From owner-structural-nmr@net.bio.net Fri Jan 02 22:00:00 1998 Path: biosci!biosci!not-for-mail From: Sunghyouk Park Newsgroups: bionet.structural-nmr Subject: DQF-COSY with WATERGATE of Jump-Return water suppression Date: 3 Jan 1998 10:59:16 -0800 Organization: University of Illinois at Chicagp Lines: 20 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <34AE8815.F62C0D33@uic.edu> Reply-To: spark20@uic.edu NNTP-Posting-Host: net.bio.net Dear NMR people. Does anyone have DQF-DOSY with WATERGATE or Jump return type of water suppression sequence in it? Other water suppression without saturation transfer to amide protons would be fine. Thanks. -- Dustine S. Park Department of Medicinal Chemistry and Pharmacognosy Center for Pharmaceutical Biotechnology University of Illinois at Chicago Chicago, Illinois 60612 Home : 312-355-7205 Fax : 312-413-9303 Lab : 312-996-0705 spark20@uic.edu From owner-structural-nmr@net.bio.net Sat Jan 03 22:00:00 1998 Path: biosci!biosci!not-for-mail From: newsmgr@merrimack.edu Newsgroups: bionet.structural-nmr Subject: MolScript v2.0 Date: 4 Jan 1998 13:12:04 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 37 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <009BFCA7.9D87D254.2@merrimack.edu> NNTP-Posting-Host: net.bio.net Relay-Version: ANU News - V6.2.0 06/23/97 OpenVMS AXP V6.2; site chasm Path: chasm!cam-news-feed2.bbnplanet.com!cam-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.algonet.se!funny.bahnhof.se!not-for-mail Newsgroups: bionet.software,bionet.xtallography,bionet.structural-nmr Subject: MolScript v2.0 Message-ID: <34AFDC07.15FB@avatar.se> From: Per Kraulis Date: Sun, 04 Jan 1998 19:59:19 +0100 Organization: Avatar Software AB Lines: 21 NNTP-Posting-Host: pm1-52.bahnhof.se Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) A major new release of MolScript (v2.0.1) is now available. MolScript is a program for creating both detailed and schematic pictures of molecular 3D structures, in particular proteins. Version 2.0.1 is now available (23 Dec 1997), with many new features! A number of different output formats are supported: PostScript, Raster3D, VRML 2.0, interactive OpenGL and image files in the SGI (RGB), JPEG, PNG and EPS formats. For more information, see the Official MolScript Web Site, where instructions and conditions for downloading the software can be found: http://www.avatar.se/molscript -- Per Kraulis mailto:pjk@avatar.se Avatar Software AB http://www.avatar.se/ address: c/o Kraulis, Heleneborgsgatan 21C, SE-117 31 Stockholm, SWEDEN. From owner-structural-nmr@net.bio.net Tue Jan 06 22:00:00 1998 Path: biosci!biosci!not-for-mail From: newsmgr@merrimack.edu Newsgroups: bionet.structural-nmr Subject: Re: MolScript v2.0 Date: 7 Jan 1998 07:43:10 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 121 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <009BFECB.1C95E9A8.7@merrimack.edu> NNTP-Posting-Host: net.bio.net Relay-Version: ANU News - V6.2.0 06/23/97 OpenVMS AXP V6.2; site chasm Path: chasm!cam-news-feed2.bbnplanet.com!cam-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!surfnet.nl!highway.leidenuniv.nl!not-for-mail Newsgroups: bionet.software,bionet.xtallography,bionet.structural-nmr Subject: Re: MolScript v2.0 Message-ID: <34B34543.8E259B6B@chemaef.leidenuniv.nl> From: Gregg Siegal Date: Wed, 07 Jan 1998 10:05:07 +0100 References: <34AFDC07.15FB@avatar.se> Organization: Leiden University, The Netherlands Lines: 104 NNTP-Posting-Host: chemaef.leidenuniv.nl Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (X11; I; IRIX 5.3 IP22) The following funded positions are currently available in the laboratory of Prof. G.W. Canters at the Gorlaeus Laboratoria of the University of Leiden, The Netherlands. Interested candidates should contact the appropriate person via email at the given address or alternatively at the following postal address by the end of January 1998. Leiden Institute of Chemistry Gorlaeus Laboratories Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands Position I LIC Ph.D. position/ dr Marcellus Ubbink M.Ubbink@chem.leidenuniv.nl The project is aimed at characterizing the structure and dynamic properties of the transient complex of two redox proteins involved in photosynthetic electron transfer, cytochrome f and plastocyanin. Diamagnetic and paramagnetic NMR experiments will form the major part of the research. It further comprises expression and purification of the proteins and characterization with other spectroscopic techniques, in particular stopped-flow absorbance and fluorescence spectroscopy. NMR facilities (see Position III) and stopped-flow are available in the lab. The candidate should have a background in biochemistry and/or experience with biomolecular NMR. Position II LIC Ph.D. position/ dr Martin Ph. Verbeet Verbeet@chem.leidenuniv.nl The Ph.D. student will participate in the project focussing on one of the big challenges in the amperometric biosensor design, i.e., to improve the efficiency of electron transfer between the sensing enzyme and the electrode. The project involves the engineering of metalloproteins, e.g., small cupredoxins like azurin, amicyanin and cytochroom-c550, and, the copper-containing enzyme, nitrite reductase, by site-directed mutagenesis for the insertion of electron-conductive linker molecules into their redox centre(s). Subsequently, from a panel of small linkers the one(s) having optimal conductive properties and, in addition, enabling the protein-linker complexes to stably immobilise on the electrode is selected. All molecular- and structural-biological techniques to generate and to characterise the mutant proteins and the electrochemistry to test the linker properties and the stability of the complex immobilised on the electrode are present. Position III LIC Ph.D. position or post-Doc (3 years)/ dr Gregg Siegal Siegal@chemaef.leidenuniv.nl Title: Development of Heteronuclear NMR Methods for paramagnetic Cu(II) Proteins We seek a highly motivated person with either a background in physics or physical chemistry or prior experience with NMR, and a strong interest in protein NMR. The successful applicant will pursue a program of NMR methodological development to enable use of multi-dimensional, heteronuclear NMR techniques for observation of paramagnetically shifted nuclei in Cu(II) proteins. Facilities include a DMX-600 NMR spectrometer with three channels and pulsed field gradients as well as a large variety of probeheads. Computational facilities include access to a 16 node IBM SP2. Double labeled and 15N-labeled samples are presently available. -- Gregg Siegal siegal@chemaef.leidenuniv.nl phone (31) 71 527 4654 or 4638 fax (31) 71 527 4593 Chemistry Dept. Gorlaeus Laboratoria Rijksuniversiteit Leiden Postbus 9502 2300 RA Leiden The Netherlands From owner-structural-nmr@net.bio.net Tue Jan 06 22:00:00 1998 Path: biosci!biosci!not-for-mail From: Istvan Pelczer Newsgroups: bionet.structural-nmr Subject: Re: NMR: T1 and T2 analysis techniques Date: 7 Jan 1998 07:41:41 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 60 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net John, This is not a direct answer to your question, but have you considered to use NMRView for analyzing your T1 and T2 data? The latest version is nicely equipped with this routine. NMRView, a very open and well designed data visualization and analysis software is free, and takes Felix data directly (among several others). There is direct conversion from NMRPipe, another free software, to NMRView as well. Take a look at www.nmrview.com . Good luck, and all the best, Istvan wwww,wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww Istvan Pelczer, Ph.D. Email: ipelczer@princeton.edu Senior NMR Spectroscopist Princeton University Department of Chemistry, Frick Lab., ph# (609) 258 2342 Washington Road fax# (609) 258 6746 Princeton, NJ 08544, USA On Mon, 5 Jan 1998, John Tomaszewski wrote: > Hi all, > Sorry that this doesn't fit exactly into either of these > newsgroups but they seemed to be my best bet. I have a couple > non-theoretical questions regarding techniques for working up T1 and T2 > 15N relaxation data. > First, for anyone using Felix to pick and name peaks for this > purpose, do you use the manual peak or autopick functions? I'm going to > do a comparison of the two this afternoon (see which method yields a > better exponential fit) but I'm curious to hear what other people think of > these Felix options. The autopick seems to box too small an area to > calculate accurate volumes, in my opinion. > Second, how do you work up the data? I should be receiving an > nawk script that will extract the relaxation times from a volumes table > but in the meantime I've been trying to use Excel. (from a post to the > Excel newsgroups): > This works fine, I can chart them with out any problem and if I > choose, plot the line equation (y=ce^-xb) on the chart. My problem is, > for these series of 40-60 values I want to extract the relaxation time > into a cell to use for further calculations, and so far the only way I can > see to do it is to read it off the graph and manually type it into a cell, > but with many data values and overlap on the chart, this isn't very > efficient. Does anyone know how to generate the line equation or the > variables into cells, independant from the chart? Any assistance would be > greatly appreciated. > > Sincerely, > > John T. > > ******************************************************************** > ** ** ** ** * ** DEPARTMENT OF CHEMISTRY ** > ** ** ** ** * ** tomasz@protein.chem.washington.edu ** > ** ** ** ** * ** (206) 616-2993 ** > ** ***** ***** JOHN TOMASZEWSKI ** > ******************************************************************** > > From owner-structural-nmr@net.bio.net Tue Jan 06 22:00:00 1998 Path: biosci!biosci!not-for-mail From: mbzlo@s-crim1.dl.ac.uk (M. Zloh) Newsgroups: bionet.structural-nmr Subject: Felix 2.3 macro needed Date: 7 Jan 1998 07:39:59 -0800 Organization: Daresbury Lab, Warrington, U.K. Lines: 65 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <6904sb$f8v@mserv1.dl.ac.uk> NNTP-Posting-Host: net.bio.net I am looking for the Felix 2.3 macro to process NMR data obtained by the BRUKER AMX NMR spectrometer using States/TPPI pulse programs. I would be grateful if somebody could send me a macro or suggest the place where I could find it. Thank you in advance. Best regards Mire ========================================================== Mr Mire Zloh | School of Pharmacy | e-mail: mzloh@ulsop.ac.uk 29 Brunswick Square | Tel: + 44 171 753 5804 London WC1N 1AX | Fax: + 44 171 278 1939 ========================================================== "There are many paths leading to the top of Mount Fuji, but there is only one summit ..." "The Art of Peace" by Morihei Ueshiba ========================================================== From owner-structural-nmr@net.bio.net Tue Jan 06 22:00:00 1998 Path: biosci!biosci!not-for-mail From: newsmgr@merrimack.edu Newsgroups: bionet.structural-nmr Subject: Re: NMR: T1 and T2 analysis techniques Date: 7 Jan 1998 13:08:36 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 104 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <009BFF02.A6D75584.14@merrimack.edu> NNTP-Posting-Host: net.bio.net Relay-Version: ANU News - V6.2.0 06/23/97 OpenVMS AXP V6.2; site chasm Path: chasm!cam-news-feed2.bbnplanet.com!cam-news-hub1.bbnplanet.com!cpk-= news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.gip.net!news.gsl.net= !gip.net!news.idt.net!nntp2.cerf.net!nntp3.cerf.net!news.msi.com!uucp Newsgroups: bionet.structural-nmr Subject: Re: NMR: T1 and T2 analysis techniques Message-ID: <34B3CE4E.41C6@msi.com> From: Sandor Szalma Date: Wed, 7 Jan 1998 18:49:50 GMT Sender: uucp@msi.com References: <68v3no$53u@net.bio.net> Organization: Molecular Simulations, Inc Lines: 73 X-Nntp-Posting-Host: iris108 Content-Type: text/plain; charset=3Diso-8859-1 Content-Transfer-Encoding: 8bit Cc: tomasz@protein.chem.washington.edu, ssz Mime-Version: 1.0 X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 6.2 IP20) X-Disclaimer: _ Unless stated otherwise, everything in this message is personal opinion and nothing in it is an official statement of Molecular Simulations Inc. John, In the latest release of Felix (Felix 97.0) there is a set of commands to deal exactly with the heteronuclear T1 and T2 data - it is part of the 2D/ND package and it is under the Measure pulldown. There are commands to extract either peak heights or volumes using optimization to define peak widths and volumes. Also there are commands to view and fit the time series with a set of improved curve fitting algorithms and extract T1 (R1), T2 (R2) and heteronuclear NOE's. Finally there is a command to prepare an input file of this information for Arthur Palmer's ModelFree program to derive order parameters ( http://cpmcnet.columbia.edu/dept/gsas/biochem/labs/palmer/). You can find more info about these new features on MSI's web pages. Cheers, Sandor \~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/ * S=E1ndor Szalma, Ph.D. * * Director, Structural Biology email: ssz@msi.com * * Molecular Simulations, Inc. tel.: 619-799-5503 * * 9685 Scranton Rd, San Diego CA 92121 http://www.msi.com * /~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\ John Tomaszewski wrote: >=20 > Hi all, > Sorry that this doesn't fit exactly into either of these > newsgroups but they seemed to be my best bet. I have a couple > non-theoretical questions regarding techniques for working up T1 and T2 > 15N relaxation data. > First, for anyone using Felix to pick and name peaks for this > purpose, do you use the manual peak or autopick functions? I'm going t= o > do a comparison of the two this afternoon (see which method yields a > better exponential fit) but I'm curious to hear what other people think= of > these Felix options. The autopick seems to box too small an area to > calculate accurate volumes, in my opinion. > Second, how do you work up the data? I should be receiving an > nawk script that will extract the relaxation times from a volumes table > but in the meantime I've been trying to use Excel. (from a post to the > Excel newsgroups): > This works fine, I can chart them with out any problem and if I > choose, plot the line equation (y=3Dce^-xb) on the chart. My problem i= s, > for these series of 40-60 values I want to extract the relaxation time > into a cell to use for further calculations, and so far the only way I = can > see to do it is to read it off the graph and manually type it into a ce= ll, > but with many data values and overlap on the chart, this isn't very > efficient. Does anyone know how to generate the line equation or the > variables into cells, independant from the chart? Any assistance would= be > greatly appreciated. >=20 > Sincerely, >=20 > John T. >=20 > ******************************************************************** > ** ** ** ** * ** DEPARTMENT OF CHEMISTRY ** > ** ** ** ** * ** tomasz@protein.chem.washington.edu ** > ** ** ** ** * ** (206) 616-2993 ** > ** ***** ***** JOHN TOMASZEWSKI ** > ******************************************************************** =20 -disclaimer- unless stated otherwise, everything in the above message is personal opi= nion and nothing in it is an official statement of molecular simulations inc. From owner-structural-nmr@net.bio.net Tue Jan 06 22:00:00 1998 Path: biosci!biosci!not-for-mail From: John Tomaszewski Newsgroups: bionet.structural-nmr Subject: NMR: T1 and T2 analysis techniques Date: 6 Jan 1998 21:27:20 -0800 Organization: University of Washington Lines: 36 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <68v3no$53u@net.bio.net> NNTP-Posting-Host: net.bio.net Hi all, Sorry that this doesn't fit exactly into either of these newsgroups but they seemed to be my best bet. I have a couple non-theoretical questions regarding techniques for working up T1 and T2 15N relaxation data. First, for anyone using Felix to pick and name peaks for this purpose, do you use the manual peak or autopick functions? I'm going to do a comparison of the two this afternoon (see which method yields a better exponential fit) but I'm curious to hear what other people think of these Felix options. The autopick seems to box too small an area to calculate accurate volumes, in my opinion. Second, how do you work up the data? I should be receiving an nawk script that will extract the relaxation times from a volumes table but in the meantime I've been trying to use Excel. (from a post to the Excel newsgroups): This works fine, I can chart them with out any problem and if I choose, plot the line equation (y=ce^-xb) on the chart. My problem is, for these series of 40-60 values I want to extract the relaxation time into a cell to use for further calculations, and so far the only way I can see to do it is to read it off the graph and manually type it into a cell, but with many data values and overlap on the chart, this isn't very efficient. Does anyone know how to generate the line equation or the variables into cells, independant from the chart? Any assistance would be greatly appreciated. Sincerely, John T. ******************************************************************** ** ** ** ** * ** DEPARTMENT OF CHEMISTRY ** ** ** ** ** * ** tomasz@protein.chem.washington.edu ** ** ** ** ** * ** (206) 616-2993 ** ** ***** ***** JOHN TOMASZEWSKI ** ******************************************************************** From owner-structural-nmr@net.bio.net Thu Jan 08 22:00:00 1998 Path: biosci!biosci!not-for-mail From: John Tomaszewski Newsgroups: bionet.structural-nmr Subject: SUMMARY: NMR: T1 and T2 analysis techniques Date: 8 Jan 1998 21:25:59 -0800 Organization: University of Washington Lines: 145 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: References: <68v3no$53u@net.bio.net> NNTP-Posting-Host: net.bio.net Thanks to all who replied to my recent question. Here's a summary of the responses I received from my query regarding the processing and analysis of T1/T2 15N relaxation data. Hope it's useful to others... EXCEL routines: 1) From: Bernard Liengme Lets assume the X values are in A2:A46 and the Y values are in B2:B46. Some where to the far right - lets say in column Q add in Q2 the formula =LN(B2) and copy this down to Q46. In the cell where you want the value of b, enter =LINEST(Q2:Q46, A2:A46) and Excel will return the value. If you first select a horizontal range of 2 cells, type the formula about, press CTRL+SHIFT+ENTER, then the first cell will contain b and the seconf LN(c). If y = cEXP(bx) Then LN(y) = LN(c) + bx ----> so we can use a linear plot with slope b and intercept c 2) From: Dana De John. You can extract the equation that excel calculates. The only way I know of is to use Visual Basic. However, for most trendlines, it is returned as text with the power raised to a non mathematical notation as x6 instead of x^6. You will have to add your own routine to extract the numbers to fit your situation. But as least, this will get you started. For now, place an embedded chart on your sheet and add a trendline to the first series. Leave cells A1 and A2 blank because this is where this routine places the equations. (Adjust these as necessary.) Adjust the accuracy of the returned number with NumberFormat. Of course, you will have to adjust most of this to fit your needs. Here is the macro. If you have any problems extracting the numbers to fit your situation, than please let me know. This took me a long time to figure out when I was in graduate school, so I'm pretty proud of this one. Sub TrendLabel() ' Select your chart here. ActiveSheet.ChartObjects(1).Activate ' Select your trendline here. With ActiveChart.SeriesCollection(1).Trendlines(1) ' The DataLabel is 1 object, ' so work with only 1 equation at a time. .DisplayEquation = True .DisplayRSquared = False ' Give it your own format .DataLabel.NumberFormat = "#,##0.0000000" Worksheets("sheet1").Range("A1").Value = .DataLabel.Text ' Now work with the R Squared .DisplayEquation = False .DisplayRSquared = True .DataLabel.NumberFormat = "#,##0.0000000" Worksheets("sheet1").Range("A2").Value = .DataLabel.Text End With End Sub --------------------------------------------------------------------------- UNIX solutions: 1) From: Istvan Pelczer This is not a direct answer to your question, but have you considered to use NMRView for analyzing your T1 and T2 data? The latest version is nicely equipped with this routine. NMRView, a very open and well designed data visualization and analysis software is free, and takes Felix data directly (among several others). There is direct conversion from NMRPipe, another free software, to NMRView as well. Take a look at www.nmrview.com . Good luck, and all the best, Istvan 2) From: Susan Baxter I recommend using Arthur Palmer's suite of macros for felix relaxation data manipulation. You can download them from his website (http://cuhhca.hhmi.columbia.edu/palmer/palmer_group.html). Felix970 purports to have these macros "built-in" but I haven't personally tried it yet. Good luck. Susan Baxter 3) From: Sandor Szalma In the latest release of Felix (Felix 97.0) there is a set of commands to deal exactly with the heteronuclear T1 and T2 data - it is part of the 2D/ND package and it is under the Measure pulldown. There are commands to extract either peak heights or volumes using optimization to define peak widths and volumes. Also there are commands to view and fit the time series with a set of improved curve fitting algorithms and extract T1 (R1), T2 (R2) and heteronuclear NOE's. Finally there is a command to prepare an input file of this information for Arthur Palmer's ModelFree program to derive order parameters ( http://cpmcnet.columbia.edu/dept/gsas/biochem/labs/palmer/). You can find more info about these new features on MSI's web pages. Cheers, Sandor 4) From: Emmanuel Brun I saw your letter on the web, it looks like you have problem with Felix peaks volumes and with the organisation of your relaxation database. Regarding the peaks volumes. My experience tell my that it is better in felix to use the peak intensity (using the "mgv" command). Or you can optimize your peak footprint by fitting them to a lorentzian or a Gaussian. If you use this optimize command the secret is to use it several time on the same peak footprint until the initial penalty = the final penalty. Regarding the organisation of the database, I have build a complete new Felix module that organise any type of 2D NMR titration. Indeed a relaxation study is like a titration where time is the substrate. This module is easy to install if you have at least FELIX 2.30. The only problem is that I haven't write any manual for it yet. Basically it allowed you to treat a serie of 2D spectra as it was a 3D spectra, organize the gestion of the peaks entity, and even visualize the titration or relaxation curves. If your are interested let me know. FELIX users are all my freinds. Manu. ******************************************************************** ** ** ** ** * ** DEPARTMENT OF CHEMISTRY ** ** ** ** ** * ** tomasz@protein.chem.washington.edu ** ** ** ** ** * ** (206) 616-2993 ** ** ***** ***** JOHN TOMASZEWSKI ** ******************************************************************** From owner-structural-nmr@net.bio.net Fri Jan 09 22:00:00 1998 Path: biosci!biosci!not-for-mail From: sajith jayasinghe Newsgroups: bionet.structural-nmr Subject: zwitterionic detergent Date: 9 Jan 1998 19:51:46 -0800 Organization: department of chemistry Lines: 10 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hello, I would like to know if anyone knows where I could obtain a deuterated Zwitterionic detergent suitable for NMR. I am in the process of of obtaining NMR spectra of a 11-mer peptide and would like t carry out the experiments in detergent. SDS (deuterated) is available commercially but would like to know if a zwitterionic detergent is available. Thankyou in advance, Sajith Jayasinghe Department of Chemistry University of Virginia. From owner-structural-nmr@net.bio.net Mon Jan 12 22:00:00 1998 Path: biosci!biosci!not-for-mail From: "Aldo Franco" Newsgroups: bionet.structural-nmr Subject: HYP Date: 13 Jan 1998 13:17:04 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <9801131240.ZM17134@chemindy.sci.fau.edu> NNTP-Posting-Host: net.bio.net I am trying to incorporate HYP into a structure, and so far I have been able to obtain a psf file that only gives 2 errors, both at %patch, but it does not tell me what residue is giving me the problem. Regardless of this I have tried to obtain a template file, but it does not recognise HYP, what files do I have to modify to have HYP in my structure? Aldo Franco, garduate student Florida Atlantic University. I would appreciate any help. From owner-structural-nmr@net.bio.net Thu Jan 15 22:00:00 1998 Path: biosci!biosci!not-for-mail From: "Philippe Picard" Newsgroups: bionet.structural-nmr Subject: Help with ROESY experiment Date: 16 Jan 1998 09:13:14 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <9801161131.ZM20169@mimosa.cristal.u-bordeaux.fr> NNTP-Posting-Host: net.bio.net Dear netters, I'm looking for a phase sensitive (TPPI) ROESY experiment for peptides with a water suppression using 3-9-19 pulse sequence with gradients. I'm working on an Br"uker DPX 400 MHz spectrometer. Does someone have the pulse program (Avance version) to perform this experiment ? Thanks in advance from Philippe PICARD -- ________________________________________________________________________________ Philippe Picard Unite de Biophysique Structurale (UBS) picard@mimosa.cristal.u-bordeaux.fr EP534 CNRS - Universite de Bordeaux 1 tel : (33) 05 56 84 28 95 351 cours de la Liberation fax : (33) 05 56 84 66 86 33405 TALENCE Cedex - France From owner-structural-nmr@net.bio.net Thu Jan 22 22:00:00 1998 Path: biosci!biosci!not-for-mail From: "wfwu@iae.syb.ac.cn" Newsgroups: bionet.structural-nmr Subject: NMR of S-Adenosyl-Methionine Date: 22 Jan 1998 20:35:18 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <34C56F58.77D3@iae.syb.ac.cn> Reply-To: wfwu@iae.syb.ac.cn NNTP-Posting-Host: net.bio.net Hello: Does anyone know where could I find the standard NMR and Infrared spectrogram of S-Adenosyl-Methionine? Thanks ahead. Ji Jianfei From owner-structural-nmr@net.bio.net Wed Jan 28 22:00:00 1998 Path: biosci!biosci!not-for-mail From: Istvan Pelczer Newsgroups: bionet.structural-nmr Subject: Re: DQF-COSY with WATERGATE of Jump-Return water suppression Date: 29 Jan 1998 11:08:29 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 45 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Sunghyouk, There is a good review on gradient-driven experiments in water which you might want to look at: A. S. Altieri, K. E. Miller, and R. A. Byrd: A comparison of Water Suppression Techniques Using Pulsed Field Gradients for High-Resolution NMR of Biomolecules Magnetic Resonance Review 17(1)(1996) 27-81. There you'll find references (and names to contact). Good luck, Istvan wwww,wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww Istvan Pelczer, Ph.D. Email: ipelczer@princeton.edu Senior NMR Spectroscopist Princeton University Department of Chemistry, Frick Lab., ph# (609) 258 2342 Washington Road fax# (609) 258 6746 Princeton, NJ 08544, USA On Sat, 3 Jan 1998, Sunghyouk Park wrote: > Dear NMR people. > Does anyone have DQF-DOSY with WATERGATE or Jump return > type of water suppression sequence in it? > Other water suppression without saturation transfer to amide protons > would be fine. > Thanks. > > -- > Dustine S. Park > Department of Medicinal Chemistry and Pharmacognosy > Center for Pharmaceutical Biotechnology > University of Illinois at Chicago > Chicago, Illinois 60612 > > Home : 312-355-7205 > Fax : 312-413-9303 > Lab : 312-996-0705 > spark20@uic.edu