From owner-structural-nmr@net.bio.net Tue Aug 01 23:00:00 1995 Newsgroups: bionet.structural-nmr Path: biosci!rutgers!uwm.edu!cs.utexas.edu!swrinde!tank.news.pipex.net!pipex!uknet!bcc.ac.uk!news From: Greg Siegal Subject: (no subject) Message-ID: <1995Aug2.111043.63407@ucl.ac.uk> Date: Wed, 2 Aug 1995 11:10:43 GMT X-Url: news:bionet.structural-nmr Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 X-Mailer: Mozilla 1.1N (X11; I; IRIX 5.3 IP22) Organization: University College London Lines: 15 Hi there, I'm in the midst of an NMR structure determination of a double labelled protein an a small problem has arisen that is so standard that I thought I'd check to see if anyone had already solved it. I have recorded a series of spectra including 15N edited NOESY + TOCSY, plus HNCO, HNCA and HN(CO)CA. I therefore have all of the backbone assignments. However, I don't have a single peak list that contains all of the relevant chemical shifts for the CBCACO(CA)HA and CBCA(CO)NH expts. The question is, has anyone written a program that can sort through input chemical shift lists and generate a requested peak list? I'd greatly appreciate any response. -- Gregg Siegal siegal@biochemistry.ucl.ac.uk phone (44) 171 391 1354 From owner-structural-nmr@net.bio.net Tue Aug 01 23:00:00 1995 Path: biosci!biophy.jussieu.fr!michel From: michel@biophy.jussieu.fr (Michel SEIGNEURET) Newsgroups: bionet.structural-nmr Subject: 8mm wide bore spinner Date: 2 Aug 1995 03:32:23 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <9508021039.AA07567@mood.biophy.jussieu.fr> NNTP-Posting-Host: net.bio.net Hi, We are in need of a teflon spinner for a 8mm solution NMR Bruker probe that is used with a wide bore Bruker magnet. It seems that Bruker is discontinuing the making of wide bore spinners and provides now a (in my opinion) less practical "bore reducer" system. Does anyone know of a NMR accesories supplier that would provide such a 8mm/widebore spinner. Thanks for your help. Michel M. Seigneuret lab. de Biophysique Cellulaire Universite Paris 7 France From owner-structural-nmr@net.bio.net Wed Aug 02 23:00:00 1995 Path: biosci!sb.com!Lesley_K_Maclachlan%notes From: Lesley_K_Maclachlan%notes@sb.com (Lesley K Maclachlan) Newsgroups: bionet.structural-nmr Subject: Protein NMR tutorial. Date: 3 Aug 1995 03:51:09 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 34 Sender: daemon@net.bio.net Distribution: world Message-ID: <9508031349.AA9344@pho018.sb.com> NNTP-Posting-Host: net.bio.net Dear fellow NMR spectroscopists, I hope that someone can help us with this problem: We frequently have part-time students, temporary workers and other visitors passing through our labs., staying from 3 months to one year, who need to be trained in the basic (and frequently the more advanced!) methodologies of protein NMR. These people are typically at the undergraduate level, some post-graduate, but usually they would have no previous NMR experience at all. I would like to know if any one knows of a tutorial/user guide/primer on the basics of practical NMR spectroscopy as applied to proteins/peptides, ie. how to tune, shim, run 1D spectra, get optimal solvent presaturation, then go on to 2D experiments like DQF-COSY, NOESY and TOCSY, which these people could work through at their own pace. We would require this for Bruker AMX spectrometers. I know that Bruker do quite a nice step-by-step guide for this for the DMX range of spectrometers. Is there anything else that could be useful out there? I would be very grateful for any suggestions. Yours, Lesley MacLachlan. Dr L K MacLachlan Analytical Science SmithKline Beecham Pharmaceuticals The Frythe Welwyn Herts. AL6 9AR United Kingdom. Tel.: +44-1438-78-2007 Fax: +44-1438-78-2570 E-mail: Lesley_K_Maclachlan%notes@sb.com From owner-structural-nmr@net.bio.net Wed Aug 02 23:00:00 1995 Path: biosci!CHIAK.KAIST.AC.KR!hkcheong From: hkcheong@CHIAK.KAIST.AC.KR (Cheong hae-kap) Newsgroups: bionet.structural-nmr Subject: [wanted] 1H-31P HETCOR pulse sequence Date: 3 Aug 1995 03:22:29 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: <199508030917.TAA07401@chiak.kaist.ac.kr> NNTP-Posting-Host: net.bio.net Dear netters: I am looking for a pulse sequence of 1H-31P HETCOR applicable to Bruker DMX-600. Referece for the pulse sequence would be: Sklenar, V., Miyoshiro, H., Zon, G., & Bax, A. (1986) FEBS Lett. 208, 94-98. So if you have such a pulse sequence, please e-mail me the sequece code, to hkcheong@chiak.kaist.ac.kr Thanks in advance for your help. From owner-structural-nmr@net.bio.net Wed Aug 02 23:00:00 1995 Path: biosci!LAPLACE.CSB.YALE.EDU!abonvin From: abonvin@LAPLACE.CSB.YALE.EDU ("Alexandre Bonvin") Newsgroups: bionet.structural-nmr Subject: Re: Full-Matrix NOE/ROE Back-calculation Software Available??? Date: 3 Aug 1995 13:21:14 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 37 Sender: daemon@net.bio.net Distribution: world Message-ID: <9508032019.AA06615@laplace.csb.yale.edu> NNTP-Posting-Host: net.bio.net Dear Dale, Here is some www addresses you want to have a look at. They should give you information about some of the relaxation matrix programs available. IRMA/DINOSAUR http://www-nmr.chem.ruu.nl/ MORASS http://www.nmr.utmb.edu/ MARDIGRAS/CORMA http://picasso.ucsf.edu/mardi.html X-PLOR also has a relaxation matrix module allowing NOE simulations and refinement (http://xplor.csb.yale.edu) BIOSYM also offers relaxation matrix calculations in their NMRrefine module. Actually IRMA is coupled to Insight. During my PhD in Utrecht I developped a direct NOE refinement suite of programs called DINOSAUR. DINOSAUR has the ability to work with BIOSYM/DISCOVER coordinates files and calculate theoretical NOE intensities. However it won't simulate an entire spectrum. It is setup to calculate only those NOE intensities for which experimental data are available, i.e. you need a peak list as starting point. Cheers, Alexandre ========================================================================== | Alexandre Bonvin PhD | Phone: (203) 432-5066 | | Mol. Biophys. & Biochemistry | Fax: (203) 432-3923 | | Yale University | Email: abonvin@laplace.csb.yale.edu | | New Haven CT 06520-8114, USA | | ========================================================================== From owner-structural-nmr@net.bio.net Wed Aug 02 23:00:00 1995 Path: biosci!bcm!news.msfc.nasa.gov!newsfeed.internetmci.com!news.sprintlink.net!howland.reston.ans.net!torn!news.bc.net!rover.ucs.ualberta.ca!news From: "Dr. Dale R. Cameron" Newsgroups: bionet.structural-nmr Subject: Full-Matrix NOE/ROE Back-calculation Software Available??? Date: 3 Aug 1995 18:56:18 GMT Organization: Computing and Network Services, U of Alberta, Edmonton, Canada Lines: 15 Message-ID: <3vr64i$qde@rover.ucs.ualberta.ca> NNTP-Posting-Host: glyco2.chem.ualberta.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; IRIX 5.2 IP22) X-URL: news:bionet.structural-nmr I am looking for a software package or packages that are capable of doing a full matrix method back-calculation of molecular dynamics data to generate theoretical noe/roe data for comparison with experimental values. I am currently using software which allows me to generate the r^-6 ensemble averages for each proton-proton pair but I would prefer a full-matrix method. Does anyone know of such software? Could you point me in the right direction? I am specifically interested in packages that are capable of interfacing with Biosym's Discover module and are capable of handling carbohydrates. I realize this is a big order but any information any of you could give me would be appreciated. Dr. Dale Cameron From owner-structural-nmr@net.bio.net Thu Aug 03 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: hong@indra.chem.umu.se (Qian Hong) Newsgroups: bionet.structural-nmr Subject: Program Date: 4 Aug 1995 08:49:04 +0100 Lines: 15 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3vsjdg$cgo@mserv1.dl.ac.uk> Original-To: str-nmr@dl.ac.uk Hello, I am looking for a program which can read and EDIT PostScripts file, like doing some text edit. Does someone out there know where I can find this kind of program in net. I have PC 486 and SGI Indigo. Any information would be appreciated. Hong Qian Organic Chem. Umea Univ. email hong@indra.chem.umu.se From owner-structural-nmr@net.bio.net Thu Aug 03 23:00:00 1995 Path: biosci!RD.ORION.ORION.mailnet.fi!PIERO.POLLESELLO From: PIERO.POLLESELLO@RD.ORION.ORION.mailnet.fi (Piero Pollesello) Newsgroups: bionet.structural-nmr Subject: NMRview-help Date: 3 Aug 1995 23:21:47 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 25 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Distribution to:NMR-discussiongroup ------------ Hallo! We are dealing with protein structure and protein-ligand interactions. We are running FELIX, NMRview and UXNMR-Bruker on a SG Indy (5.2) workstation in order to compare their performances. (We wish also to try Pronto, Pencil and other software in the future). We have two problems and maybe someone has the solutions. (a) is it possible (and how) to open a Bruker 2D spectrum on NMRview? (b) when I open in NMRview a 2D spectrum from FELIX format and I want to pick. .. the operation is not allowed in the window where you have, e.g., the four buttons "Fold": the button "Pick" remains "dead", only "Close" works. We posted the same question also in the "NMRview-discussion-group". Thanks for helping Piero Pollesello NMR-lab, Chem.Res.Dept. Orion-Farmos P.O.box 65 FIN-02101 Espoo, FINLAND tel.:int-358-0-429-4191 fax.:int-358-0-429-2924 e-mail:piero.pollesello@rd.orion.orion.mailnet.fi URL:http://poly01.tbs.trieste.it/figpp.html From owner-structural-nmr@net.bio.net Thu Aug 03 23:00:00 1995 Path: biosci!PETER.BPC.UNI-FRANKFURT.DE!rolfi From: rolfi@PETER.BPC.UNI-FRANKFURT.DE (Rolf Winkelmann) Newsgroups: bionet.structural-nmr Subject: 13C Chemical-Shift References Date: 4 Aug 1995 10:12:48 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: <9508041826.AA27007@peter.bpc.uni-frankfurt.de> NNTP-Posting-Host: net.bio.net I am running heteronuclear spectra on 13C- and 15N-fully labeled samples. My problem is how to find a appropriate calibration for 13C and 15N . It is not possible to use an internal standard. Would anybody have a solution for this ?? Maybe a reference from the literature ?! From owner-structural-nmr@net.bio.net Fri Aug 04 23:00:00 1995 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: [wanted] 1H-31P HETCOR pulse sequence Date: 5 Aug 1995 00:08:02 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 101 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <199508030917.TAA07401@chiak.kaist.ac.kr> NNTP-Posting-Host: net.bio.net On 3 Aug 1995, Cheong hae-kap wrote: > Dear netters: > > I am looking for a pulse sequence of 1H-31P HETCOR applicable to Bruker DMX-600. > > Referece for the pulse sequence would be: > Sklenar, V., Miyoshiro, H., Zon, G., & Bax, A. (1986) FEBS Lett. 208, 94-98. > > So if you have such a pulse sequence, please e-mail me the sequece code, to > hkcheong@chiak.kaist.ac.kr > > Thanks in advance for your help. > > Please, find below a pulse program we have used with success here, in Frankfurt. I'd suggest to use dispersive phasing in both F2 and F1 dimensions in order to take advantage of enhanced sensitivity of the central signal which replaces the four-peak pattern and that of simplified appearance of the spectrum (there is an illustration of this effect in our review on nD data processing (Pelczer & Carter, in: Techniques in Protein NMR, in the series of Methods in Molecular Biology, Ed.: D. G. Reid, Humana Press, NJ, in press). Good luck, Istvan ================================ Istvan Pelczer, Ph.D. Res. Assist. Professor Chemistry Department, CST Bldg. Syracuse University Syracuse, NY 13244-4100 ph: (315) 443 1023 or x-5932 fax: x-1022(lab) or x-4070(dept) Temporary address until Aug-14, 1995: c/o Prof. Heinz Ruterjans J.W. Goethe - Universitat Inst. fur Biophysikalische Chemie Biozentrum, N230 Marie-Curie-Str. 9 60439 Frankfurt am Main, Germany ph# 49 69 798 29630 or 31, fax# x-32 **************************************************** the sequence: ; ; ph_cosypsA_i ; ; 31P,1H COSY, according to: ; Sklenar, V., et al, FEBS Lett., 94(1986)208 ; for the DMX, with presaturation of the water ; ; Istvan Pelczer 7/6/95 (ipelczer@mailbox.syr.edu) ; #include d25=(p10-p1) ; compensate different pulse lengths 1 ze 2 d10 pl2:f2 ; additional relaxation delay [min. 30ms!] 3 d11 4 d20 pl18:f1 ; switch to low power for... p18:f1 ph18 ; ...CW presat on the H2O d20 pl1:f1 ; switch to high power 5 p1*2:f1 ph18 ; 180 deg 1H pulse d22 ; interpulse delay for saturation [30-50 ms] lo to 5 times l10 ; ... repeated l10 times, for ; proton presaturation p10:f2 ph1 ; 90 deg 31P pulse d0 ; incremented delay -- t1 (p10:f2 ph2) (d25 p1:f1 ph3) ; 90 deg pulses both, 13P and 1H go=2 ph4 ; acquisition d10 do wr #0 if #0 zd ip1 ; R & I for t1 lo to 3 times 2 ; hypercomplex acquisition d11 id0 ; increment t1 lo to 4 times l1 ; l1 complex points in t1 exit ph1 = 0 2 ph2 = 0 ph3 = 0 ph4 = 0 2 ph18 = 0 ; processing with "States-TPPI" in Bruker From owner-structural-nmr@net.bio.net Sat Aug 05 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!usc!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!vixen.cso.uiuc.edu!newsrelay.iastate.edu!news.iastate.edu!baker From: baker@iastate.edu (Wayne R. Baker) Newsgroups: bionet.structural-nmr Subject: Re: 13C Chemical-Shift References Date: 6 Aug 1995 01:11:33 GMT Organization: Biochemistry & Biophysics, Iowa State University Lines: 13 Message-ID: <4014s5$29b@news.iastate.edu> References: <9508041826.AA27007@peter.bpc.uni-frankfurt.de> NNTP-Posting-Host: pv0a0d.vincent.iastate.edu In bionet.structural-nmr, Rolf Winkelmann wrote : :I am running heteronuclear spectra on 13C- and 15N-fully labeled samples. :My problem is how to find a appropriate calibration for 13C and 15N . :It is not possible to use an internal standard. Would anybody have a solution :for this ?? Maybe a reference from the literature ?! Wishart & Sykes (1994) Meth Enz vol 239 p363. Wayne Baker (baker@iastate.edu) Maybe a great magnet pulls Biochemistry & Biophysics All souls towards truth Iowa State University -- k. d. lang, "Constant Craving" From owner-structural-nmr@net.bio.net Sun Aug 06 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!newsfeed.internetmci.com!news.sprintlink.net!sunic!sunic.sunet.se!news.uni-c.dk!news From: Mogens Kjaer Newsgroups: bionet.structural-nmr Subject: Re: making noe cartoons from xplor Date: 7 Aug 1995 07:11:18 GMT Organization: News Server at UNI-C, Danish Computing Centre for Research and Education. Lines: 566 Message-ID: <404eam$ib8@news.uni-c.dk> References: <01HTIOERBA2Q8Y8BL9@bcvms.bc.edu> NNTP-Posting-Host: lgbppp39.uni-c.dk Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="-------------------------------27443224246936" X-Mailer: Mozilla 1.1S (X11; I; IRIX 5.3 IP22) X-URL: file:/indy2/mk/irix5/FAQ/FAQ950331 This is a multi-part message in MIME format. ---------------------------------27443224246936 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii MARKMANO@BCVMS.BC.EDU wrote: >Does anybody know of aprogram to produce >noe data presentation cartoons from Xplor data >is there a program available? > Ofer Markman You could try using Pronto 3D: You can assign your NMR spectra, export NOE's to X-PLOR, and import calculated structures from X-PLOR. The structures can be visualized, and you can draw lines between atoms representing NOE's between them. It is also possible to display helices as cylinders and beta-sheets as arrows. The displayed structures can be exported in a format used by raytracers, thus making it possible to produce pictures with shadows, reflections, texture- mapping, transparent atoms, etc. etc. etc. You can get Pronto from several FTP sites, you must send me a mail to get the license code after installation; it does not cost anything. Check the FAQ attached. -- 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 ---------------------------------27443224246936 Content-Transfer-Encoding: 7bit Content-Type: text/plain =============================================== ###### # # ##### #### # # ##### #### # # # # # # ## # # # # ###### # # # # # # # # # # # ##### # # # # # # # # # # # # # # ## # # # # # # #### # # # #### ####### # ##### # # # # # # # # # # ##### # # # # # ####### # # # # # # # # # # # #### # ##### ####### ### ##### ##### # # # # # # # # # # ## # # # # # # # # # ###### ###### # # ##### ##### # # # # # # # # # # # # # # # # # # # ##### ##### ### ##### ##### ##### =============================================== Frequently asked questions about the Pronto program - and their answers: History: This is version 950331. The second release of this faq. Contents: 1. What is Pronto/3D? !1.1 What is Pronto/3D^2? !2. Where can I find Pronto/3D? 3. What kind of spectra can Pronto read? 3.1 Where should the spectra be located? !4. What is MNMR? 5. Misc. questions: 5.1 Help, my screen is full of windows! 5.2 How do I use the backups? 5.3 Why does Pronto use so much memory? 5.4 Why can't I zoom in the contour diagram using the mouse? 5.5 How do I analyze a series of NOESY spectra? 5.6 How do I read in the assignments I already have made? 5.7 Why doesn't the measure distance tool work? 5.8 How do I change colors and fonts? 5.9 Why doesn't the help system work? !5.10 Why doesn't Pronto display serial number? !5.11 I press a button and nothing happens, why? !6. Future plans? 7. Where can I get further information? Q1: What is Pronto/3D? Pronto: The PROtein Nmr TOol Pronto/3D is a computer program, running on UNIX workstations. The interface to the program uses X-Windows. All information obtained about the moleculed studied is maintained in a data base. The input to the program is a series of processed nD spectra (n>1). The output from the program is a list of constraints to be used in structure calculations. The program was primarily designed to handle spectra of peptides and proteins, but has also been used to assign carbohydrates and nucleic acids. The program has the following main features: a. Display of spectra. One or more spectra can be displayed in one or more windows simultaneously. Cross peaks are labeled. 2D and 3D spectra can be contoured in the same window. b. Locating cross peaks. This can be done automatically or inter- actively. c. Build up of spin systems. Starting from a single cross peak, e.g. a HN-HA peak in a COSY spectrum, the rest of the spin system is built using the cross peaks in the data base. 2D and 3D spectra can be used. Spin systems identified as a specific residue can be labeled so, or as belonging to a class of residues, e.g. an AMX spin system. d. Assign cross peaks. Identify the atoms to which a certain cross peak is linked. A PDB structure file can be consulted to measure atom distances. e. Sequential assignments. Spin systems are linked together using assigned or unassigned cross peaks. The primary sequence is consulted to match residue types. f. A set of check routines are used to find possible errors in the assignment process, i.e. multiple assigned cross peaks. g. Tools for integrating cross peaks and measurement of coupling constants. h. Report facilities for printing or plotting out information. A list of assigned NOE's and their intensity class can be produced, ready for an X-PLOR calculation. Currently, versions for Silicon Graphics and Sun SPARC workstations are distributed. Pronto was designed in a collaboration between Carlsberg Laboratory, CRI A/S, and Bruker Analytische Messtechnik, GmbH. After the design phase, Pronto Software - Development and Distribution was set up at Carlsberg Research Center to handle distribution and further development. This was made in close contact with people doing protein and carbohydrate NMR at Carlsberg Laboratory, using the Pronto program in the assignment phase. At January 1, 1995, the Pronto Software - Development and Distribution project was closed, and Pronto/3D, version 930401, is now available by anonymous ftp for all interested. Q1.1: What is Pronto/3D^2? Pronto/3D^2 is the latest version of Pronto. A few bugs in the 930401 version have been corrected, some tools for the analysis of triple resonance spectra have been added, and mainly, a tool for the display of structures. The structure display facility can show one or more structures simultaneously, as sticks, balls, cartoons, or ribbons. Lines showing NOE's between atoms can be shown. The structure display window can work on an X11 terminal, but better results are obtained on a Silicon Graphics workstation, running GL. Q2. Where can I find Pronto/3D? Pronto/3D, version 930401, is available at the following FTP sites: Address: Directory: ftp.nmrfam.wisc.edu /pub/pronto nmr.utmb.edu /pub/pronto ftp.dfh.dk nmr/pronto The program is stored in a gzip'ed tar file. The 930401I.tar.gz file contains the SGI version, and 930401S.tar.gz contain the Sun SPARC version. A PostScript file with the manual is stored in the manual subdirectory. Two files exist, one formatted for letter size paper and one for A4 sized paper. The manual is approx. 20 Mb when uncompressed, due to a number of screen dumps in the file. The manual is 117 pages. The latest version of Pronto 3D^2 is available for SGI only. The name of the tar archive is: 950331I.tar.gz Q3. What kind of spectra can Pronto read? Pronto can read spectra processed by the following software: a. MNMR This is the library of programs used at the Carlsberg Laboratory for processing of NMR spectra. See later in this FAQ. b. Felix Felix files, compressed or uncompressed .mat files are read. c. Varian files. d. NMR2 files. NMR2 files are not in submatrix format. Contouring of non-submatrix spectra uses a lot of memory. e. Spectra processed by UXNMR or Xspec from Bruker or Spectrospin. - I think that there are still some problems when some of the parameter files are in binary, and some in ASCII... Q3.1 Where should the spectra be located? Pronto determines the type of the spectrum from the directory in which it is found. Each spectrum location is identified by the following parameters, set up in the spectrum catalog in Pronto: Max. 15 characters Max. 15 characters Max. 15 characters Specify an integer Specify an integer Note, not all of the parameters are used for all file formats. The character based parameters may contain the "/" character, specifying an extra subdirectory level. a. MNMR: //nmr//data/ b. Felix: //felix//data/ c. Varian: ///exp/datdir/phasefile d. NMR2: //nmri//data/ e. UXNMR et al.: 2D: //data//nmr///pdata//2rr 3D: //data//nmr///pdata//3rrr Note, also the files: acqus, acqu2s, acqu3s, proc, procs, proc2, proc2s, proc3, proc3s are necessary (the files containing "3" only for 3D spectra). Example: To read the MNMR file /usr/people/nmr/mk/data/COSY.2x2 specify the following parameters: disk: usr/people user: mk name: COSY.2x2 The expno and procno numbers are not used. If the directory layout does not match yours, try setting up some symbolic links. Remember the 15 character limit on the disk, user, and name fields. Q4. What is MNMR? MNMR (Multidimensional NMR) is a set of programs for the processing of nD spectra. n is greater than one, and (currently) less than or equal to ten. MNMR contains programs for: FFT (reading various types of FID files): The program does one dimension at a time, applying the window function, linear prediction phase correction, etc. Determine constants for phase correction Display of 3D spectra Making contour plots Baseline corrections Calculation of relaxation parameters Calculation of projections A set of routines to read and write spectrum files are provided. Use them for your own programs! MNMR is distributed as source code only! You'll need a C and a FORTRAN compiler in order to use the system. You probably would have to spend some time to modify the Makefiles to make it compile on your system. The system compiles on Silicon Graphics, Sun SPARC, IBM RS/6000, and HP workstations. You might need to obtain some fft libraries from various other ftp sites. The program is mainly written for IRIX 4.0.1, so expect to spend some time in getting it to run on other UNIX versions, even newer IRIX versions. Currently, MNMR has not been put on an anonymous ftp server. Send me a mail, and I'll send you the tar archive as a uuencoded, gzip'ed file. The size of this file is 1.4 Mb. Q5. Misc. questions: Q5.1 Help, my screen is full of windows! The first impression people get when they watch a demonstration of the program, or watching someone actually using the program is: Why all those windows? However, when you actually use the program, this is really not a problem. There are some things to remember: a. Close the windows not in use. b. Use a smaller font if the windows are too big. c. Start Pronto/3D with the flag "-2d" or "-3d" if you are only analysing 2D or 3D spectra: Some of the windows will be smaller in this case. d. Open the window survey window to see a list of windows currently open. e. Opening a lot of windows with small fonts makes it more difficult for you boss to see what you are doing... :-) The Pronto/3D^2 program stores a list of windows that were open when you exit, and reopens them at the same place the next time. Q5.2 How do I use the backups? This might sound simple, but we have had cases where people have lost several weeks of work because they used the backup system in a wrong manner. When Pronto/3D is running, it works on a copy of the data base, located in the directory pointed out by the environment variable PRONTO_WORK. If the machine crashes during this, the copy of the data base in PRONTO_WORK is left in an unknown state, and can't/shouldn't be used further. When you exit Pronto/3D, you can save a copy of the PRONTO_WORK data base in another directory. Do this! If you start Pronto/3D with the command: "Pronto" or "Pronto -2D", it will continue to work on the data base in PRONTO_WORK, if Pronto/3D was exited correctly the last time. You can also start with the command "Pronto ", and the contents of PRONTO_WORK will be overwritten with a copy of the data base stored under . Pressing "Backup" in the Pronto/3D program does the following: The access to the data base is closed, and the contents of PRONTO_WORK is stored under the name: backup. After a system crash, the contents of backup can be reloaded by starting the program by: "Pronto backup". The backup will be reloaded into PRONTO_WORK: Now comes the important thing: If you do this, you are adviced to exit Pronto/3D immediately, and store the data base under a new name. Never make it a habbit to start Pronto/3D with "Pronto backup" unless you really need to reload the backup. The scene when people have lost data was as follows: The user presses backup in Pronto/3D. The machine crashes during this. Now, it is important to remember that in this case, the contents of PRONTO_WORK will be OK, and the contents of the backup directory will miss some data. So, if the program is started with "Pronto backup", the good data base in PRONTO_WORK will be overwritten with the partial data base in backup! So: Press backup often! Store under a name when you exit Pronto/3D Clean up old data bases in the PRONTO_DATA directory Think before starting "Pronto backup" Q5.3 Why does Pronto use so much memory? During the contouring process, the last set of contours are stored as vectors in Pronto/3D. This area is released, when new contours are plotted. However, the memory is not released from the running process. The release storage is reused, but can sometimes get so fragmented that new storage is necessary to hold new contours. If you often contour large areas, you might need to exit and enter Pronto a couple of times during the day. The contouring in Pronto/3D has been specifically designed to make it fast to contour small (e.g. 0.1x0.1 ppm) areas quickly. Use the mcnt program in MNMR (also distributed with Pronto/3D) to contour whole spectra. Q5.4 Why can't I zoom in the contour diagram using the mouse? This is normally not needed. In most cases, the contouring regions are set by importing ppm values from the other windows in Pronto/3D. The ppm values are taken from the cross peak list, the spin system list, the spin system buildup tool, or from the cross peak assignment tool. You can move up, down, left, or right and zoom in and out by using the arrows and other buttons in the contouring setup window. During manual cross peak identification, these buttons are used to contour the spectrum in 1x1 ppm areas to locate the cross peaks. Q5.5 How do I analyze a series of NOESY spectra? Start by assigning the cross peaks in ONE of the spectra. Use the one in a series with the most intense peaks. Use the "copy" button in the spectrum catalog window to copy all information (including cross peaks and assignments) to a new spectrum name, and insert the information about the new spectrum. Now you can reintegrate the new spectrum, using the same cross peak positions and integration limits as used for the first spectrum. Q5.6 How do I read in the assignments I already have made? Pronto/3D does not contain any direct way of importing information like cross peaks or spin system assignments. An indirect way exists: When Pronto/3D data bases are converted from one version of the program to a newer version, a temporary, ASCII representation of the data base is used. This is created by the $PRONTO_DIR/$PRONTO_VER/prog/expIO program. This is inserted in the new data base using the corresponding impIO program. In theory, one could code the assignments in this undocumented ASCII format and insert (impIO appends to the data base) it into the database. However, you must be careful as little check is done by the impIO program for inconsistencies, etc. The way of doing it manually is as follows: To insert a spin system in Pronto/3D, fill in the ppm values of all the atoms in the spin system in the contouring setup window and display the spin system in small windows. If the ppm list is correct, you should see the relevant cross peaks in the center of each subwindow. Now it is easy to click in the new peaks and build the spin system using the spin system assignment tool. Q5.7 Why doesn't the measure distance tool work? This is a very old bug in the program, still only partially solved. It normally only shows up when we demonstrate the program for people, or when some of the programmers are looking the other way. In order for the distance to be measured, the following should be done: A PDB file should be specified, "Dist On" should be set for exactly two dimensions, and an atom should be selected in each of the two, selected dimensions. If the bug appear, the program still doesn't show any distances. Closing and reopening the window might help... Also, I think the problem is related to starting Pronto/3D with the "-2D" or "-3D" switch. Q5.8 How do I change colors and fonts? Most colors are controlled by the Pronto resource file. This is by default the file: $PRONTO_DIR/$PRONTO_VER/Resources/pronto_res You can make your own copy of this file and set the environment variable PRONTO_RES to point to the directory containing the file. The fonts used for the display of Pronto windows can be set in your own .Xdefaults file: prontoIO*font: -misc-fixed-medium-r-normal--20-*-*-*-c-*-iso8859-1 saveloadIO*font: -misc-fixed-medium-r-normal--15-*-*-*-c-*-iso8859-1 Change "IO" after pronto to "SO" for the SPARC version. The resource file generally contain a section for each window or tool in Pronto/3D. Most of the definitions in this file is the text displayed in the buttons in Pronto/3D. Some user relevant definitions: *Cur_wnd_color: Background color of current window *Add_wnd_color: Background color of additional window *##_lines: Number of browser lines in the ## window *cnt_cache: Number of sets of contours cached *cnt_color0: Colors for contouring *cntp_cnt.labelFont: Font used when cross peaks a labelled with cross & text *cntp_cnt.axisColor: Color number used to draw the axes Definitions only relevant to Pronto/3D^2: *stp_plot.labelFont: Font used to label atoms drawn by X11 *stp_plot.fontSize: Size of font, in points *stp_plot.fmFont: Font used by GL *stp_plot.rGBMode: Use RGB mode? *stp_plot.doubleBuffer: Use double buffering? *stp_plot.zBuffer: Use Z-buffer? *stp_plot.depthCue: Do depth cueing? *stp_plot.zClip: Clip in z dimension? *stp_plot.dcZmin: Z minimum for clip *stp_plot.dcZmax: Z maximum for clip *struc_color0: Colors of atoms... *smooth_factor: Smoothing of the spline function. *swidth: Width of sheet. *sthick: Thickness of sheet. *rthick: Thickness of ribbon. *nsubdiv: No. of subdivisions of sheet plots. *halfBond: Plot half bond from atoms. Normally, a bond is only plotted if both of the atoms involved are selected. If this is set to true, you will see a "half" bond going out from each selected atom. *nwormdiv: No. of subdivisions for worm display. Q5.9 Why doesn't the help system work? This is first implemented in the Pronto/3D^2 version. Don't use the help button in version 930401; the program might crash! Q6. Future plans? Currently, we are working on an improvement on Pronto/3D^2 making it possible to write BASIC-like programs running in the data base environment. This is called Pronto Interactive Language System, PILS. This would make it possible to write small programs for numerous tasks: Analysing structures, e.g. plots of RMSD by residue or Ramachandran plots. Make a program that reads a file of assignments and insert them into the data base. Test algorithms for automatic assignments. The 950331 version contains some parts of the PILS system, but wait until later this summer to get a more useful version. Q7. Where can I get further information? Send me a mail/fax/email: Mogens Kjaer Carlsberg Laboratory, Dept. of Chemistry Gamle Carlsberg Vej 10 DK-2500 Valby Denmark Phone: +45 33 27 53 25 Fax: +45 33 27 47 08 Email: carlmk@unidhp.uni-c.dk ---------------------------------27443224246936-- From owner-structural-nmr@net.bio.net Mon Aug 07 23:00:00 1995 Path: biosci!PETER.BPC.UNI-FRANKFURT.DE!rolfi From: rolfi@PETER.BPC.UNI-FRANKFURT.DE (Rolf Winkelmann) Newsgroups: bionet.structural-nmr Subject: To Mr. Kristofferson Date: 8 Aug 1995 03:59:29 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <9508081222.AA05487@peter.bpc.uni-frankfurt.de> NNTP-Posting-Host: net.bio.net Dear Mr. Kristofferson I suppose that I only get personal e-mail messages instead off getting both personal and general messages from the network !? I do not know what the reason for this. Probably you can set me on the list for reciving general messages. If any other problem is responsable for this please contact me. Sincerely yours Rolf Winkelmann From owner-structural-nmr@net.bio.net Mon Aug 07 23:00:00 1995 Path: biosci!BCVMS.BC.EDU!MARKMANO From: MARKMANO@BCVMS.BC.EDU Newsgroups: bionet.structural-nmr Subject: NMR- reference to use of cs changes in structural studies Date: 7 Aug 1995 17:44:08 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HTSZ9ETYDE8Y8WZ2@bcvms.bc.edu> Reply-To: markmano@bcvms.bc.edu NNTP-Posting-Host: net.bio.net Thank for the help with the toons, Apparantly there is nothing directly made for X-plor cartoons outputs, but the options to use pronto-3d is available. Pronto-3d seem to have a wide vriety of graphical outputs. As other options, there is nothing for xplor. While I am at it, here is another Q. I am looking for a good reference to the use of changes in Chemical shifts as a way to assign constraints for phosphate binding. I am studing the interaction of phosphate-organic compound to protein, I have NOEs but not enough to constrain and get a tight clustering, I have nice changes in CS in the area of the binding site can I assign constraint for that in somehow a rigorous way? I'll appriciate references, but would take any advice. thanks much Ofer Markman From owner-structural-nmr@net.bio.net Tue Aug 08 23:00:00 1995 Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!EU.net!howland.reston.ans.net!nctuccca.edu.tw!news.cc.nctu.edu.tw!news.sinica!news From: Chen Chang Newsgroups: bionet.structural-nmr Subject: postdoc. in MRI/S Date: 9 Aug 1995 13:34:15 GMT Organization: Inst. of Biomedical Sciences Lines: 17 Message-ID: <40adgn$4g3@gate.sinica.edu.tw> NNTP-Posting-Host: 140.109.40.244 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) X-URL: news:bionet.structural-nmr A postdoctoral position is available immediately for recent Ph.D. with experience in NMR imaging and in vivo spectroscopy. Studies focus primarily on the correlation between brain function and metabolism. The NMR center at institute of Biomedical Sciences, Academia Sinica in Taipei, Taiwan is well equipped with three modern spectrometers, a Bruker AMX 600, a Bruker AMX 400WB equipped with microimaging accessories and a Biospec BMT 47/40 in vivo animal system. In addition, four SGI personal IRIS workstations are available for imaging processing and spectroscopic data analysis. Send curriculum vitae and three letters of reference to Dr. C. Chang, Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei 11529, Taiwan. Tel: 011-886-2-789-9027, Fax: 011-886-2-785-3569 Email:BMCCHEN@ccvax.sinica.edu.tw From owner-structural-nmr@net.bio.net Wed Aug 09 23:00:00 1995 Path: biosci!BIOSYM.COM!mjf From: mjf@BIOSYM.COM (Mark J Forster) Newsgroups: bionet.structural-nmr Subject: Re: Full-Matrix NOE/ROE Back-calculation Software Available??? Date: 10 Aug 1995 11:30:30 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 31 Sender: daemon@net.bio.net Distribution: world Message-ID: <199508101827.LAA17898@iris120.biosym.com> NNTP-Posting-Host: net.bio.net Alexandre Bonvin has kindly pointed out > BIOSYM also offers relaxation matrix calculations in their NMRrefine module. > Actually IRMA is coupled to Insight. The NMR_Refine module of v950 insightII has the IRMA NOE backcalculation code, which uses matrix diagonalisation methods. In addition it also offers the matrix doubling procedure which produces near identical results but is much more efficient, scaling as order O(N). This procedure is used in Discover 2.9x along with novel and efficient NOE gradient calculation to implement direct NOE refinement in a way is more rigourous than that offered by DINOSAUR, which in effect of considers the first two terms in the Taylor series expansion of the NOE matrix. In v950 Felix the matrix doubling procedure will be used for NOE back calculation of 2D NOESY and 3D NOE-NOE intensities. Hope this helps. Best Wishes. Mark J Forster ------------------------------------------------------------------ There are many types of football namely american, australian rules, rugby football, association football (a.k.a. soccer). Of course the only one worthy of the name is the latter in which most of the work is done with the feet not the hands - that is just too easy !!! Follower of Manchester United FC => top of the food chain. ------------------------------------------------------------------ From owner-structural-nmr@net.bio.net Wed Aug 09 23:00:00 1995 Path: biosci!rutgers!gatech!newsfeed.internetmci.com!usenet.eel.ufl.edu!news.gmi.edu!msunews!harbinger.cc.monash.edu.au!usenet From: Brendan Duggan Newsgroups: bionet.structural-nmr Subject: Re: NMR- reference to use of cs changes in structural studies Date: 10 Aug 1995 04:04:17 GMT Organization: Victorian College of Pharmacy, Monash University Lines: 8 Message-ID: <40c0g1$isi@harbinger.cc.monash.edu.au> References: <01HTSZ9ETYDE8Y8WZ2@bcvms.bc.edu> NNTP-Posting-Host: biochem.vcp.monash.edu.au Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Windows; I; 16bit) I'm also studying ligand-protein binding and have lots of variations in proton chemical shifts. If anybody knows of any references correlating direction and magnitude of change in chemical shift with the type of interacting group, I'd be very grateful. Brendan From owner-structural-nmr@net.bio.net Wed Aug 09 23:00:00 1995 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: Full-Matrix NOE/ROE Back-calculation Software Available??? Date: 10 Aug 1995 09:41:00 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 50 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <9508101557.AA02879@laplace.csb.yale.edu> NNTP-Posting-Host: net.bio.net One can license the (standalone) new MARDIGRAS version directly from Tom James (ca. $200 -- to my best recollection); it includes CARNIVAL. Worth to take a look. Best regards, Istvan ================================ Istvan Pelczer, Ph.D. Res. Assist. Professor Chemistry Department, CST Bldg. Syracuse University Syracuse, NY 13244-4100 ph: (315) 443 1023 or x-5932 fax: x-1022(lab) or x-4070(dept) Temporary address until Aug-14, 1995: c/o Prof. Heinz Ruterjans J.W. Goethe - Universitat Inst. fur Biophysikalische Chemie Biozentrum, N230 Marie-Curie-Str. 9 60439 Frankfurt am Main, Germany ph# 49 69 798 29630 or 31, fax# x-32 On 10 Aug 1995, Alexandre Bonvin wrote: > > PS.: There is also some new relaxation matrix code from Thomas James lab for > > ROESY intensities called CARNIVAL (J. Magn. Reson. B107 51 (1995)). > > Alexandre > > ========================================================================== > | Alexandre Bonvin PhD | Phone: (203) 432-5066 | > | Mol. Biophys. & Biochemistry | Fax: (203) 432-3923 | > | Yale University | Email: abonvin@laplace.csb.yale.edu | > | New Haven CT 06520-8114, USA | http://xplor.csb.yale.edu | > ========================================================================== > > From owner-structural-nmr@net.bio.net Wed Aug 09 23:00:00 1995 Path: biosci!LAPLACE.CSB.YALE.EDU!abonvin From: abonvin@LAPLACE.CSB.YALE.EDU ("Alexandre Bonvin") Newsgroups: bionet.structural-nmr Subject: Re: Full-Matrix NOE/ROE Back-calculation Software Available??? Date: 10 Aug 1995 09:35:58 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 49 Sender: daemon@net.bio.net Distribution: world Message-ID: <9508101633.AA02990@laplace.csb.yale.edu> NNTP-Posting-Host: net.bio.net It seems that my first answer got lost somewhere in the net. Here it is again: Dear Dale, Here is some www addresses you want to have a look at. They should give you information about some of the relaxation matrix programs available. IRMA/DINOSAUR http://www-nmr.chem.ruu.nl/ MORASS http://www.nmr.utmb.edu/ MARDIGRAS/CORMA http://picasso.ucsf.edu/mardi.html X-PLOR also has a relaxation matrix module allowing NOE simulations and refinement (http://xplor.csb.yale.edu) BIOSYM also offers relaxation matrix calculations in their NMRrefine module. Actually IRMA is coupled to Insight. During my PhD in Utrecht I developped a direct NOE refinement suite of programs called DINOSAUR. DINOSAUR has the ability to work with BIOSYM/DISCOVER coordinates files and calculate theoretical NOE intensities. However it won't simulate an entire spectrum. It is setup to calculate only those NOE intensities for which experimental data are available, i.e. you need a peak list as starting point. Cheers, Alexandre ========================================================================== | Alexandre Bonvin PhD | Phone: (203) 432-5066 | | Mol. Biophys. & Biochemistry | Fax: (203) 432-3923 | | Yale University | Email: abonvin@laplace.csb.yale.edu | | New Haven CT 06520-8114, USA | | ========================================================================== From owner-structural-nmr@net.bio.net Wed Aug 09 23:00:00 1995 Path: biosci!LAPLACE.CSB.YALE.EDU!abonvin From: abonvin@LAPLACE.CSB.YALE.EDU ("Alexandre Bonvin") Newsgroups: bionet.structural-nmr Subject: Re: Full-Matrix NOE/ROE Back-calculation Software Available??? Date: 10 Aug 1995 08:59:32 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: <9508101557.AA02879@laplace.csb.yale.edu> NNTP-Posting-Host: net.bio.net PS.: There is also some new relaxation matrix code from Thomas James lab for ROESY intensities called CARNIVAL (J. Magn. Reson. B107 51 (1995)). Alexandre ========================================================================== | Alexandre Bonvin PhD | Phone: (203) 432-5066 | | Mol. Biophys. & Biochemistry | Fax: (203) 432-3923 | | Yale University | Email: abonvin@laplace.csb.yale.edu | | New Haven CT 06520-8114, USA | http://xplor.csb.yale.edu | ========================================================================== From owner-structural-nmr@net.bio.net Sun Aug 13 23:00:00 1995 Path: biosci!GENETICS.COM!tmcdonagh From: tmcdonagh@GENETICS.COM (Tom McDonagh) Newsgroups: bionet.structural-nmr Subject: Position available in Protein Structure Determination Lab Date: 14 Aug 1995 07:44:42 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 50 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Structural Biology Department Small Molecule Drug Discovery Genetics Institute, Inc. 85 Bolton Street Cambridge, Ma. 02140 The structural biology department is seeking applicants for a Staff Scientist position. The successful candidate will have a Ph.D. and at least 2 years post-doc experience in the determination of protein solution structures(>10kDa). The Small Molecule Drug Discovery group includes a multi-disciplinary team of fifty scientists working in our Cambridge facility. The group is currently pursuing several novel targets including signal transduction proteins and intracellular regulatory enzymes. The NMR facility is equipped with a Varian 600 MHz Unity+ spectrometer with PFG, 4 channel capability, and deuterium decoupling. Computer resources within the lab include SGI R8000 workstations and a SGI Challenge series 8-CPU compute server. Genetics Institute (NASDAQ:GENIZ) is a leading biopharmaceutical firm engaged in the discovery, development, and commercialization of human pharaceuticals through recombinant DNA and other technologies. The company has a diversified portfolio of licenced and proprietary products at various stages of development, including treatments for anemia, hemophilia, cancer, bone damage, heart disease, inflammatory conditions, and immune system disorders. Please forward all e-mail responses to tmcdonagh@genetics.com Groundmail should be directed to Thomas McDonagh at the above address. ____________________________________________________________________________ Thomas McDonagh Small Molecule Drug Discovery#| Phone: (617)-498-8962 Genetics Institute, Inc.#| Fax: (617)-498-8993 85 Bolton Street | E-mail: tmcdonagh@genetics.com Cambridge, MA 02140 From owner-structural-nmr@net.bio.net Sun Aug 13 23:00:00 1995 Path: biosci!NODDY.CM.UTEXAS.EDU!dave From: dave@NODDY.CM.UTEXAS.EDU (david w. hoffman) Newsgroups: bionet.structural-nmr Subject: (none) Date: 14 Aug 1995 06:50:39 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <9508141348.AA05457@noddy.cm.utexas.edu> NNTP-Posting-Host: net.bio.net Dear NMR-netters, I am looking for a few suggestions for "up to date" (or nearly so) books from which a graduate student in chemistry or biochemistry could learn something about modern NMR spectroscopy, with an emphasis on solution NMR, protein/nucleic acid structure, multi-dimensional NMR, and maybe carbohydrate and "organic molecule" applications. Either respond directly to me, or post your response to the "net", since this may be of general interest. Thanks. Dave Hoffman Univ. of Texas at Austin e-mail: dave@noddy.cm.utexas.edu From owner-structural-nmr@net.bio.net Mon Aug 14 23:00:00 1995 Path: biosci!agate!spool.mu.edu!uwm.edu!homer.alpha.net!solaris.cc.vt.edu!news.bluesky.net!news.sprintlink.net!sunic!sunic.sunet.se!seunet!news2.swip.net!mailgate.astra.com!usenet From: Bob Carter Newsgroups: bionet.structural-nmr Subject: Head of the ASTRA Structural Chemistry Laboratory Date: 15 Aug 1995 11:57:11 GMT Organization: Astra AB Lines: 43 Message-ID: <40q22n$m0m@mailgate.astra.com> NNTP-Posting-Host: 157.96.200.39 Astra is a pharmaceutical company in a phase of rapid growth. The company's operations, which are highly international, consist of research, production and marketing of pharmaceuticals through subsidiaries, agents and licensees all over the world. Sales in 1994 amounted to SEK 28 billion (USD 3.65 billion). A central Structural Chemistry Laboratory is to be established for the Astra group, with the mission to provide the projects of the Astra product companies with structural information on macromolecular targets of therapeutic interest. The Laboratory is projected to be operational during 1997, with a staff of 14 scientists, and will be located at the Astra Haessle site in Gothenborg, Sweden. The scientific disciplines initially available at the Laboratory will be protein crystallography (state-of-the-art instrumentation), NMR spectroscopy (750, 600, 400 MHz), and protein biochemistry. Implementation of additional technologies is foreseen for the future. We are now looking for a highly experienced and motivated scientist as Head of the Structural Chemistry Laboratory. The successful candidate will have a strong background in the physical organic, bioorganic, or biophysical sciences, and will have had experience with research management in an appropriate field. Documented experience in the field of macromolecular structure determination is a prerequisite. Experience with structural chemistry in drug discovery in the pharmaceutical industry is an advantage. The Head of the Laboratory will be expected to take an active part in the recruitment of key scientific personnel, and in the build up of the facilities. The position involves responsiblilty for operations and management, as well as for the maintenance of the Laboratory at state-of-the-art level. Strong interpersonal communications skills are important, as well as experience in managing people in a multidisciplinary team. The Head of the Laboratory will be expected to collaborate fully with project teams at the product companies. For more information, please contact Bob Carter, +46 31 776 1621 or Bertil Samuelsson, +46 31 776 1350 Applications marked E-98/95 Head of the Astra Structural Chemistry Laboratory should be sent to the following address: Astra Haessle AB, Human Resources, Att. Paula Wallklev, S-431 83 Molndal, Sweden. Fax: +46 31 776 3746. From owner-structural-nmr@net.bio.net Mon Aug 14 23:00:00 1995 Newsgroups: bionet.announce.bionet.biology.computational,bionet.physics,bionet.general,bionet.info-theory,bionet.structural-nmr,bionet.software,can.med.misc,fj.sci.bio,fj.sci.medical,sci.bio,sci.bio.technology,sci.engr.biomed,sci.image.processing,sci.med,sci.med.informatics,sci.med.pathology,sci.med.physics Path: biosci!galaxy.ucr.edu!library.ucla.edu!info.ucla.edu!newsfeed.internetmci.com!news.sprintlink.net!dispatch.news.demon.net!demon!uknet!liv!ch0s4005 From: ch0s4005@liverpool.ac.uk (Mr DJ Beechs) Subject: 3D RECONSTRUCTION OF TERMINAL DUCTS Message-ID: Keywords: lung terminal duct sids 3d reconstruction Sender: news@liverpool.ac.uk (News System) Nntp-Posting-Host: elm-21.liv.ac.uk Organization: The University of Liverpool Date: Tue, 15 Aug 1995 12:47:27 GMT Lines: 27 Xref: biosci bionet.general:16525 bionet.info-theory:3567 bionet.structural-nmr:713 bionet.software:12990 sci.bio:18365 sci.bio.technology:3594 sci.engr.biomed:4231 sci.image.processing:14926 sci.med:89273 sci.med.informatics:3382 sci.med.pathology:1154 sci.med.physics:3328 > Please help! I am currently studying for a PhD, looking into anatomical defects in the lungs and kidneys of cot death (SIDS) victims. I want to 3 dimensionally reconstruct the terminal duct complex of SIDS and non-SIDS infants, using microscopy and histology. If anyone has any information could they please contact me. Many thanks, DARREN J. BEECH Department of Fetal and Infant Pathology RLCH Mulberry St LIVERPOOL L7 7DG UK Phone - +44 151 794 3856 Fax - +44 151 794 3854 E-Mail - ch0s4005@liverpool.ac.uk From owner-structural-nmr@net.bio.net Mon Aug 14 23:00:00 1995 Newsgroups: bionet.structural-nmr Path: biosci!rutgers!gatech!news.uoregon.edu!vixen.cso.uiuc.edu!news.ecn.bgu.edu!news.moneng.mei.com!news.inc.net!news.sprintlink.net!rockyd!notes From: cowburn Subject: Job available. X-Nntp-Posting-Host: mr_pc2.rockefeller.edu Message-ID: Sender: notes@rockyd.rockefeller.edu (News Administrator) Organization: Rockefeller University Date: Tue, 15 Aug 1995 18:48:47 GMT Lines: 5 I am looking for someone interested in a postdoctoral opportunity in Molecular/Structural Biology related to Signal Transduction. Experience in cloning and expression is required. Training or interest in structural biology is essential. E-mail cowburn@rockvax.rockefeller.edu with an outline cv and names of three references. From owner-structural-nmr@net.bio.net Mon Aug 14 23:00:00 1995 Path: biosci!SAVBA.SAVBA.SK!uachmalk From: uachmalk@SAVBA.SAVBA.SK (Vladimir Malkin) Newsgroups: bionet.structural-nmr Subject: CS <--> structure correlations Date: 15 Aug 1995 09:59:57 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 110 Sender: daemon@net.bio.net Distribution: world Message-ID: <199508151656.AA16961@savba.savba.sk> NNTP-Posting-Host: net.bio.net Dear str-NMR netters, Last week two questions concerning a possibility to use the changes in chemical shifts (CS) as a way to assign constraints for ligand-protein binding have been asked. Unfortunately, there is a deficiency of such correlations based on experimental data. As an alternative to such "experimental" correlations one can, in principle, develop theoretical correlations based on quantum-chemical calculations of CS. From our point of view, this is a very promising direction and we expect that many groups might be interested in such "theoretical" correlations. As one of the authors of the recently developed SOS-DFPT (Sum-Over-States Density Functional Perturbation Theory) approach for CS calculations [1,2] I believe that we can do a good job in this direction using our method and code (which is very fast and reliable). As we know, some groups already use our code for such studies and we have some positive responses. Since I believe that much more efforts should be spend in this field I am playing with an idea to organize a wide cooperation on this topic. Being involved in some of such studies we still mostly work in the field of "quantum-chemical method development" and we would be very glad to see a response from the people for whom this direction (development of NMR CS <---> structure correlations) is very topical. Responses from the people who would like to participate actively in such project are especially welcome. Looking forward to learn your opinions, Vladimir Malkin PS. See some enclosed information about the method and list of references below. *************************************************************** * Dr. Vladimir G. Malkin * * Senior Research Scientist * * Institute of Inorganic malkin@savba.sk * * Chemistry, SAV Phone (42-7) 378-2923 * * Dubravska cesta 9 Fax (42-7) 373-541 * * SK-84236 Bratislava * * Slovakia * *************************************************************** About our method: ----------------- Sum-Over-States Density Functional Perturbation Theory (SOS-DFPT) approach implemented in the deMon/NMR code produces reliable results for chemical shift calculations. The SOS-DFPT approach with the IGLO choice of gauge origin [1,2] leads to superior results in comparison with the uncoupled DFT approach or Hartree-Fock approaches (IGLO, GIAO or other choice of gauge origin). Providing the results almost as good as MP2 for 13-C chemical shifts in systems with relatively small correlation effects and significantly more reliable for systems with strong correlation [3]. The real "break-through" for SOS-DFPT (being more efficient than Hartree-Fock and post-Hartree-Fock methods) is the ability to compute larger molecules (including biosystems and transition metal complexes [1-11]) with reasonable accuracy. It might be also of your interest our (also recently developed) approach for spin-spin coupling constant calculations [2,8] which yields very reliable results for C-C, C-H, H-H couplings [2,8]. REFERENCES ---------- 1) {\bf Malkin V.G., Malkina O.L., Casida M.E., and Salahub D.R.} "Nuclear Magnetic Resonance Shielding Tensors Calculated with a Sum-Over-States Density Functional Perturbation Theory", J. Am. Chem. Soc., 116 (1994) 5898. 2) {\bf Malkin V.G., Malkina O.L, Eriksson L.A., and Salahub D.R.} "The Calculation of NMR and ESR Spectroscopy Parameters Using Density Functional Theory", in: "Theoretical and Computational Chemistry", vol. 2, "Modern Density Functional Theory: A Tool For Chemistry", edited by J.M. Seminario and P. Politzer, Elsevier, Amsterdam, 1995. 3) {\bf Kaupp M., Malkin V.G., Malkina O.L., and Salahub D.R.} "Calculation of Ligand NMR-Chemical Shifts in Transition-Metal Complexes Using ab Initio Effective-Core Potentials and Density Functional Theory.", Chem. Phys. Lett. 235 (1995) 382-388. 4) {\bf Malkin V.G., Malkina O.L., and Salahub D.R.} "Influence of Intermolecular Interactions on the NMR Shielding Tensors in Solid alpha-Glycine.", J. Am. Chem. Soc. 117 (1995) 3294-3295. 5) Kaupp M., Malkin V.G., Malkina O.L., and Salahub D.R. "Calculation of Ligand NMR Chemical Shifts in Transition-Metal Complexes Using ab Initio Effective-Core Potentials and Density Functional Theory", {\it Chem. Phys. Lett.}, { 235} (1995) 382. 6) Kaupp M., Malkin V.G., Malkina O.L., and Salahub D.R. "Scalar Relativistic Effects on 17-O NMR Chemical Shifts in Transition-Metal Oxo Complexes. An ab Initio ECP/DFT Study", {\it J. Am. Chem. Soc.}, { 117} (1995) 1851. 7) Kaupp M., Malkin V.G., Malkina O.L., and Salahub D.R. "An ab Initio ECP/DFT Calculation and Interpretation of Carbon and Oxygen NMR Chemical Shift Tensors in Transition-Metal Carbonyl Complexes", {\it Chem. Euro. J.} (1995), submitted for publication. 8) {\bf Malkin V.G., Malkina O.L., and Salahub D.R.} "Calculation of Spin-Spin Coupling Constants Using Density Functional Theory", Chem. Phys. Lett. 221 (1994) 91. 9) {\bf Malkin V.G., Malkina O.L., G. Steinebrunner and H. Huber} "Solvent effect on the NMR chemical shieldings in water calculated by a combination of molecular dynamics and density functional theory", {\it Chem. Euro. J.} (1995), submitted for publication. 10) {\bf Woolf T.B., Malkin V.G., Malkina O.L., Salahub D.R., and Roux B.} "The Backbone $^{15}$N Chemical Shift Tensor of the Gramicidin Channel: A Molecular Dynamics and Density Functional Study", Chem. Phys. Lett. 239 (1995) 186. 11) {\bf C. Maerker, P. von R. Schleyer, D.R. Salahub, O.L. Malkina, and V.G Malkin} "Accuracy and Performance of Density Functional Computation of 13-C NMR Chemical Shifts", to be submitted. From owner-structural-nmr@net.bio.net Tue Aug 15 23:00:00 1995 Path: biosci!lab.takeda.co.jp!murakami From: murakami@lab.takeda.co.jp (Morio Murakami) Newsgroups: bionet.structural-nmr Subject: NMR research of beta-amyloid peptide fragments Date: 16 Aug 1995 02:29:23 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 56 Sender: daemon@net.bio.net Distribution: world Message-ID: <9508160900.AA21136@lab.takeda.co.jp> NNTP-Posting-Host: net.bio.net Daer str-NMR list members, I am very interested in the 42-residue beta-amyloid protein implicated in the formation of insoluble plaques in Alzheimer's disease. Now I am studying the interaction of beta-amyloid peptide fragment 25-35 with biological model membranes using various spectroscopy . I am encouraged at E.Terzi at al.'s work named "Alzheimer beta-Amyloid Peptide 25-35: Electrostatic Interactions with Phospholipid Membranes ", Biochemistry, 33, 7434-7441 (1994). I am attempting to track down NMR research on beta-amyloid protein and its fragment. For example, I know of the following the works: Ref.1 beta-amyloid fragment 1-28 Michael G. Zagorski et al., "NMR Studies of amyloid beta-peptides: Proton Assignments, Secondary Structure, and Mechanism of an alpha-Helix → beta-Sheet Conversion for a Homologous, 28-Residue, N-Terminal Fragment", Biochemistry, 31, 5621-5631 (1992) Ref.2 beta-amyloid fragment 1-28 Joseph Talafous et al., "Solution Structure of Residues 1-28 of the Amyloid beta-Peptide" Biochemistry, 33, 7788-7796 (1994) Ref.3 beta-amyloid fragment 10-35 Jonathan P. Lee at al., "1H NMR of beta-Amyloid Peptide Congeners in Water Solution. Conformational Change Correlate with Plaque Competence" Biochemistry, 34, 5191-5200 (1995) Does anyone know any works and references about the comformation determination of beta-amyloid peptide fragments using NMR spectroscopy? And also I am looking for the reference about the interaction of beta-myloid with the biological membranes. I will summarize the responses accordingly. Sincerely, Morio Murakami ************************************************* Morio Murakami Molecular Chemistry Laboratory Pharmaceutical Research Division Takeda Chemical Industries, LTD. 2-17-85, Jusohonmachi, Yodogawa-ku, Osaka 532, JAPAN E-mail. murakami@lab.takeda.co.jp FAX 81-6-300-6306 TEL 81-6-300-6618 ************************************************* From owner-structural-nmr@net.bio.net Tue Aug 15 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!hookup!news.mathworks.com!news.bluesky.net!news.sprintlink.net!in2.uu.net!shore!news3.near.net!loki.novalink.com!usenet From: "Richard H. Siderits" Newsgroups: bionet.announce.bionet.biology.computational,bionet.physics,bionet.general,bionet.info-theory,bionet.structural-nmr,bionet.software,can.med.misc,fj.sci.bio,fj.sci.medical,sci.bio,sci.bio.technology,sci.engr.biomed,sci.image.processing,sci.med,sci.med.informatics,sci.med.pathology,sci.med.physics Subject: Re: 3D RECONSTRUCTION OF TERMINAL DUCTS Date: 16 Aug 1995 06:05:01 GMT Organization: HFMC Lines: 7 Distribution: inet Message-ID: <40s1qd$anq@loki.novalink.com> References: NNTP-Posting-Host: ppp-151.dialup-1.novalink.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Windows; I; 16bit) Xref: biosci bionet.general:16539 bionet.info-theory:3568 bionet.structural-nmr:717 bionet.software:13000 sci.bio:18379 sci.bio.technology:3600 sci.engr.biomed:4240 sci.image.processing:14950 sci.med:89377 sci.med.informatics:3389 sci.med.pathology:1161 sci.med.physics:3332 For simple 3D recon you might try an old wire frame program called PC3D and an image capture board with a digitizing tablet. Its pretty straight forward. I did a few 3D and 4D recons with the Pittsburgh supercomputing center. They are another good resource and they provide "Starter" grants for allocation of the PSC resources. 412-268-4960 From owner-structural-nmr@net.bio.net Wed Aug 16 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!simtel!harbinger.cc.monash.edu.au!news.uwa.edu.au!madvax!watson From: watson@madvax (Dave Watson) Newsgroups: bionet.general,bionet.info-theory,bionet.structural-nmr,bionet.software,sci.bio.technology,sci.engr.biomed,sci.image.processing,sci.med,sci.med.informatics,sci.med.pathology,sci.med.physics Subject: Re: 3D RECONSTRUCTION OF TERMINAL DUCTS Followup-To: bionet.general,bionet.info-theory,bionet.structural-nmr,bionet.software,sci.bio.technology,sci.engr.biomed,sci.image.processing,sci.med,sci.med.informatics,sci.med.pathology,sci.med.physics Date: 17 Aug 1995 00:14:48 GMT Organization: The University of Western Australia Lines: 23 Message-ID: <40u1lp$uc0@styx.uwa.edu.au> References: NNTP-Posting-Host: madvax.maths.uwa.edu.au X-Newsreader: TIN [version 1.2 PL1] Xref: biosci bionet.general:16548 bionet.info-theory:3570 bionet.structural-nmr:719 bionet.software:13005 sci.bio.technology:3604 sci.engr.biomed:4251 sci.image.processing:14977 sci.med:89489 sci.med.informatics:3403 sci.med.pathology:1167 sci.med.physics:3335 Mr DJ Beechs (ch0s4005@liverpool.ac.uk) wrote: : > Please help! : I am currently studying for a PhD, looking into anatomical : defects in the lungs : and kidneys of cot death (SIDS) victims. : I want to 3 dimensionally reconstruct the terminal duct complex of SIDS and : non-SIDS infants, using microscopy and histology. : If anyone has any information could they please contact me. I market a program, derma-c, which will do what you ask. If you send me a series of crossections, expressed as bitmaps, I will reconstruct the solid object that they represent as approximated by a set of triangular facets, as a demonstration. -- Dave Watson, PhD Spatial Interpolation Specialist P.O. Box 734 watson@iinet.com.au Claremont, WA 6010 Australia Tel: (61 9) 385 2227 See my web page - http://www.iinet.com.au/~watson/ From owner-structural-nmr@net.bio.net Fri Aug 18 23:00:00 1995 Path: biosci!agate!ames!neuron.arc.nasa.gov!kevin From: kevin@neuron.arc.nasa.gov (Kevin Montgomery) Newsgroups: bionet.announce.bionet.biology.computational,bionet.physics,bionet.general,bionet.info-theory,bionet.structural-nmr,bionet.software,can.med.misc,fj.sci.bio,fj.sci.medical,sci.bio,sci.bio.technology,sci.engr.biomed,sci.image.processing,sci.med,sci.med.informatics,sci.med.pathology,sci.med.physics Subject: Re: 3D RECONSTRUCTION OF TERMINAL DUCTS Date: 19 Aug 1995 21:29:52 GMT Organization: NASA-Ames Biocomputation Center Lines: 16 Distribution: world Message-ID: <415l4k$is2@news.arc.nasa.gov> References: NNTP-Posting-Host: neuron.arc.nasa.gov Keywords: lung terminal duct sids 3d reconstruction Xref: biosci bionet.general:16572 bionet.info-theory:3573 bionet.structural-nmr:721 bionet.software:13023 sci.bio.technology:3626 sci.engr.biomed:4271 sci.image.processing:15051 sci.med:89805 sci.med.informatics:3431 sci.med.pathology:1195 sci.med.physics:3346 In article , ch0s4005@liverpool.ac.uk (Mr DJ Beechs) writes: |> I want to 3 dimensionally reconstruct the terminal duct complex of SIDS and |> non-SIDS infants, using microscopy and histology. I'd like to point everyone to the 3D Reconstruction Web Site- it contains information on around 70 different software packages, on-line data sets, an extensive reference bibliography, images/movies of reconstructions, and pointers to related information available on the Internet. It covers reconstruction from MRI, CAT, PET, and microscopy (light, confocal, EM). The URL for this site is: http://biocomp.arc.nasa.gov/3dreconstruction Enjoy! Kevin From owner-structural-nmr@net.bio.net Mon Aug 21 23:00:00 1995 Path: biosci!jk.uni-linz.ac.at!Alexej.Jerschow From: Alexej.Jerschow@jk.uni-linz.ac.at (Alexej Jerschow) Newsgroups: bionet.structural-nmr Subject: WinNMR2D file format Date: 22 Aug 1995 09:47:13 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <199508221645.AA03044@alijku06.edvz.uni-linz.ac.at> NNTP-Posting-Host: net.bio.net Dear Netters, Does anyone out there know the WinNMR2D file format ? UXNMR 2D-file format would do as well ! Thanx Sincerely AJ ---------------------------------------------------------------- Alexej Jerschow Organic Chemistry, Johannes Kepler University Linz, Austria Tel: +43-732-2468-777 (or 748 or 777) or +43-732-246202 (home) Fax: +43-732-2468-747 From owner-structural-nmr@net.bio.net Tue Aug 22 23:00:00 1995 Path: biosci!jk.uni-linz.ac.at!Alexej.Jerschow From: Alexej.Jerschow@jk.uni-linz.ac.at (Alexej Jerschow) Newsgroups: bionet.structural-nmr Subject: WinNMR2D file format Date: 23 Aug 1995 00:54:13 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <199508230752.AA11095@alijku06.edvz.uni-linz.ac.at> NNTP-Posting-Host: net.bio.net Dear Netters, Since I was asked, which WinNMR-file format I meant, I send the message again: Does anyone out there know the WinNMR2D file format (The 2rr format) ? UXNMR 2D-file format would do as well ! Thanx Sincerely AJ ---------------------------------------------------------------- Alexej Jerschow Organic Chemistry, Johannes Kepler University Linz, Austria Tel: +43-732-2468-777 (or 748 or 777) or +43-732-246202 (home) Fax: +43-732-2468-747 From owner-structural-nmr@net.bio.net Tue Aug 22 23:00:00 1995 Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!EU.net!uknet!bhamcs!news.ox.ac.uk!nmra.ocms!smb From: smb@bioch.ox.ac.uk (Simon Brocklehurst) Newsgroups: bionet.structural-nmr Subject: ANNOUNCE: NMR structure refinement module Date: 23 Aug 1995 13:32:41 GMT Organization: Oxford University Lines: 50 Message-ID: <41falp$5co@news.ox.ac.uk> NNTP-Posting-Host: nmra.ocms.ox.ac.uk NAOMI - Module Announcement (Please note, NAOMI is provided at zero charge for academic use) (e-mail contact smb@bioch.ox.ac.uk) The NMR structure refinement module of NAOMI is available now. It allows hydrogen bond restraints to be "sorted out" objectively, and automatically. Existing users should request a FEATURE 5 license key, and upgrade to Version 2.10c of the program. ____________________________________________________________________________ An extract from the User Guide is shown below: Hydrogen bond restraints are important in defining the three-dimensional structure of proteins in many NMR structure determinations. But it is difficult (and often impossible) to identify hydrogen bonding partners by direct observation by using current NMR experiments. One of the best ways to attack this problem is to analyse ensembles of structures calculated without hydrogen bond restraints, to see where donor-acceptor pairs can be identified unambiguously. In combinatation with hydron exchange NMR experiments, this approach can, in favourable cases allow identification of both donor and acceptor partners of: both regular and distorted secondary structural hydrogen bonds. main-chain - main-chain tertiary hydrogen bonds side-chain - main-chain hydrogen bonds involving amide-proton donors _____________________________________________________________________________ See the User Guide on NAOMI WWW site at: http://www.ocms.ox.ac.uk/~smb/Software/N_details/naomi.html for more details and example output. _____________________________________________________________________________ NB NAOMI works only on Silicon Graphics workstations running IRIX 5.* _____________________________________________________________________________ | | ,_ o Simon M. Brocklehurst, | / //\, Oxford Centre for Molecular Sciences, Department of Biochemistry, | \>> | University of Oxford, Oxford, UK. | \\, E-mail: smb@bioch.ox.ac.uk | WWW: http://www.ocms.ox.ac.uk/~smb/ |____________________________________________________________________________ From owner-structural-nmr@net.bio.net Wed Aug 23 23:00:00 1995 Path: biosci!agate!newsxfer.itd.umich.edu!news.itd.umich.edu!usenet From: Rick Neubig Newsgroups: bionet.structural-nmr Subject: Re: WinNMR2D file format Date: 23 Aug 1995 19:26:48 GMT Organization: University of Michigan Lines: 16 Message-ID: <41fvdo$1pf@lastactionhero.rs.itd.umich.edu> References: <199508221645.AA03044@alijku06.edvz.uni-linz.ac.at> NNTP-Posting-Host: warbler.med.umich.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Windows; I; 16bit) To: Alexej.Jerschow@jk.uni-linz.ac.at Alexej.Jerschow@jk.uni-linz.ac.at (Alexej Jerschow) wrote: >Dear Netters, > Does anyone out there know the WinNMR2D file format ? UXNMR 2D-file >format would do as well ! What is WinNMR2D? Is it for Microsoft Windows or is it a Unix program? Thanks in advance for putting up with a naive question. Rick _________________________________________________________ Rick Neubig RNeubig@umich.edu University of Michigan Phone (313) 763-3650 http://www.umich.edu/~rneubig FAX (313) 763-4450 From owner-structural-nmr@net.bio.net Thu Aug 24 23:00:00 1995 Path: biosci!rutgers!gatech!swrinde!howland.reston.ans.net!vixen.cso.uiuc.edu!newsrelay.iastate.edu!news.iastate.edu!kintanar From: kintanar@iastate.edu (Agustin Kintanar) Newsgroups: bionet.structural-nmr Subject: JOB ANNOUNCEMENT Date: 24 Aug 1995 16:06:51 GMT Organization: Iowa State University, Ames, Iowa USA Lines: 17 Message-ID: <41i82r$jkt@news.iastate.edu> NNTP-Posting-Host: pv0a0b.vincent.iastate.edu Originator: kintanar@pv0a0b.vincent.iastate.edu The Department of Biochemistry & Biophysics at Iowa State University seeks an NMR specialist to perform routine maintenance, train instrument users, as well as to design, implement and analyze experiments on a Varian UNITY 500 NMR spectrometer. A Ph.D. in biophysics, biochemistry or physical chemistry, along with expertise in current applications of NMR to biological macromolecules is essential. Collaborative research using NMR and other biophysical techniques is encouraged. Send C.V. and three letters of reference to: Dr. Basil Nikolau c/o Donna Nelson, Dept. of Biochemistry & Biophysics, 1210 Molecular Biology Bldg., ISU, Ames, IA 50011-3260 From owner-structural-nmr@net.bio.net Mon Aug 28 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.sprintlink.net!sundog.tiac.net!cil.tiac.net!tasha From: tasha@isotope.com (Tasha Agreste) Newsgroups: bionet.structural-nmr Subject: bacterial expression Date: Tue, 29 Aug 1995 14:52:45 Organization: Cambridge Isotope Laboratories Lines: 14 Message-ID: NNTP-Posting-Host: cil.tiac.net X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] I recently received a survey questionaire from an unidentified individual containing several questions regarding label incorporation into induced bacterial expression systems. The individual is from the northern New Jersey area as indicated by the post-mark. I would be more than happy to answer his/her questions, however no name, address or phone number was written on the survey. If this individual subscribes to this news group please contact me at the address below. I would be happy to discuss your inquiry. Tasha Agreste Cambridge Isotope Laboratories 50 Frontage Rd Andover MA 01810 1-800-322-1174 tasha@isotope.com From owner-structural-nmr@net.bio.net Tue Aug 29 23:00:00 1995 Path: biosci!DINO.FOLD.FCCC.EDU!hong From: hong@DINO.FOLD.FCCC.EDU (Hong Cheng) Newsgroups: bionet.structural-nmr Subject: (none) Date: 30 Aug 1995 06:16:19 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <199508301314.JAA02273@dino.fold.fccc.edu> NNTP-Posting-Host: net.bio.net subscribe hong@dino.fold.fccc.edu From owner-structural-nmr@net.bio.net Tue Aug 29 23:00:00 1995 Path: biosci!SUNNSC.NSC.SYR.EDU!kerwood From: kerwood@SUNNSC.NSC.SYR.EDU (Deborah Kerwood) Newsgroups: bionet.structural-nmr Subject: subscribe Date: 30 Aug 1995 13:41:30 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <9508301943.AA08494@sunnsc.nsc.syr.edu> NNTP-Posting-Host: net.bio.net From owner-structural-nmr@net.bio.net Tue Aug 29 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!spool.mu.edu!sdd.hp.com!news.cs.indiana.edu!purdue!mozo.cc.purdue.edu!not-for-mail From: eog@mace.cc.purdue.edu (Vicki Finkenstadt) Newsgroups: bionet.structural-nmr Subject: Faculty Search - Food NMR - Purdue U. Date: 29 Aug 1995 18:54:52 -0500 Organization: Purdue University Lines: 72 Message-ID: <4209cc$i5d@mace.cc.purdue.edu> NNTP-Posting-Host: mace.cc.purdue.edu Keywords: faculty professor job search nmr p-chem food employment PhD ***** A copy of this announcement is resident in: URL: http://www.foodsci.purdue.edu/~vicki/nmrpost.html More information on the Carbohydrate Center, Food Science Department, and Purdue University is available from this page. ***** PURDUE UNIVERSITY DEPARTMENT OF FOOD SCIENCE ACADEMIC POSITION ANNOUNCEMENT SOLIDS NMR SPECTROSCOPIST POSITION: Tenure-track faculty position in NMR spectroscopy as applied to food and agriculture involving fundamental and applied research and teaching. LOCATION: Department of Food Science, 1160 Smith Hall, Purdue University, West Lafayette, IN 47907-1160 APPOINTMENT AND SALARY: Assistant or Associate Professor on a 10-month appointment. Salary commensurate with experience. Up to three months supplemental salary from external funding is possible. Appointment will be 70% research, 20% teaching, 10% extension. QUALIFICATIONS: Ph.D. in physical chemistry, biophysics, food science, or a related discipline with an emphasis on solids NMR spectroscopy applied to biological materials. Good teaching, communication, interactive skills, and a desire to work with companies on practical problems are essential. RESPONSIBILITIES: The person selected for the position will be expected to establish an innovative research program in solids NMR spectroscopy of biological materials. Examples of areas of investigation are examination of behavioral characteristics of starches, food gums, and other biopolymers; textures and stabilities of food products; identification and quantitation of individual components; determinations of molecular events underlying the functionalities of individual components; and changes in composition of phases over time. The person is expected to conduct fundamental research related to practical problems, to collaborate with other faculty of the Department of Food Science and the School of Agriculture and with scientists from food and food ingredient companies, to secure external research funding, and to supervise the Food Science NMR facility. Teaching expectations include a graduate course in the area of specialization and, perhaps, a general course in the physical chemistry of foods. STARTING DATE: open APPLICATION DEADLINE: until the position is filled. APPLICATION: Send letter of application; curriculum vitae; the names, addresses, and telephone numbers of three references; and a 1-3 page description of research interests and a proposed research program to: James N. BeMiller Department of Food Science 1160 Smith Hall Purdue University West Lafayette, IN 47907-1160 Email inquiries to: wccr@foodsci.purdue.edu *NO* electronic submissions accepted. Snail mail package to above address. Purdue University is an Equal Opportunity/Affirmative Action Employer -- Vicki Finkenstadt eog@mace.cc.purdue.edu Carbohydrate Center vicki@kiwi.foodsci.purdue.edu Purdue University http://www.foodsci.purdue.edu/~vicki "There is much that is true, wise and beautiful in this world." From owner-structural-nmr@net.bio.net Wed Aug 30 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!newsrelay.iastate.edu!news.iastate.edu!baker From: baker@iastate.edu (Wayne R. Baker) Newsgroups: bionet.structural-nmr,sci.techniques.mag-resonance,bionet.jobs,bionet.molec-model Subject: NMR Spectroscopist Position Available Date: 31 Aug 1995 02:08:14 GMT Organization: Biochemistry & Biophysics, Iowa State University Lines: 25 Message-ID: <4235ie$sr0@news.iastate.edu> Reply-To: nmr-search@iastate.edu NNTP-Posting-Host: pv0a05.vincent.iastate.edu Xref: biosci bionet.structural-nmr:732 sci.techniques.mag-resonance:1154 bionet.molec-model:570 NMR SPECIALIST The Department of Biochemistry & Biophysics, Iowa State University, Ames, Iowa, seeks an NMR specialist to perform routine maintenance, to train users, as well as to design, implement and analyze experiments on a Varian UNITY 500 NMR. A Ph.D. or the equivalent experience in biophysics, biochemistry or physical chemistry, along with expertise in current application of NMR to biological macromolecules is essential. Collaborative research using NMR and other biophysical techniques is encouraged. Send C.V. and three letters of reference to: Dr. Basil Nikolau c/o Donna Nelson Dept. of Biochemistry & Biophysics 1210 Molecular Biology Bldg. Iowa State University Ames, IA 50011-3260 From owner-structural-nmr@net.bio.net Wed Aug 30 23:00:00 1995 Path: biosci!rutgers!uwm.edu!spool.mu.edu!usenet.eel.ufl.edu!newsfeed.internetmci.com!tank.news.pipex.net!pipex!sunsite.doc.ic.ac.uk!hgmp.mrc.ac.uk!nimr.mrc.ac.uk!m-gradwe From: m-gradwe@nimr.mrc.ac.uk (Mike Gradwell) Newsgroups: bionet.structural-nmr Subject: spin simulation Date: 31 Aug 1995 09:11:03 GMT Organization: National-Institute-for-Medical-Research Lines: 5 Distribution: world Message-ID: <423ub7$9a3@mercury.hgmp.mrc.ac.uk> NNTP-Posting-Host: nimsb42.nimr.mrc.ac.uk We are looking for a recent spin simulation program. Does anyone have any relevant details? Thanking you in advance Mike Gradwell National Institute for Medical Research From owner-structural-nmr@net.bio.net Wed Aug 30 23:00:00 1995 Path: biosci!agate!spool.mu.edu!howland.reston.ans.net!tank.news.pipex.net!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: th@mrc-cpe.cam.ac.uk (Tim Hubbard) Newsgroups: bionet.structural-nmr Subject: ANNOUNCEMENT: have you a protein to predict? FINAL Call for prediction targets Date: 31 Aug 1995 11:13:51 +0100 Lines: 40 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <42420v$9d3@mserv1.dl.ac.uk> X-Sender: th@ind1.mrc-lmb.cam.ac.uk Original-To: pdb-l@pdb.pdb.bnl.gov, bioforum@dl.ac.uk, bionews@dl.ac.uk, biophys@dl.ac.uk, bio-soft@dl.ac.uk, comp-bio@dl.ac.uk, methods@dl.ac.uk, molmodel@dl.ac.uk, proteins@dl.ac.uk, xtal-log@dl.ac.uk, str-nmr@dl.ac.uk Announcement: FINAL Call prediction targets =========================================== IRBM practical course: frontiers of protein structure prediction Organizers: Tim Hubbard (CPE, MRC), Anna Tramontano (IRBM) Instructors: G. Barton (Oxford), T. Hubbard (Cambridge), D. Jones (London), M. Sippl (Salzburg), A. Valencia (Madrid) Lecturers: A. Lesk (Cambridge), J. Moult (Rockville), B. Rost (Heidelberg), C. Sander (Cambridge) Dates: 8-17 October 1995 The aim of the workshop is to predict as much as possible about the structure of a number of proteins of biological interest, taking advantage of the most recent methodologies for fold recognition and ab initio prediction. If you are interested in a structure prediction being made on a protein for which there is no sign of an experimental structure and does not appear to be homologous to any known structure, please consider submitting it as a target for this course. Applications for this practical course closed 1st July, however we are still accepting target submissions until 15 September 1995. For further information and on-line target submission forms see: http://www.mrc-cpe.cam.ac.uk/predict/ Tim Hubbard, (Centre for Protein Engineering, MRC Centre, Cambridge, UK) Anna Tramontano, (Istituto di Ricerche di Biologia Molecolare, Roma, Italy) From owner-structural-nmr@net.bio.net Wed Aug 30 23:00:00 1995 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!swrinde!tank.news.pipex.net!pipex!sunsite.doc.ic.ac.uk!daresbury!is.bbsrc.ac.uk!news From: (Computing) Newsgroups: bionet.structural-nmr Subject: carbohydrates database Date: 31 Aug 1995 08:04:29 GMT Organization: IFR NL Lines: 13 Message-ID: <423qed$6ck@is.bbsrc.ac.uk> Reply-To: boetzel@bbsrc.ac.uk NNTP-Posting-Host: pc0517.ifrn.bbsrc.ac.uk X-Newsreader: WinVN 0.91.6 Hi! Does anybody know if there is a database for 13C NMR spectra of sugars and polysaccharides in the Net or on CD-ROM??? Thanks a lot Ruth ************************************************************************* Dr. Ruth Boetzel IFR Norwich UK E-mail: boetzel@bbsrc.ac.uk ************************************************************************* From owner-structural-nmr@net.bio.net Thu Aug 31 23:00:00 1995 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: spin simulation Date: 31 Aug 1995 23:39:15 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 32 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <423ub7$9a3@mercury.hgmp.mrc.ac.uk> NNTP-Posting-Host: net.bio.net I would like to know about such things myself. In addition to the usual capabilities, I am particularly interested in the input/output file format. I am looking for something capable with as open and transparent data structure as possible. I would like to simulate DNMR phenomena as well. Thanks, Istvan =========================================================================== Istvan Pelczer, Ph.D. (ipelczer@mailbox.syr.edu) Res. Assist. Professor Visiting Assist. Professor Chemistry Department, CST Bldg. SUNY ESF, Chemistry Department Syracuse University One Forestry Drive Syracuse, NY 13244-4100 Syracuse, NY 13210-2778 ph: (315) 443 1023 or x-5932 ph# (315) 470 6596 or x-6855(Dept.) fax: x-1022 or x-4070(Dept.) On 31 Aug 1995, Mike Gradwell wrote: > We are looking for a recent spin simulation program. Does anyone have any relevant > details? > Thanking you in advance > Mike Gradwell > National Institute for Medical Research > > From owner-structural-nmr@net.bio.net Thu Aug 31 23:00:00 1995 Path: biosci!WWITCH.UNL.EDU!rshoe From: rshoe@WWITCH.UNL.EDU (Richard Shoemaker) Newsgroups: bionet.structural-nmr Subject: Re: spin simulation Date: 1 Sep 1995 09:49:12 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 43 Sender: daemon@net.bio.net Distribution: world Message-ID: <9509011643.AA08681@wwitch.unl.edu.unl.edu> NNTP-Posting-Host: net.bio.net Regarding the following: >> >>We are looking for a recent spin simulation program. Does anyone have >any relevant >>details? >>Thanking you in advance >>Mike Gradwell >>National Institute for Medical Research > >There are several programs: >a) DSYMPC from the Institute of AC1 in Duesseldorf, Germany. You can get >it from their ftp server. >b) PERCH from Prof. Laatikainen in Kuopio >c) Win-Daisy, a very powerful program now being distributed by Bruker. > >Ruth > >************************************************************************* >Dr. Ruth Boetzel >IFR Norwich >Norwich, UK >E-mail: boetzel@bbsrc.ac.uk >************************************************************************* I've spent lots of time during the past year using Aconr NMR's "Nuts" program to do spin simulations on high-order P-31 spectra. Although it's a commercial program (i.e. not free), it does a very nice job most of the time. One very nice feature is that Nuts will read in most every NMR data format directly, with no fiddling around. This won't help Istvan, and others who want to simulate dynamic systems. We have a group that uses an older version of DNMR5, and they get pretty good results, but getting the data in isn't the most convenient thing in the world. Best Regards, Richard Shoemaker, Ph.D. Phone--(402) 472-6255 Instrumentation Director, Chemistry FAX---- -6964 Research Associate Professor, Chemistry University of Nebraska-Lincoln URL: http://wwitch.unl.edu/nmrlab.html From owner-structural-nmr@net.bio.net Thu Aug 31 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.sprintlink.net!dispatch.news.demon.net!demon!sunsite.doc.ic.ac.uk!daresbury!is.bbsrc.ac.uk!news From: (Computing) Newsgroups: bionet.structural-nmr Subject: Re: spin simulation Date: 1 Sep 1995 07:57:28 GMT Organization: IFR NL Lines: 24 Message-ID: <426ed8$c79@is.bbsrc.ac.uk> References: <423ub7$9a3@mercury.hgmp.mrc.ac.uk> Reply-To: boetzel@bbsrc.ac.uk NNTP-Posting-Host: pc0517.ifrn.bbsrc.ac.uk X-Newsreader: WinVN 0.91.6 In article <423ub7$9a3@mercury.hgmp.mrc.ac.uk>, m-gradwe@nimr.mrc.ac.uk (Mike Gradwell) says: > >We are looking for a recent spin simulation program. Does anyone have any relevant >details? >Thanking you in advance >Mike Gradwell >National Institute for Medical Research There are several programs: a) DSYMPC from the Institute of AC1 in Duesseldorf, Germany. You can get it from their ftp server. b) PERCH from Prof. Laatikainen in Kuopio c) Win-Daisy, a very powerful program now being distributed by Bruker. Ruth ************************************************************************* Dr. Ruth Boetzel IFR Norwich Norwich, UK E-mail: boetzel@bbsrc.ac.uk *************************************************************************