with xyz gradients, and a molecular graphics/ workstation laboratory, which includes several Silicon Graphics Indigo2 R4400 and Indy R4400 computers. In addition, multiuser access Challenge and Onyx systems are being utilized. Software being used includes FELIX 950, XEASY, XPLOR, INSIGHT, MOLMOL, QUANTA, NMR Structure Determination, and other molecular graphics display programs. Three other postdoctoral associates are in the laboratory. Salary for a first year postdoctoral is $21,000 with raises with subsequent years of experience. Start date for the position is as early as Sept 1996. Send c.v. and names of three references to: Dr. Greg Mullen, Department of Biochemistry, UCONN Health Center, Farmington, CT 06032; Email: gmullen@panda.uchc.edu For background see the publications: Liu, D-J., DeRose, E. F., Prasad, R., Wilson, S. H., and Mullen, G. P., "Assignments of 1H, 15N, and 13C Resonances for the Backbone and Side Chains of the N-Terminal Domain of DNA Polymerase beta. Determination of the Secondary Structure and Tertiary Contacts," Biochemistry, 33, 9537-9545, (1994). Mullen, G. P., "Solution Structure of DNA Polymerases and DNA Polymerase- Substrate Complexes," Methods Enzymol., 262, 147-171 (1995). Liu, D-J., DeRose, E. F., Prasad, R., Wilson, S. H., and Mullen, G. P., "Three-dimensional Solution Structure of the N-terminal Domain of DNA polymerase beta and Mapping of the ssDNA Interaction Interface," Biochemistry, 35, 6188-6200, (1996). Liu, T., DeRose, E. F., and Mullen, G. P., "Determination of the Structure of the DNA Binding Domain of gamma,delta Resolvase in Solution," Protein Sci. 3, 1286-1295 (1994). _____________________________________________________________________________ -- Walfrido Antuch Ph.D. University of Connecticut Health Center Department of Biochemistry 263 Farmington Avenue, Farmington Connecticut, CT 06032 USA phone: (860)679-3117 fax: (860)679-3408 eMail: antuch@panda.uchc.edu www: http://www.uchc.edu/~antuch/ From owner-structural-nmr@net.bio.net Thu May 30 23:00:00 1996 Path: biosci!PHOENIX.PRINCETON.EDU!ipelczer From: ipelczer@PHOENIX.PRINCETON.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: Question: noise along D1? Date: 30 May 1996 18:26:33 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 50 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <4ol3ht$10k4@chem.Stanford.EDU> NNTP-Posting-Host: net.bio.net Hi Michael, It is not clear to me what do you mean that you "turned on digital processing". I suppose you might have used LP replacement of the first section of the FID in t2 (D1). This process can lead to unstable results, in turn, to sharp ridges. Perhaps some -- relatively simple -- frequency domain baseline correction could improve the output. The instability is a function of the parameters used (polynomial order, for example; the less the more stable, especially in vectors which carry no real intensities). The other alternative is the time domain filter, which may be done by running averaging or by polynomial fit of the FID (or both). This causes less errors usually, but you may have to shift the virtual carrier position on top of the peak to be suppressed if it was not in the center. Good luck, Istvan wwww,wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww Istvan Pelczer, Ph.D. Email: ipelczer@princeton.edu Senior NMR Spectroscopist Princeton University Department of Chemistry ph# (609) 258 2342 Frick Laboratory fax# (609) 258 6746 Washington Road Princeton, NJ 08544 On 30 May 1996, Michael Frederick Koehler wrote: > Hello there. I am a graduate student working on 2D NMR structural > studies of various organic molecules. I am doing my spectroscopy on > a Varian UNITY 500, and working up the data in Felix 2.30. In my > most recent spectra, I have ENORMOUS lines running along D1 in the > tranformed spectra. 1D slices through D1 and D2 show normal looking > spectra, but the baseline of the slices along D1 has a DC offset that > varies, forming sharp peaks when viewed along D2. The only difference > between these spectra and some that I have transformed successfully is > that I turned on digital signal processing to eliminate a baseline roll > produced by the large 1H-benzene peak (spectra were performed in > D6-benzene). Is Felix somehow unequipped to handle this? I have read > the Magnetic Moments article on digital filtering, which implies that > using the digital filters can produce a DC offset. Is that what I'm > seeing? > > Any suggestions are greatly appreciated. > > Michael Koehler > > From owner-structural-nmr@net.bio.net Thu May 30 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!sgigate.sgi.com!nntp.coast.net!fu-berlin.de!cs.tu-berlin.de!sandmann.prz.tu-berlin.de!kowall From: kowall@sispa.chem.TU-Berlin.de (Martin Kowall) Newsgroups: bionet.structural-nmr Subject: influence of Ammoniumacetat to COSY- and TOCSY-crosspeaks Date: 31 May 1996 12:36:18 GMT Organization: PRZ/TU-Berlin Lines: 19 Message-ID: <4omp42$9n7@sandmann.prz.tu-berlin.de> NNTP-Posting-Host: sispa.chem.tu-berlin.de X-Newsreader: TIN [version 1.2 PL0] Hallo. I am a graduate student working on 2D NMR structural studies of Surfactin a cyclic heptapeptid with a beta-hydroxy-fatty acid: fatty acid-Glu1-Leu2-Leu3-Val4-Asp5-Leu6-Leu7 - lactone bond to fatty acid. 2D COSY and TOCSY spectra of surfactin show seven clearly separated NH - C(alpha)H crosspeaks. A surfactin sample which contained some ammoniumacetat as pollution show an effect I could not explain. Some crosspeaks show only up to 30 percent loss of signalintensity due to linebroadening, but other crosspeaks show nearly zero intensity. COSY spectra show only crosspeaks for Val4, Asp5 and Leu7; TOCSY spectra show all seven crosspeaks but the intensity of Glu1, Leu2, Leu3 and Leu6 are much smaller than the intensity of the other 3 aminoacids. Now I am looking for an explanation of this amino acid specific loss of crosspeakintensity when ammoniumacetat is present in the NMR sample. Thanks, Martin Kowall From owner-structural-nmr@net.bio.net Thu May 30 23:00:00 1996 Path: biosci!SBNMR1.SKI.MSKCC.ORG!bouaziz From: bouaziz@SBNMR1.SKI.MSKCC.ORG (Serge Bouaziz) Newsgroups: bionet.structural-nmr Subject: (none) Date: 31 May 1996 15:01:19 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: <199605312200.SAA03007@sbnmr1.ski.mskcc.org> NNTP-Posting-Host: net.bio.net subscribe Best regards ******************************************** * * * Serge Bouaziz * * Memorial Sloan Kettering Cancer Center * * * * 1275 York Avenue Box 557 * * New York, NY 10021 USA * * Tel: (212) 639 7225 * * Fax: (212) 717 3066 * * Email: bouaziz@sbnmr1.mskcc.org * * * ******************************************** From owner-structural-nmr@net.bio.net Thu May 30 23:00:00 1996 Path: biosci!sfu.ca!cushley From: cushley@sfu.ca (Robert Cushley) Newsgroups: bionet.structural-nmr Subject: NMR post-doc position Date: 31 May 1996 14:15:05 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 33 Sender: daemon@net.bio.net Distribution: world Message-ID: <199605312111.VAA12102@beaufort.sfu.ca> NNTP-Posting-Host: net.bio.net NMR POST-DOCTORAL POSITION Multidimensional NMR studies of proteins associated with heart disease. Several years experience with Bruker nD pulse sequences is essential. Study with Senior Investigator on Bruker AMX600 Major Installation, with triple resonance and z-gradients. Also available: Bruker AMX400, Aspectstation (XWinNMR), SGI Indigo2 (Felix, NMRPipe, Pronto, InsightII, Xplor, Naomi). Send resume with names and addresses of three referees. Salary $28,000 - $30,000 per annum, depending on qualifications. Information about Simon Fraser University and Vancouver may be obtained from http://www.sfu.ca/ -- xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx Professor Robert J. Cushley Institute of Molecular Biology and Biochemistry Simon Fraser University Burnaby, British Columbia V5A 1S6 CANADA Phone: (604)291-4230; FAX: (604)291-5583 e-mail (Internet): cushley@sfu.ca xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx From owner-structural-nmr@net.bio.net Thu May 30 23:00:00 1996 Path: biosci!aol.com!Resourcemr From: Resourcemr@aol.com Newsgroups: bionet.structural-nmr Subject: Employment Opportunity Date: 31 May 1996 12:21:16 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 50 Sender: daemon@net.bio.net Distribution: world Message-ID: <960531151716_404631769@emout09.mail.aol.com> NNTP-Posting-Host: net.bio.net NMR Sales Position Available M R Resources is currently seeking a qualified individual to market our NMR engineering services, parts and accessories. Specifically, these products include field service, in house service, service contracts, probes, circuit boards and system peripherals. 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