From owner-structural-nmr@net.bio.net Wed Nov 01 22:00:00 1995 Path: biosci!bcm.tmc.edu!pendragon.jsc.nasa.gov!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!sunsite.doc.ic.ac.uk!charlie.lif.icnet.uk!usenet From: Robert Russell Newsgroups: bionet.molbio.proteins,bionet.software,bionet.structural-nmr,bionet.xtallography Subject: ANNOUNCE- *** PROTEIN 3D STRUCTURE ALIGNMENT SOFTWARE - STAMP v4.0 *** Date: 2 Nov 1995 18:18:48 GMT Organization: Imperial Cancer Research Fund Lines: 41 Message-ID: <47b228$b0d@charlie.lif.icnet.uk> NNTP-Posting-Host: bonsai.lif.icnet.uk 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) To: gjb@bioch.ox.ac.uk X-URL: news:bionet.molbio.proteins Xref: biosci bionet.molbio.proteins:6167 bionet.software:13809 bionet.structural-nmr:868 bionet.xtallography:2137 NEW RELEASE OF STAMP (Structural Alignment of Multiple Proteins) Version 4.0 STAMP is a package comprising 15 programs for alignment and analysis of protein three-dimensional structures. The major features are: 1) Fast alignment and superimposition of two or more protein structures 2) Generation and display superimposed protein 3D structures and sequence alignments 3) Comparison of a protein 3D structure to a database of other 3D structures 4) Direct interface to MOLSCRIPT and ALSCRIPT drawing programs 5) A clear method for assigning which regions within a family of proteins are structurally equivalent, without the need for graphical intervention. STAMP is available free of charge to non-profit organisations, and to others for a fee. A license must be completed by all prospective users. Users of previous versions of STAMP can obtain the new version with the same license. The new version (4.0) has corrected several bugs, ontains a much improved manual and includes several new programs, including those for the generation of MOLSCRIPT input, and for the generation of averaged structures. For further details as to the program and licenses, see: WWW http://geoff.biop.ox.ac.uk/ FTP ftp://geoff.biop.ox.ac.uk/README ftp://geoff.biop.ox.ac.uk/STAMP.LIC or contact Geoff Barton via mailto:gjb@bioch.ox.ac.uk Robert B. Russell Biomolecular Modelling, Imperial Cancer Research Fund 44 Lincoln's Inn Fields, P.O. Box 123, London, WC2A 3PX, U.K. Tel: 44 171 269 3583 FAX: 44 171 269 3479 mailto:russell@icrf.icnet.uk WWW http://bonsai.lif.icnet.uk/people/rob/rob.html From owner-structural-nmr@net.bio.net Wed Nov 01 22:00:00 1995 Newsgroups: bionet.structural-nmr Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!sunsite.doc.ic.ac.uk!daresbury!yama.mcc.ac.uk!liv!uknet!newsfeed.ed.ac.uk!leeds.ac.uk!news From: garyt@resumix.portal.com (Gary Thompson) Subject: Felix 95 Message-ID: <1995Nov2.153042.21420@leeds.ac.uk> Reply-To: garyt@resumix.portal.com NNTP-Posting-Host: chmsun10.leeds.ac.uk Organization: Resumix, Inc., Santa Clara, CA Date: Thu, 2 Nov 1995 15:30:42 +0000 (GMT) References: <478bqk$2kd@gap.cco.caltech.edu> Lines: 22 Hi Does anyone have info on the cost of the Latest Felix ie Felix95 at academic rates. Someone has told me that there has been a major rise in prices since the merger with MSI. Is there a particular eason for this??? Alos can someone give me a url for NMRPipe on the NIH ftp site gary --- ________________________________________________________________________________ Dr G. S. Thompson. quote of the day/week/month/eternity: Biomolecular Structure Group. Department of Chemistry. University of Leeds. "If everyone stands on tiptoes noone Leeds LS2 9JT. can see any better..." Phone 0113 233 6578. e-mail: garyt@chem.leeds.ac.uk _______________________________________________________________________________ From owner-structural-nmr@net.bio.net Wed Nov 01 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.sprintlink.net!news.cc.sunysb.edu!delbruck!culli From: culli@delbruck (David Cullinan) Newsgroups: bionet.structural-nmr Subject: Re: Xplor_NOESY_algorithm Date: 2 Nov 1995 15:31:26 GMT Organization: State University of New York at Stony Brook Lines: 30 Message-ID: <47ao8e$2qi@abel.cc.sunysb.edu> NNTP-Posting-Host: delbruck.pharm.sunysb.edu X-Newsreader: TIN [version 1.2 PL2] I tried to reply to the original poster by mail, but it bounced back to me, and all finger queries I made indicated that the host did not exist. Very strange... Anyway, this is what I tried to mail. In article <479vml$9tg@idefix.eunet.fi> you wrote: : Does someone know which is the exact algorithm used in Xplor to : transform nOe intensities into distances and viceversa (in obtaining : symulated nOe intensities from molecular models)? : I know the basic of it (nOe=k/r**6 , where r is the distance between Hi : and Hj) but I wish to have the correct algorithm as written in the : program. Do someone know where it is stored? The executable are not very : informative. What I was told to do when I first started working with this sort of stuff (which was only a couple of years ago, so I don't have vast experience at it), was to plot a graph of intensity vs mixing time, and try to find the initial slope of that graph. Using that number, use the k/r^6 rule to determine the distances, using one of the geometrically fixed distances (like cytosine H5-H6, which I think is 2.45 angstroms, but check that), as a ruler. In other words, you know the intensity of the 'ruler' peaks, you know their distances, and you know the intensity of the other peaks. From that and the k/r^6 rule, you can get the distances. Hope that helps! -Dave Cullinan graduate student Dept of Biophysics SUNY Stony Brook culli@delbruck.pharm.sunysb.edu From owner-structural-nmr@net.bio.net Wed Nov 01 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!EU.net!news.eunet.fi!newsmaster From: piero pollesello Newsgroups: bionet.structural-nmr Subject: Xplor_NOESY_algorithm Date: 2 Nov 1995 08:32:21 GMT Organization: POLYbios, Area scientific park, trieste Lines: 24 Message-ID: <479vml$9tg@idefix.eunet.fi> NNTP-Posting-Host: mac545.espoo.orion.fi Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) X-URL: news:bionet.structural-nmr Does someone know which is the exact algorithm used in Xplor to transform nOe intensities into distances and viceversa (in obtaining symulated nOe intensities from molecular models)? I know the basic of it (nOe=k/r**6 , where r is the distance between Hi and Hj) but I wish to have the correct algorithm as written in the program. Do someone know where it is stored? The executable are not very informative. Thanks for help Piero Piero Pollesello NMR-lab, Chem.Res.Dept. Orion-Farmos, Orion Corp. FIN-02101 Espoo FINLAND tel.int-358-0-429-4191 fax.int-358-0-429-2924 e-mail(direct):piero.pollesello@rd.orion.orion.mailnet.fi From owner-structural-nmr@net.bio.net Wed Nov 01 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!news.luc.edu!uchinews!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!not-for-mail From: mbmorton@ix.netcom.com (michelle morton ) Newsgroups: bionet.structural-nmr,sci.bio,sci.engr,sci.misc,sci.physics,sci.physics.research Subject: biophysics vs. biochem speculatin' Date: 2 Nov 1995 18:11:55 -0500 Organization: Netcom Lines: 27 Sender: pfiglio@dustbunny.physics.indiana.edu Approved: pfiglioz@indiana.edu Message-ID: <47bj7r$kkt@dustbunny.physics.indiana.edu> NNTP-Posting-Host: dustbunny.physics.indiana.edu Xref: biosci bionet.structural-nmr:870 sci.engr:15017 sci.misc:7829 sci.physics:105176 sci.physics.research:2869 Got a question that's been puzzling me. My cat's fur is so soft that petting him is like touching a cashmere or angora sweater. Is this *softness* due to: a) the **physical** arrangement of the peptide bonds - ie, do the amino acids line up in a smooth, rather than jagged or discrete, surface? b) the sequencing of the amino acids themselves? c) the tertiary or quarternary folding of the protein(s) in his fur - ie, do the proteins have some special arrangement that we experience as being *soft* or, d) some other phenomenom (phenomena) that completely escapes me right now? Obviously, as a student, I have wwwaaaaaaayyyyyy too much time on my hands :>!! This is one of several "philosophy" of chemistry questions I have that completely prevent me from ever getting around to figuring out how to solve world hunger or bring about total global peace on earth or other really important stuff like that! :> :> :> If you could help me out, I'd really appreciate it. Thanx in advance for your info. michelle (my mind's awanderin', awanderin', just awanderin' away) m- From owner-structural-nmr@net.bio.net Wed Nov 01 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!lade.news.pipex.net!pipex!news00.sunet.se!sunic!news99.sunet.se!columba.udac.uu.se!rigel.bmc.uu.se!gerard From: gerard@rigel.bmc.uu.se (Gerard Kleijwegt) Newsgroups: bionet.structural-nmr Subject: Re: molecular topology and parameter in xplor Date: 2 Nov 1995 18:42:45 GMT Organization: Uppsala University Lines: 55 Distribution: world Message-ID: <47b3f5$m3u@columba.udac.uu.se> References: NNTP-Posting-Host: rigel.bmc.uu.se In article , ccchuang@GATE.SINICA.EDU.TW (Chyh-chong Chuang) writes: |> |> To Xplor experts: |> |> how to creat a topology and parameter for a residue not appear on |> standard xplor topology and parameter file? |> |> I had read the inp file for generate cyclosporin A, and tried to |> learn some there. But I had problem in assigning the charge of atoms. |> Do there are some "rules" when do this? (I mean assigning the parameters) |> |> I also had problem in assignment of a improper group. How and |> when to assign a impropers? |> |> Any help will be great appreciated. |> |> Thanks all |> |> ============================================ |> Chyh-Chong Chuang |> Institude of Biological Chemistry, |> Academia Sinica,Taipei, Taiwan |> -------------------------------------------- |> P.O. BOX 23-106, Phone: 886-2-362-0261 ext 2021 |> Taipei, Taiwan, Fax: 886-2-363-5038 |> R.O.C. E-Mail: ccchuang@gate.sinica.edu.tw |> ============================================ |> XPLO2D is a little jiffy program, free for academics, which contains an option to generate X-PLOR topology and parameter files from a PDB file. The only drawback for NMR users is that it hates hydrogens, so you would have to add those yourself. As for charges: either stick your thumb into the air and make a wild guess, or switch off the electro- statics term in X-PLOR ;-) I also have a collection of ~1,000 hetero-entities from published PDB structures which you can use as input to XPLO2D (the coordinates are taken from the highest- resolution X-ray structure; if a compound does not occur in any X-ray structure, it is taken from an NMR model). This collection is available free-of-charge to anyone interested (i.e., including commercial users). Both can be found on rigel.bmc.uu.se, directory pub/heteros. The program exists in SGI, ESV and Alpha/OSF1 versions. The hetero-collection is called hetero.pdb.Z. By the way: there's a dedicated Newsgroup for X-PLOR users of all religions (X-rayers, NMRists and people who don't need experimental data ;-): bionet.software.x-plor. --gerard kleywegt bmc, uppsala From owner-structural-nmr@net.bio.net Thu Nov 02 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.sprintlink.net!news.crd.ge.com!rebecca!news From: shelton bank Newsgroups: bionet.xtallography,bionet.structural-nmr Subject: Re: General Questions re NMR Date: 3 Nov 1995 19:37:11 GMT Organization: The University at Albany Lines: 3 Message-ID: <47dr17$lvl@rebecca.albany.edu> References: NNTP-Posting-Host: bankpc.chem.albany.edu 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.xtallography:2143 bionet.structural-nmr:876 The Horst Friebolin text Basic One and Two Dimensional NMR is both readable and correct From owner-structural-nmr@net.bio.net Thu Nov 02 22:00:00 1995 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: biophysics vs. biochem speculatin' Date: 3 Nov 1995 02:03:50 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 36 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <47bj7r$kkt@dustbunny.physics.indiana.edu> NNTP-Posting-Host: net.bio.net I guess there is and answer at a bit higher structural level (at least part of it). To my best knowledge the cat's hair has a different macroscopic structure than that of the dog's, for example; there are fine "hooks" on the surface which keep it fluffier and soft when touching. Actually, once in a while I have had a very interesting conversation with someone back in Hungary, a professional manufacturer of the traditional hats made of animals' hair. She told me that when for some reason the material just did not wnt to keep together in the process, the workers grabbed the nearest cat in the workshop (there were always some, to keep the mice away), teared off a handful of her/his hair and mixed into the bulk of other hair -- it kept it together... This might be a superficial, or partial answer only, but there is something else. Jeremy Sanders (in Cambridge) with his colleagues has measured relaxation times of sipder webb's proteins. The lucky creature was well fed with 13C labeled sugar then developed the webb (13C labeled in large proportion). This webb was rolled up on a tiny glass rod and put into the NMR tube. Since I have heard this from Jeremy I recall seeing some poster about some similar thing lately. I think this is a great idea -- however, a bit more difficult to apply to the cat... All the best, 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.) From owner-structural-nmr@net.bio.net Thu Nov 02 22:00:00 1995 Path: biosci!TRACER.CHEM.UH.EDU!hong From: hong@TRACER.CHEM.UH.EDU (Hong Yu Liu) Newsgroups: bionet.structural-nmr Subject: 3D NMR data processing Date: 2 Nov 1995 17:04:06 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 30 Sender: daemon@net.bio.net Distribution: world Message-ID: <199511030102.TAA28643@Tracer.chem.uh.edu> NNTP-Posting-Host: net.bio.net Hi, Everyone: I'm new to this newsgroup and the NMR field. So I have some questions which might sound trivial to most of the people here. But here it is: I'm trying to process my 3D 1H-15N-1H NOESY-HMQC data on the felix 2.3 ND mode. This data was acquired on a bruker 600 MHz AMX with the size of 1024 X 256 X 32. But the problem start here: 1) What conversion program should I use to convert 3D data files from bruker format to felix format? I was using /BRUKER/X32/ux2ftnmrb to convert 2D data and it works fine. Will it work for 3D? 2) But I use the above mentioned conversion program anyway. It went through fine and did not give me any error message. But I noticed that the data size of the file changed from 33554432 to 33652736 upon conversion. Is this correct? 2D seems to do sth similiar. 3) Then I went ahead and try to process it. by using EZ 3D transform d1 (type 1 as well as type 2) using the following matrix size (512 X 512 X 32), but the data processing stop half way at tier 17 always. What's wrong? Would some one pls help me? Thanks a million. My e-mail : hong@tracer.chem.uh.edu tel: 713-743-3301 Regards hong From owner-structural-nmr@net.bio.net Thu Nov 02 22:00:00 1995 Path: biosci!BIOC01.UTHSCSA.EDU!raman From: raman@BIOC01.UTHSCSA.EDU (C.S.RAMAN) Newsgroups: bionet.structural-nmr Subject: Newsgroup Moderation Poll - Please read Date: 2 Nov 1995 16:27:37 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 59 Sender: daemon@net.bio.net Distribution: world Message-ID: <9511030025.AA01877@bioc01.uthscsa.edu> NNTP-Posting-Host: net.bio.net Dear Str-NMR members: I have been approached by many who follow this newsgroup regarding the recent spams we have experienced and possible solutions to avoid the same in future. Well, I have discussed this problem in detail with Dr. Dave Kristofferson - coordinator of the BIONET newsgroups and here is a summary: 1. It appears that we are not the only newsgroup to be hit by spams. Almost always the other BIONET newsgroups get cross-posted with the same message from these spammers. 2. Can we do anything about spams? Other than using the all powerful "DELETE" key, not much. In fact, the spammers are getting to be real smart in that it is become increasingly difficult to track them down. 3. I am told that moderation of the newsgroup (considering the low volume of messages), str-nmr, shouldn't take more than about 5 minutes per day. 4. Should the newsgroup be moderated, we have the capability to filter out messages that have no relevance to str-nmr. Of course, such moderation can only guarantee that e-mail subscribers to this newsgroup be immune to spams. Although, BIONET administrators make sure that irrelevant posts get deleted or not mirrored by NEWS servers, it is always possible for these spammers to overcome this hurdle. Having said all of this, I would like to ask all the readers of STR-NMR the following question: WOULD YOU LIKE THIS NEWSGROUP TO BE MODERATED? I would be happy to do it, since the time it takes to do the same is quite small and it appears to work well in other BIONET moderated newsgroups. I would appreciate if you could email me directly your thoughts on this subject. Cheers -raman -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ C.S.RAMAN _/ _/ Department of Biochemistry _/ _/ University of Texas Health Science Center _/ _/ 7703 Floyd Curl Drive _/ _/ San Antonio, TX 78284-7760 _/ _/ USA _/ _/ _/ _/ Tel: (210) 567-6623 _/ _/ Fax: (210) 567-6595 _/ _/ E-mail: raman@bioc01.uthscsa.edu _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ How can it be that mathematics, a product of human thought _/ _/ independent of experience, is so admirably adapted to the _/ _/ objects of reality? -Albert Einstein _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From owner-structural-nmr@net.bio.net Thu Nov 02 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!newsfeed.ACO.net!sbg.ac.at!news From: Thomas HEISTRACHER Newsgroups: bionet.molec-model,bionet.molbio.proteins,bionet.xtallography,bionet.structural-nmr,bionet.biophysics,sci.chem,sci.comp-aided Subject: Re: Internet Drug Design Course Date: 3 Nov 1995 09:42:45 GMT Organization: uni.sbg Lines: 30 Message-ID: <47co6l$dt3@dwst13.edvz.sbg.ac.at> References: <47241o$1r3@holly.sandwich.pfizer.com> NNTP-Posting-Host: dbio26.bio.sbg.ac.at Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 32bit) To: hartla@edvz.sbg.ac.at Xref: biosci bionet.molec-model:650 bionet.molbio.proteins:6177 bionet.xtallography:2138 bionet.structural-nmr:874 bionet.biophysics:1384 sci.chem:42399 sci.comp-aided:929 jpo@siris7 (John Overington) wrote: > We (Peter Murray-Rust of Glaxo Wellcome, and John Overington of Pfizer) >would like to announce an initiative in industrial training for medicinal >chemists interested in applying protein structure-based drug design (SBDD) >techniques as part of their jobs. Additionally, skills in effectively using >the internet as a scientific resource will also be developed. The course will >use self-paced, internet-based training, coupled to close contact with >course 'tutors', working in the pharmaceutical industry. > > We are currently looking for further partners to offer financial support, >and course material. Partners need to have a presence in the UK to qualify for >potential funding under a Technology Foresight grant; although the basic >course material will be generally accessible over the internet to the wider >community. > > Further details, and a draft prospectus can be found at >http://www.cryst.bbk.ac.uk/SBDD/course.html > > If you have any further questions, we would be pleased to answer them. > > John Overington jpo@guitar.rockefeller.edu > Peter Murray-Rust ubcg09q@cryst.bbk.ac.uk > >-- >Dr. John Overington email: overingtonj@pfizer.com >Pfizer Central Research phone: +44-(0)1304-618467 >Sandwich, Kent, CT13 9NJ fax: +44-(0)1304-618422 >United Kingdom cc-mail: overington_j@sandwich.pfizer.com From owner-structural-nmr@net.bio.net Thu Nov 02 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!tank.news.pipex.net!pipex!dispatch.news.demon.net!demon!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: bryan@freja.fkem2.lth.se (Bryan Finn) Newsgroups: bionet.structural-nmr Subject: Re: Xplor_NOESY_algorithm Date: 3 Nov 1995 08:57:17 -0000 Lines: 40 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <47clhd$hhs@mserv1.dl.ac.uk> Original-To: str-nmr@dl.ac.uk In article <479vml$9tg@idefix.eunet.fi> you wrote: : Does someone know which is the exact algorithm used in Xplor to : transform nOe intensities into distances and viceversa (in obtaining : symulated nOe intensities from molecular models)? : I know the basic of it (nOe=k/r**6 , where r is the distance between Hi : and Hj) but I wish to have the correct algorithm as written in the : program. Do someone know where it is stored? The executable are not very : informative. There are several algorithms used depending on how one treates the multiple-proton problem (i.e. with or without pseudo-atom correction, etc.) Your best bet is just to contact Axel Brunger, the author of X-plor: brunger@laplace.csb.yale.edu or cross-post your question to the x-plor newgroup: bionet.software.x-plor Bryan ___________________________________________________________________ | | | Dr. Bryan Finn | | Department of Physical Chemistry 2 Tel: +46-46-222-8254 | | Chemical Center Fax: +46-46-222-4543 | | University of Lund | | POB 124 | | S-221 00 Lund Sweden e-mail: bryan@freja.fkem2.lth.se | | WWW: http://www.fkem2.lth.se/personnel/bryan/finn.html | |_________________________________________________________________| From owner-structural-nmr@net.bio.net Fri Nov 03 22:00:00 1995 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!scripps.edu!usenet From: Christoph Weber Newsgroups: bionet.structural-nmr Subject: Re: 3D NMR data processing Date: Fri, 03 Nov 1995 16:56:10 -0800 Organization: The Scripps Research Institute, La Jolla, CA Lines: 36 Message-ID: <309ABA2A.167E@scripps.edu> References: <199511030102.TAA28643@Tracer.chem.uh.edu> NNTP-Posting-Host: bianca.scripps.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0b1N (X11; I; IRIX 5.3 IP22) Hong Yu Liu wrote: (some stuff deleted) > I'm trying to process my 3D 1H-15N-1H NOESY-HMQC data on the felix > 2.3 ND mode. This data was acquired on a bruker 600 MHz AMX with the size of > > 1) What conversion program should I use to convert 3D data files from > bruker format to felix format? I was using /BRUKER/X32/ux2ftnmrb to convert 2D > data and it works fine. Will it work for 3D? Yes, although I'd recommend ux2flx in the gifts section. > 3) Then I went ahead and try to process it. by using EZ 3D transform > d1 (type 1 as well as type 2) using the following matrix size (512 X 512 X 32), > but the data processing stop half way at tier 17 always. What's wrong? > Don't know what's wrong, but as a general suggestion: Once you're advancing to 3D NMR, it is probably high time to learn at least some of the versatile macro language in FELIX to set up your own processing scheme. Start with a good, hard look into the command reference manual and use the EZ 3D macros as a template, boiled down to the essentials. You will also learn more about NMR and digital signal processing this way, which will never hurt in our profession ;-). The macro language - easy to understand, versatile and forgiving - is the real power of FELIX and should be a mainstay of any demanding user (in my opinion). It has so far proved to do most of what I needed from a NMR processing package (we're doing some fairly involved stuff around here) and I would recommend FELIX to anyone contemplating serious ND work. This as an aside and a late follow-up to the recent discussion on SW packages. Cheers, Christoph -- | Christoph Weber Sen. Research Associate | Dept.of Molecular Biology, MB2 The Scripps Research Institute | La Jolla CA 92037 weber@scripps.edu | 619-554-8754 (phone) 619-554-3757 (FAX) From owner-structural-nmr@net.bio.net Sun Nov 05 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!not-for-mail From: Robert Miller Newsgroups: bionet.structural-nmr,sci.bio,sci.engr,sci.misc,sci.physics,sci.physics.research Subject: Re: biophysics vs. biochem speculatin' Date: 6 Nov 1995 18:16:20 -0500 Organization: RJM & Associates Lines: 9 Sender: pfiglio@anthrax.physics.indiana.edu Approved: pfiglioz@indiana.edu Message-ID: <47kd3q$mc8@shellx.best.com> References: <47bj7r$kkt@dustbunny.physics.indiana.edu> NNTP-Posting-Host: anthrax.physics.indiana.edu To: mbmorton@ix.netcom.com Xref: biosci bionet.structural-nmr:882 sci.engr:15110 sci.misc:7921 sci.physics:105760 sci.physics.research:2893 My guess is "d - some other ...". The "softness" you feel is on a macro-level not the molecular level. Try looking at fatty acid, vitamin E or some other oil like materials as a component of hair pores etc. Robert >mbmorton@ix.netcom.com (michelle morton ) wrote: >Got a question that's been puzzling me. My cat's fur is so soft that >petting him is like touching a cashmere or angora sweater. Is this >*softness* due to.... From owner-structural-nmr@net.bio.net Sun Nov 05 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!newsfeed.ACO.net!fstgal00.tu-graz.ac.at!balu.kfunigraz.ac.at!email.kfunigraz.ac.at!zangger From: zangger@email.kfunigraz.ac.at (Klaus Zangger) Newsgroups: bionet.structural-nmr Subject: multi-site exchange Date: Mon, 6 Nov 1995 17:55:09 Organization: Institut für organische Chemie Lines: 13 Distribution: world Message-ID: NNTP-Posting-Host: boch04.kfunigraz.ac.at X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Dear Netters ! For a special type of NMR-experiment I am looking for an organic compound which shows a mutli-site (3 to 6 different sites) exchange equilibrium. If the different sites have the same energy it would be advantageous. The exchange constants should be in the range of Hertz (slow exchange on the NMR time scale). The compound should also be commercially available. Suggestions would be appreciated. Thanks in advance. Klaus From owner-structural-nmr@net.bio.net Sun Nov 05 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!news00.sunet.se!sunic!news99.sunet.se!columba.udac.uu.se!rigel.bmc.uu.se!gerard From: gerard@rigel.bmc.uu.se (Gerard Kleijwegt) Newsgroups: bionet.structural-nmr Subject: Re: Newsgroup Moderation Poll - Please read Date: 6 Nov 1995 19:04:02 GMT Organization: Uppsala University Lines: 4 Distribution: world Message-ID: <47lm72$1nn2@columba.udac.uu.se> References: <9511030025.AA01877@bioc01.uthscsa.edu> NNTP-Posting-Host: rigel.bmc.uu.se with fewer than 10 postings per day I don't think moderation is really necessary; the S/N is still considerably > 2 --gerard From owner-structural-nmr@net.bio.net Mon Nov 06 22:00:00 1995 Path: biosci!mr.unit.no!Alexej.Jerschow From: Alexej.Jerschow@mr.unit.no ("Alexej Jerschow") Newsgroups: bionet.structural-nmr Subject: AU program for data processing in Xwinnmr Date: 7 Nov 1995 15:18:21 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 46 Sender: daemon@net.bio.net Distribution: world Message-ID: <9511080015.ZM26186@linus.mr.sintef.no> NNTP-Posting-Host: net.bio.net Dear All, I would like to write an AU program for processing data in 2rr files using the xwinnmr program on an SGI (R4000, Irix 5.3, or R8000, Irix 6.0.1). To do this I would need some advice and clarification of the following 1) Can I write AU programs in a way that I can run them without xwinnmr (e.g. for testing). What changes are then to be made to make them run from within xwinnmr again ? 2) Can I write the programs using the GNU Compiler and/or Libraries ? 3) Can I use a Debugger when compiling AU programs from within xwinnmr ? 4) Can I define subroutines ? 5) Can I include C++ code ? 6) Can I run AU commands in queues ? (So that the user can specify to run time intensive processes sequentially) 7) Do there exist AU program libraries to take as an example other than the ones that come with the normal xwinnmr distribution ? 9) Do there exist predefined functions to access easily rows and cols in a processed (2rr) 2D file ? (Read and write) I would be very glad if someone could give me an answer to the above questions. Thank you very much Regards Alexej Jerschow -- ------------------------ Alexej Jerschow present address: MR-Center, SINTEF UNIMED N-7034 Trondheim, Norway Tel: +47-73 99 89 36 Fax: +47-73 99 00 08 From owner-structural-nmr@net.bio.net Mon Nov 06 22:00:00 1995 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: moderation Date: 7 Nov 1995 02:57:02 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 25 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Netters, I should not keep away from the polls in concern of moderation of the newsgroup. I understand that these "spams" (I learned this word as new for me in this context...) are of nuissance for all of us. It would be a convenient arrangement to make one person responsible for sweeping such message right into the garbage can, but I think I can do it myself with little inconvenience involved. Thanks, cheers, 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.) From owner-structural-nmr@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!URANO.MIA.UV.MX!fmontes From: fmontes@URANO.MIA.UV.MX (Fernando M. Montes Gonzalez) Newsgroups: bionet.structural-nmr Subject: Positions on protein analysis on immune recognition available in Mexico Date: 7 Nov 1995 17:17:21 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 66 Sender: daemon@net.bio.net Distribution: world Message-ID: <9511080116.AA03749@urano.mia.uv.mx> NNTP-Posting-Host: net.bio.net Two positions are available for research in protein sequences and structure analysis applied to the Study of the Immune Molecular Recognition Process. Our group in Molecular Bioinformatics and Immune Recognition are opening a new laboratory in protein modeling and sequence analysis. We are seeking for two Ph.D. with experience in sequence and/or structure analysis of proteins or in the the study of the molecular mechanism of immune recognition. Our area of research is the study of the molecular basis of immune recognition. This problem is studied from a wide spectrum that goes from the analysis of the structural diversity of the germline repertoire, the comparison of the immune molecular recognition strategies in vertebrates, the construction of a 3-d specialized database of Igs, Mhc and Tcr and it analysis, molecular dynamics studies of the Fv, etc. We try to integrate these studies in the context of theoretical models and the general theory of the immune response. We are planing to extend in the future our studies to other recognition models like those of the endocrine or nervous systems. The two positions available are for a period of three years of renewal. After this period, if the work is evaluated as satisfactory the position will come permanent. The new laboratory is the result from an agreement between the National University of Mexico and the Veracruzana University. The seat of the laboratory will be the City of Xalapa at the state of Veracruz. Xalapa (1500 m. over the sea level) is a medium size city (300,000) and is the capital of the state of Veracruz. For information about the Veracruzana University please see at: http://www.coacade.uv.mx/ For information about our Molecular Biology Laboratory here in Xalapa please see at: http://uv4.ivest.uv.mx/ The candidates must send their curriculum vitae with all its publications to the e-address indicated at the end of this message. You can find information about our research in: J. Mol. Evol. (1994) 38:100 J. Mol. Evol. (1995) 41:98 Biosystems (1995) 32:25 J. Mol. Biol. (1995) 246:74 Int. J. Pept. Prot. Res. (1995) 45:180 Prot. Sci. (1995) 4:1708. Immunogenenics (1995) in press. J. Mol. Biol. (1995) in press. Please contact with Dr. Enrique Vargas-madrazo at: evargas@uv4.invest.uv.mx or evargas@speedy.coacade.uv.mx --QAC07330.815790199/net.bio.net-- From owner-structural-nmr@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!URANO.MIA.UV.MX!fmontes From: fmontes@URANO.MIA.UV.MX (Fernando M. Montes Gonzalez) Newsgroups: bionet.structural-nmr Subject: Positions on protein analysis on immune recognition available in Mexico Date: 7 Nov 1995 16:14:03 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 62 Sender: daemon@net.bio.net Distribution: world Message-ID: <9511080012.AA03661@urano.mia.uv.mx> NNTP-Posting-Host: net.bio.net Two positions are available for research in protein sequences and structure analysis applied to the Study of the Immune Molecular Recognition Process. Our group in Molecular Bioinformatics and Immune Recognition are opening a new laboratory in protein modeling and sequence analysis. We are seeking for two Ph.D. with experience in sequence and/or structure analysis of proteins or in the the study of the molecular mechanism of immune recognition. Our area of research is the study of the molecular basis of immune recognition. This problem is studied from a wide spectrum that goes from the analysis of the structural diversity of the germline repertoire, the comparison of the immune molecular recognition strategies in vertebrates, the construction of a 3-d specialized database of Igs, Mhc and Tcr and it analysis, molecular dynamics studies of the Fv, etc. We try to integrate these studies in the context of theoretical models and the general theory of the immune response. We are planing to extend in the future our studies to other recognition models like those of the endocrine or nervous systems. The two positions available are for a period of three years of renewal. After this period, if the work is evaluated as satisfactory the position will come permanent. The new laboratory is the result from an agreement between the National University of Mexico and the Veracruzana University. The seat of the laboratory will be the City of Xalapa at the state of Veracruz. Xalapa (1500 m. over the sea level) is a medium size city (300,000) and is the capital of the state of Veracruz. For information about the Veracruzana University please see at: http://www.coacade.uv.mx/ For information about our Molecular Biology Laboratory here in Xalapa please see at: http://uv4.ivest.uv.mx/ The candidates must send their curriculum vitae with all its publications to the e-address indicated at the end of this message. You can find information about our research in: J. Mol. Evol. (1994) 38:100 J. Mol. Evol. (1995) 41:98 Biosystems (1995) 32:25 J. Mol. Biol. (1995) 246:74 Int. J. Pept. Prot. Res. (1995) 45:180 Prot. Sci. (1995) 4:1708. Immunogenenics (1995) in press. J. Mol. Biol. (1995) in press. Please contact with Dr. Enrique Vargas-madrazo at: evargas@uv4.invest.uv.mx or evargas@speedy.coacade.uv.mx From owner-structural-nmr@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!server-b.cs.interbusiness.it!dsi.unimi.it!sirio.cineca.it!nmrlab.ciam.unibo.it!mauro From: "M.A. Cremonini" Newsgroups: bionet.structural-nmr Subject: Re: moderation Date: Wed, 8 Nov 1995 15:13:57 +0100 Organization: Cineca Lines: 38 Message-ID: References: NNTP-Posting-Host: nmrlab.ciam.unibo.it Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In-Reply-To: On 7 Nov 1995, Istvan Pelczer wrote: > > Dear Netters, > > I should not keep away from the polls in concern of moderation of the > newsgroup. I understand that these "spams" (I learned this word as new > for me in this context...) are of nuissance for all of us. It would be a > convenient arrangement to make one person responsible for sweeping such > message right into the garbage can, but I think I can do it myself with > little inconvenience involved. > Thanks, cheers, > > Istvan > Hi everybody, I did not follow the newsgroup for a while and now I understand that someone has raised the problem about newsgroup moderation. I completely agree with Istvan. Since we are not dealing with hundreds of messsages per day we can erase the unwanted or off-topics messages ourselves. And I think that we also should simply *ignore* offensive or stupid messages, so as not to give any satisfaction to stupid folks. Ciao to all. Mauro ============================================ Dr. Mauro Andrea Cremonini Institute of Agricultural Chemistry University - Bologna - Italy FAX:+39.51.243362 e-mail: m.a.cremonini@nmrlab.ciam.unibo.it 73 de IK4QIX ============================================ From owner-structural-nmr@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!LILY.CHEM.WESLEYAN.EDU!phbolton From: phbolton@LILY.CHEM.WESLEYAN.EDU (Philip H. Bolton) Newsgroups: bionet.structural-nmr Subject: labeled d-arginine Date: 7 Nov 1995 18:36:08 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Does anyone know of a source of uniformly 13C/15N labeled d-arginine? This is for a project with a biotech firm so price is not that important (if you know someone who would be willing to prepare it for money that is fine). Need a couple of hundred milligrams. If double labeled material is not available then 13C would do and 15N in a pinch. Cambridge does not have it and Martek apparently does not. Best, Philip Bolton From owner-structural-nmr@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!URANO.MIA.UV.MX!fmontes From: fmontes@URANO.MIA.UV.MX (Fernando M. Montes Gonzalez) Newsgroups: bionet.structural-nmr Subject: Positions on protein analysis available Date: 8 Nov 1995 13:28:51 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 64 Sender: daemon@net.bio.net Distribution: world Message-ID: <9511081801.AA04421@urano.mia.uv.mx> NNTP-Posting-Host: net.bio.net Two positions are available for research in protein sequences and structure analysis applied to the Study of the Immune Molecular Recognition Process. Our group in Molecular Bioinformatics and Immune Recognition are opening a new laboratory in protein modeling and sequence analysis. We are seeking for two Ph.D. with experience in sequence and/or structure analysis of proteins or in the the study of the molecular mechanism of immune recognition. Our area of research is the study of the molecular basis of immune recognition. This problem is studied from a wide spectrum that goes from the analysis of the structural diversity of the germline repertoire, the comparison of the immune molecular recognition strategies in vertebrates, the construction of a 3-d specialized database of Igs, Mhc and Tcr and it analysis, molecular dynamics studies of the Fv, etc. We try to integrate these studies in the context of theoretical models and the general theory of the immune response. We are planing to extend in the future our studies to other recognition models like those of the endocrine or nervous systems. The two positions available are for a period of three years of renewal. After this period, if the work is evaluated as satisfactory the position will come permanent. The new laboratory is the result from an agreement between the National University of Mexico and the Veracruzana University. The seat of the laboratory will be the City of Xalapa at the state of Veracruz. Xalapa (1500 m. over the sea level) is a medium size city (300,000) and is the capital of the state of Veracruz. For information about the Veracruzana University please see at: http://www.coacade.uv.mx/ For information about our Molecular Biology Laboratory here in Xalapa please see at: http://uv4.ivest.uv.mx/ The candidates must send their curriculum vitae with all its publications to the e-address indicated at the end of this message. You can find information about our research in: J. Mol. Evol. (1994) 38:100 J. Mol. Evol. (1995) 41:41 Biosystems (1995) 32:25 J. Mol. Biol. (1995) 246:74 Int. J. Pept. Prot. Res. (1995) 45:180 Prot. Sci. (1995) oct. issue. Immunogenenics (1995) in press. J. Mol. Biol. (1995) in press. Please contact with Dr. Enrique Vargas-madrazo at: evargas@uv4.invest.uv.mx or evargas@speedy.coacade.uv.mx From owner-structural-nmr@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!WWITCH.UNL.EDU!rshoe From: rshoe@WWITCH.UNL.EDU (Richard Shoemaker) Newsgroups: bionet.structural-nmr Subject: Q...Career Advice for Student Date: 8 Nov 1995 10:54:44 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 51 Sender: daemon@net.bio.net Distribution: world Message-ID: <9511081847.AA29448@wwitch.unl.edu.unl.edu> NNTP-Posting-Host: net.bio.net Dear Biomolecular NMR People: I have an acquaintance who has come to me for advice on the best way to go about entering the field of Biomolecular NMR Spectroscopy, and although I "dabble" in the area, I'm certainly no "big gun" in the field of Protein/DNA NMR structure determination. She has a BS degree in Chemistry, and has worked for a couple of years for a major manufacturer of bio-analytical/analytical instrumentation located here in Lincoln, NE. She is _very_ talented, has the potential to be quite successful in any area of science, and sees Bio-NMR as an important/growing research field. She has specific questions like: 1) Who's doing leading-edge work in the field? (I can help her w/ this one, but I'm sure that there are many doing good work that I don't know about.) 2) Of "(1)" above, what is the market for new, inexperienced grad-students, and what is the best way for her to contact potential research advisors? 3) What does the future look like for the field? (i.e. which areas are "hot" now, and which are likely to stay that way?) With the difficulty many Chemistry-related Ph.D.s are having getting good jobs, she seems to feel that Biomolecular NMR is an area where she will have a career after she finishes the onerous task of acheiving the degree. I'm not even sure that I can give a good answer to whether this assumption is correct or not? I found myself somewhat taken aback by these questions, which means that I haven't spent much time of late stepping back and looking at the "big picture" of this group's research area. I'm going to send her to the library (first of all), and give her some guidance WRT surfing the NMR-related stuff on the Net, but I would appreciate any helpful comments/suggestions on any/all of the above...especially from those of you who are "neck-deep" in the area of Biomolecular NMR Structure work! I hope such a general/ambiguous question is welcomed by the group...At least I'm not SELLING anything (like phone-sex, or get-rich-quick schemes)! 8-) Best Regards, Rich Shoemaker ---- 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 Tue Nov 07 22:00:00 1995 Path: biosci!anti.irkutsk.su!krivdin From: krivdin@anti.irkutsk.su ("Leonid B. Krivdin") Newsgroups: bionet.structural-nmr Subject: Re: biophysics vs. biochem speculatin' Date: 7 Nov 1995 18:33:58 -0800 Organization: ANGARSK TECHNOLOGY INSTITUTE Lines: 40 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <47bj7r$kkt@dustbunny.physics.indiana.edu> NNTP-Posting-Host: net.bio.net > Got a question that's been puzzling me. My cat's fur is so soft that > petting him is like touching a cashmere or angora sweater. Is this > *softness* due to: > > a) the **physical** arrangement of the peptide bonds - ie, do the amino > acids line up in a smooth, rather than jagged or discrete, surface? > > b) the sequencing of the amino acids themselves? > > c) the tertiary or quarternary folding of the protein(s) in his fur - > ie, do the proteins have some special arrangement that we experience as > being *soft* or, > > d) some other phenomenom (phenomena) that completely escapes me right > now? Obviously, this interesting phenomenon you observe with your cat is due to the proper feeding and good care and none of the given above reasonings (a) - (c). Good luck to your cat. Rgds, Leonid Krivdin. *************************************************** Dr Leonid B. Krivdin Professor of Chemistry Angarsk Technological Institute 60 Chaikovsky Ave. Angarsk 665835, Russia E-mail: krivdin@anti.irkutsk.su *************************************************** From owner-structural-nmr@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!URANO.MIA.UV.MX!fmontes From: fmontes@URANO.MIA.UV.MX (Fernando M. Montes Gonzalez) Newsgroups: bionet.structural-nmr Subject: Positions on protein analysis on immune recognition available in Mexico Date: 7 Nov 1995 17:21:21 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 66 Sender: daemon@net.bio.net Distribution: world Message-ID: <9511080116.AA03750@urano.mia.uv.mx> NNTP-Posting-Host: net.bio.net Two positions are available for research in protein sequences and structure analysis applied to the Study of the Immune Molecular Recognition Process. Our group in Molecular Bioinformatics and Immune Recognition are opening a new laboratory in protein modeling and sequence analysis. We are seeking for two Ph.D. with experience in sequence and/or structure analysis of proteins or in the the study of the molecular mechanism of immune recognition. Our area of research is the study of the molecular basis of immune recognition. This problem is studied from a wide spectrum that goes from the analysis of the structural diversity of the germline repertoire, the comparison of the immune molecular recognition strategies in vertebrates, the construction of a 3-d specialized database of Igs, Mhc and Tcr and it analysis, molecular dynamics studies of the Fv, etc. We try to integrate these studies in the context of theoretical models and the general theory of the immune response. We are planing to extend in the future our studies to other recognition models like those of the endocrine or nervous systems. The two positions available are for a period of three years of renewal. After this period, if the work is evaluated as satisfactory the position will come permanent. The new laboratory is the result from an agreement between the National University of Mexico and the Veracruzana University. The seat of the laboratory will be the City of Xalapa at the state of Veracruz. Xalapa (1500 m. over the sea level) is a medium size city (300,000) and is the capital of the state of Veracruz. For information about the Veracruzana University please see at: http://www.coacade.uv.mx/ For information about our Molecular Biology Laboratory here in Xalapa please see at: http://uv4.ivest.uv.mx/ The candidates must send their curriculum vitae with all its publications to the e-address indicated at the end of this message. You can find information about our research in: J. Mol. Evol. (1994) 38:100 J. Mol. Evol. (1995) 41:98 Biosystems (1995) 32:25 J. Mol. Biol. (1995) 246:74 Int. J. Pept. Prot. Res. (1995) 45:180 Prot. Sci. (1995) 4:1708. Immunogenenics (1995) in press. J. Mol. Biol. (1995) in press. Please contact with Dr. Enrique Vargas-madrazo at: evargas@uv4.invest.uv.mx or evargas@speedy.coacade.uv.mx --QAC07330.815790199/net.bio.net-- From owner-structural-nmr@net.bio.net Wed Nov 08 22:00:00 1995 Path: biosci!INTNET.UPJ.COM!kafarley From: kafarley@INTNET.UPJ.COM Newsgroups: bionet.structural-nmr Subject: subscribe Date: 9 Nov 1995 13:37:07 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: <9511092130.AA18970@intnet.upj.com> NNTP-Posting-Host: net.bio.net I would like to subscribe to the structural NMR network. Thanks, Kathleen Farley kafarley@intnet.upj.com From owner-structural-nmr@net.bio.net Wed Nov 08 22:00:00 1995 Path: biosci!biosci!not-for-mail From: Fred Hughson Newsgroups: bionet.xtallography,bionet.structural-nmr,bionet.jobs.offered Subject: ASST. PROF./Structural Biology/Princeton Univ. Date: 8 Nov 1995 22:30:36 -0800 Organization: Princeton University Lines: 28 Sender: biohelp@net.bio.net Approved: biojobs-moderator@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Xref: biosci bionet.xtallography:2159 bionet.structural-nmr:893 bionet.jobs.offered:494 ====================================================== ASSISTANT PROFESSOR Structural Biology Department of Molecular Biology Princeton University The Department of Molecular Biology at Princeton University invites applications for a tenure track position in structural biology and biochemistry at the Assistant Professor level. Exceptional senior level scientists may also be considered. Candidates must have a Ph.D. degree or equivalent and several years of postdoctoral experience. Qualified applicants should send their curriculum vitae, a summary of research interests, and three letters of reference to: Structural Biology Search Committee Department of Molecular Biology Princeton University Princeton, NJ 08544 Application deadline: December 1, 1995. [Princeton University is an Equal Opportunity/ Affirmative Action Employer.] ===================================================== From owner-structural-nmr@net.bio.net Thu Nov 09 22:00:00 1995 Path: biosci!anti.irkutsk.su!krivdin From: krivdin@anti.irkutsk.su ("Leonid B. Krivdin") Newsgroups: bionet.structural-nmr Subject: E-mail address of Poul E. Hansen Date: 9 Nov 1995 22:03:18 -0800 Organization: ANGARSK TECHNOLOGY INSTITUTE Lines: 29 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Fri: 10 Nov 95 Dear Netters: I should greatly appreciate getting E-mail address and Fax of Professor Poul E. Hansen from Roskilde University Center (Denmark). You are kindly encouraged to send this information directly to krivdin@anti.irkutsk.su. Thank you in advance, Leonid Krivdin. *************************************************** Dr Leonid B. Krivdin Professor of Chemistry Angarsk Technological Institute 60 Chaikovsky Ave. Angarsk 665835, Russia E-mail: krivdin@anti.irkutsk.su *************************************************** From owner-structural-nmr@net.bio.net Sat Nov 11 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.sprintlink.net!news.crd.ge.com!rebecca!news From: shelton bank Newsgroups: bionet.structural-nmr Subject: Re: labeled d-arginine Date: 10 Nov 1995 19:27:56 GMT Organization: The University at Albany Lines: 8 Message-ID: <48093s$hl9@rebecca.albany.edu> References: NNTP-Posting-Host: bankpc.chem.albany.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: phbolton@LILY.CHEM.WESLEYAN.EDU Phil I just called my contacts at ICON and they will get back to you about the arginine. hope it works best regards shel bank From owner-structural-nmr@net.bio.net Sat Nov 11 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!demon!sunsite.doc.ic.ac.uk!uknet!bhamcs!news.ox.ac.uk!news From: "Simon M. Brocklehurst" Newsgroups: bionet.structural-nmr Subject: ANNOUNCE: NAOMI Version 2.3 Date: Sun, 12 Nov 1995 18:52:09 +0000 Organization: Oxford University Lines: 67 Message-ID: <30A64259.1CFBAE39@bioch.ox.ac.uk> NNTP-Posting-Host: nmrv.ocms.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0b1N (X11; I; SunOS 4.1.3_U1 sun4m) NAOMI - Version Upgrade Announcement (Please note, NAOMI is provided at zero charge for academic use) (e-mail contact smb@bioch.ox.ac.uk) _____________________________________________________________________________ The computer program NAOMI Version 2.3 is available as of now from the NAOMI Web site at: http://www.ocms.ox.ac.uk/~smb/Software/N_details/naomi.html or via anonymous ftp from: nmrz.ocms.ox.ac.uk in directory pub/smb/naomi/ Users of versions older than 2.10 will need new license keys to allow the upgrade to work (please contact the author in this case). _____________________________________________________________________________ Upgrade features : machine-parsable output for interface to bioinformatics software, main-chain modelling, general residue selection, new solvent accessibility commands, additions to NMR structure refinement module. Fixes of minor bugs in pdb output and molscript output commands. _____________________________________________________________________________ What is NAOMI? NAOMI is an easy-to-use, state-of-the-art computer program which is aimed at both specialist and non-specialist researchers who make use of three-dimensional structures of proteins in their work. It has hundreds of users Worldwide. Some facilities offered by the program for working with structure include: automatic 'key' residue identification automatic hydrophobic core/packing analysis automatic hydrogen bonds main-chain and side-chain identification (including high quality energy calculations) automatic secondary structure (helix, strand and turn) classification using fuzzy logic automatic supersecondary structure classification (beta-hairpin loops) conformational parameters: phi,psi,chi1,chi2,chi3,chi4,chi5 etc solvent accessibility (both absolute and percentage) calculations automatic identification of disulphide bonds, salt bridges, chain-breaks side-chain modelling and manipulation applying symmetry operators automatic structure repair (building in missing atoms) NMR structure refinement module interfaces to graphics programs (MOLSCRIPT (and thus Raster3D), INSIGHT, QUANTA to allow automatic preparation of figures More details are available on the Web site. NB NAOMI currently 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 Sat Nov 11 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.sprintlink.net!news.crd.ge.com!rebecca!news From: shelton bank Newsgroups: bionet.structural-nmr Subject: Re: labeled d-arginine Date: 10 Nov 1995 19:27:43 GMT Organization: The University at Albany Lines: 8 Message-ID: <48093f$hl9@rebecca.albany.edu> References: NNTP-Posting-Host: bankpc.chem.albany.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: phbolton@LILY.CHEM.WESLEYAN.EDU Phil I just called my contacts at ICON and they will get back to you about the arginine. hope it works best regards shel bank From owner-structural-nmr@net.bio.net Sat Nov 11 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!uwm.edu!msunews!harbinger.cc.monash.edu.au!news.cs.su.oz.au!metro!news.une.edu.au!metz.une.edu.au!not-for-mail From: cgarvey@metz.une.edu.au (Christopher J. Garvey) Newsgroups: bionet.structural-nmr Subject: Re: Newsgroup Moderation Poll - Please read Date: 12 Nov 1995 03:03:50 GMT Organization: University of New England, NSW, Australia Lines: 27 Distribution: world Message-ID: <483o6m$iqj@grivel.une.edu.au> References: <9511030025.AA01877@bioc01.uthscsa.edu> <47lm72$1nn2@columba.udac.uu.se> NNTP-Posting-Host: metz.une.edu.au X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Gerard Kleijwegt (gerard@rigel.bmc.uu.se) wrote: : with fewer than 10 postings per day I don't : think moderation is really necessary; the : S/N is still considerably > 2 : --gerard Indeed, the best cure for spam is to ignore it and leave it on the plate. chris -- "For these gnostics fatherhood and mirrors are abominable since they dilute and disseminate the universe." Jorge Luis Borges ______________________________________ ************************************** -------------------------------------- Christopher J. Garvey Tamworth Agricultural Research Centre AUSTRALIA email cgarvey@metz.une.edu.au ======================================= /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-structural-nmr@net.bio.net Sat Nov 11 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.sprintlink.net!news.crd.ge.com!rebecca!news From: shelton bank Newsgroups: bionet.structural-nmr Subject: Re: labeled d-arginine Date: 10 Nov 1995 19:28:55 GMT Organization: The University at Albany Lines: 6 Message-ID: <48095n$hl9@rebecca.albany.edu> References: NNTP-Posting-Host: bankpc.chem.albany.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Windows; I; 16bit) Phil I called the people at icon and they will get back to you I hope shel bank From owner-structural-nmr@net.bio.net Mon Nov 13 22:00:00 1995 Path: biosci!INDIANA.EDU!mpagel From: mpagel@INDIANA.EDU (Marty Pagel) Newsgroups: bionet.structural-nmr Subject: Re: QCPE site Date: 14 Nov 1995 08:11:23 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 34 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <4899q8$5ib@leonard.anu.edu.au> Hi Chris, Since QCPE is just down the road from us, it's easier for us to visit. There is no QCPE web page listed at Indiana University, nor do they list an ftp site. Their address and phone # listed in the QCPE catalogue is: QCPE Creative Arts Building 181 Indiana University Bloomington, IN 47405, USA (812)-855-4784 You may want to call them to learn more about their policies. Marty Pagel mpagel@indiana.edu --- __o Department of Chemistry Phone: (812)-855-6492 --- \<, Indiana University Fax: (812)-855-8300 --- ()/ () Bloomington, IN 47405-4001 http://nmrsg1.chem.indiana.edu/~mpagel On 14 Nov 1995, Christopher J Blake wrote: > Does anyone know if there is a web or ftp site for QCPE programs? > We are looking for iterative simulation programs for exchanging NMR > systems, a la DNMR5, but preferably something that has been written (or > updated) in the last decade. What I'm really hoping to find is something > written in well documented C or C++ (anything but Fortran) so that I have > some hope of understanding how the program works, but that may be asking > too much! > > Chris Blake Chris.Blake@anu.edu.au > University N.M.R. Centre phone 61 6 279-8074 > Australian National University fax 61 6 249-0750 > > From owner-structural-nmr@net.bio.net Mon Nov 13 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!newsfeed.internetmci.com!chi-news.cic.net!simtel!harbinger.cc.monash.edu.au!newshost.anu.edu.au!leonard.anu.edu.au!not-for-mail From: cjb505@leonard.anu.edu.au (Christopher J Blake) Newsgroups: bionet.structural-nmr Subject: QCPE site Date: 14 Nov 1995 16:35:04 +1100 Organization: Australian National University Lines: 12 Message-ID: <4899q8$5ib@leonard.anu.edu.au> NNTP-Posting-Host: 150.203.2.15 Keywords: QCPE exchange X-Newsreader: NN version 6.5.0 #12 (NOV) Does anyone know if there is a web or ftp site for QCPE programs? We are looking for iterative simulation programs for exchanging NMR systems, a la DNMR5, but preferably something that has been written (or updated) in the last decade. What I'm really hoping to find is something written in well documented C or C++ (anything but Fortran) so that I have some hope of understanding how the program works, but that may be asking too much! Chris Blake Chris.Blake@anu.edu.au University N.M.R. Centre phone 61 6 279-8074 Australian National University fax 61 6 249-0750 From owner-structural-nmr@net.bio.net Tue Nov 14 22:00:00 1995 Path: biosci!rutgers!concert!gatech2!usenet.eel.ufl.edu!spool.mu.edu!news.sol.net!news.inc.net!news.sprintlink.net!newsfeed.internetmci.com!in2.uu.net!brighton.openmarket.com!decwrl!lll-winken.llnl.gov!taco.cc.ncsu.edu!bch48.bch.ncsu.edu!stuart From: stuart@bch48.bch.ncsu.edu (John Stuart) Newsgroups: bionet.structural-nmr Subject: Re: QCPE site Date: 14 Nov 1995 22:49:24 GMT Organization: ncsu biochemistry Lines: 29 Message-ID: <48b6dk$82o@taco.cc.ncsu.edu> References: <4899q8$5ib@leonard.anu.edu.au> NNTP-Posting-Host: bch48.bch.ncsu.edu Keywords: QCPE exchange Christopher J Blake wrote: >Does anyone know if there is a web or ftp site for QCPE programs? >We are looking for iterative simulation programs for exchanging NMR >systems, a la DNMR5, but preferably something that has been written (or >updated) in the last decade. What I'm really hoping to find is something >written in well documented C or C++ (anything but Fortran) so that I have >some hope of understanding how the program works, but that may be asking >too much! Hi, QCPE *does* have an ftp/gopher site. You can either ftp to: qcpe6.chem.indiana.edu or point your WWW browser to: < gopher://gopher.gdb.org:70/1ftp%3aqcpe6.chem.indiana.edu%40/ > One can also telnet for on-line searching. To carry out a search simply do the following: telnet 129.79.74.206 login: anonymous (There is no password) When you have logged in give the command 'Catsrch'. The search program will provide instructions as to how to proceed. This site should have all the information you need. Later, John W Stuart stuart@bch48.bch.ncsu.edu From owner-structural-nmr@net.bio.net Tue Nov 14 22:00:00 1995 Newsgroups: bionet.software.x-plor,bionet.structural-nmr Path: biosci!rutgers!concert!gatech2!wa4mei!gatech!udel!darwin.sura.net!nih-csl!loglady.ninds.nih.gov!johnk From: johnk@spasm.niddk.nih.gov (John Kuszewski) Subject: Re: Gly phi constraints Message-ID: <1995Nov15.215448.9529@alw.nih.gov> Sender: postman@alw.nih.gov (AMDS Postmaster) Nntp-Posting-Host: spasm.niddk.nih.gov Reply-To: johnk@spasm.niddk.nih.gov (John Kuszewski) Organization: National Insts. of Health References: <48d4q1$36b@news.ox.ac.uk> Date: Wed, 15 Nov 1995 21:54:48 GMT Lines: 42 Xref: biosci bionet.software.x-plor:204 bionet.structural-nmr:911 In article <48d4q1$36b@news.ox.ac.uk>, Kristy Downing writes: |> Dear All, |> |> I have extracted coupling constants corresponding to Gly HA1-HN and HA2-HN from |> a HNHA experiment, and I would now like to use this information to derive |> backbone phi constraints. I have two questions: |> |> (i) How do the couplings relate to the phi angle? For example, if one HA-HN |> coupling constant is 4.0 Hz and the other is 7.4 Hz, what equation do I use to |> derive phi? (If anyone knows of a reference, I would be very grateful!) I just talked to Andy Wang, one of Ad Bax's postdocs, about this. The Karplus curve that Vuister and Bax published (as well as a re-worked version that Andy and Ad have in-press) does not work well for gly. I wouldn't try to include phi restraints from gly 3J HnHa couplings. |> |> (ii) Are glycine phi constraints encoded the same way in X-PLOR as other |> backbone torsion angle constraints, i.e., using the atoms of C(i-1), N, CA, and |> C? Yes, although better ways of dealing with this information, such as my direct refinement techniques, have been developed too. -- _____________ | ___/_ | |/ / -- /\ // /-- || || / /|| || || / / || || ||/ / || John Kuszewski || |/ /| || johnk@spasm.niddk.nih.gov || / /|| || \/ / / || \/ that's MISTER protein G to you! |/__/| | /_________| "Biophysics has driven me to an attitude of apocalyptic doom" --Frank Delaglio From owner-structural-nmr@net.bio.net Tue Nov 14 22:00:00 1995 Path: biosci!BIOC01.UTHSCSA.EDU!raman From: raman@BIOC01.UTHSCSA.EDU (C.S.RAMAN) Newsgroups: bionet.structural-nmr Subject: postdoctoral positions Date: 15 Nov 1995 11:38:06 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 54 Sender: daemon@net.bio.net Distribution: world Message-ID: <9511151935.AA00393@bioc01.uthscsa.edu> NNTP-Posting-Host: net.bio.net POSITION OPEN: Postdoctoral Research Associates INSTITUTION: Yale University ADDRESS: 266 Whitney Ave. Box 208114 New Haven, CT 06520-8114 CONTACT PERSON: Steven Smith PHONE: 203-432-5095 FAX: 203-432-5175 EMAIL: smith@loki.csb.yale.edu DATE OF AVAILABILITY: December 1, 1995 (first available start date) DURATION: Two - three years JOB DESCRIPTION: Two postdoctoral positions are currently available. The general research area involves structure/function studies of membrane proteins involved in signal transduction and ion transport. Specific projects focus on the development and application of magic angle spinning NMR methods for measuring internuclear distances. Applicants with backgrounds in NMR spectroscopy and an interest in biological systems are encouraged to apply. For more information about the lab and current publications, see the Smithlab homepage (http://loki.csb.yale.edu/smithlab/smithlab). APPLICATION REQUIREMENTS: Send a CV and two letters of recommendation to Prof. Steven Smith at the address above. APPLICATION DEADLINE: March 1, 1996 -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ C.S.RAMAN _/ _/ Department of Biochemistry _/ _/ University of Texas Health Science Center _/ _/ 7703 Floyd Curl Drive _/ _/ San Antonio, TX 78284-7760 _/ _/ USA _/ _/ _/ _/ Tel: (210) 567-6623 _/ _/ Fax: (210) 567-6595 _/ _/ E-mail: raman@bioc01.uthscsa.edu _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ How can it be that mathematics, a product of human thought _/ _/ independent of experience, is so admirably adapted to the _/ _/ objects of reality? -Albert Einstein _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From owner-structural-nmr@net.bio.net Tue Nov 14 22:00:00 1995 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!news.sprintlink.net!tank.news.pipex.net!pipex!demon!sunsite.doc.ic.ac.uk!warwick!bham!bhamcs!news.ox.ac.uk!news From: Kristy Downing Newsgroups: bionet.software.x-plor,bionet.structural-nmr Subject: Gly phi constraints Date: 15 Nov 1995 16:34:09 GMT Organization: University of Oxford Lines: 23 Message-ID: <48d4q1$36b@news.ox.ac.uk> NNTP-Posting-Host: nmru.ocms.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1IS (X11; I; IRIX 5.3 IP22) X-URL: news:bionet.software.x-plor Xref: biosci bionet.software.x-plor:202 bionet.structural-nmr:909 Dear All, I have extracted coupling constants corresponding to Gly HA1-HN and HA2-HN from a HNHA experiment, and I would now like to use this information to derive backbone phi constraints. I have two questions: (i) How do the couplings relate to the phi angle? For example, if one HA-HN coupling constant is 4.0 Hz and the other is 7.4 Hz, what equation do I use to derive phi? (If anyone knows of a reference, I would be very grateful!) (ii) Are glycine phi constraints encoded the same way in X-PLOR as other backbone torsion angle constraints, i.e., using the atoms of C(i-1), N, CA, and C? Thanks very much, Kristy Downing -- Dr. A. Kristina Downing Oxford University tel. 01865-275956 Department of Biochemistry fax. 01865-275253 Oxford OX1 3QU ENGLAND e-mail: kristy@bioch.ox.ac.uk From owner-structural-nmr@net.bio.net Tue Nov 14 22:00:00 1995 Path: biosci!UNITY.NCSU.EDU!idshin From: idshin@UNITY.NCSU.EDU ("Dan Shin") Newsgroups: bionet.structural-nmr Subject: Re: (none) Date: 15 Nov 1995 07:15:47 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 39 Sender: daemon@net.bio.net Distribution: world Message-ID: <9511151103.ZM12487@152.1.38.71> NNTP-Posting-Host: net.bio.net Dave, Here is the info about the book. Title: A Handbook of Nuclear Magnetic Resonance By Ray Freeman, Oxford University Longman Scientific & Technical Copublished in the United States with John Wiley & Sons, Inc. New York ISBN 0-582-00390-3 Hope this helps. On Nov 15, 6:31am, david w. hoffman wrote: > Subject: (none) > Hi - > > I am trying to find a copy of a book > by Ray Freeman called "A Handbook of NMR" > or something like that. If anyone was > this book, could you e-mail me the name > of the publisher, the exact title, year > published, etc. > > Thanks. > > Dave Hoffman > Univ. of Texas at Austin > > e-mail: dave@noddy.cm.utexas.edu > > > > >-- End of excerpt from david w. hoffman -- Dan Shin dan_shin@ncsu.edu (919) 515-2248 From owner-structural-nmr@net.bio.net Tue Nov 14 22:00:00 1995 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: (none) Date: 15 Nov 1995 07:04:37 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 44 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <9511151427.AA02882@noddy.cm.utexas.edu> NNTP-Posting-Host: net.bio.net "A Handbook of Nuclear Magnetic Resonance" Longman/John Wiley & Sons, Inc. New York, 1988 (what we have here) ISBN 0-582-00390-3 (CSD) 0-582-00574-4 (PPR) Enjoy! (I am sure you will.) All the best, 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 15 Nov 1995, david w. hoffman wrote: > Hi - > > I am trying to find a copy of a book > by Ray Freeman called "A Handbook of NMR" > or something like that. If anyone was > this book, could you e-mail me the name > of the publisher, the exact title, year > published, etc. > > Thanks. > > Dave Hoffman > Univ. of Texas at Austin > > e-mail: dave@noddy.cm.utexas.edu > > > From owner-structural-nmr@net.bio.net Tue Nov 14 22:00:00 1995 Path: biosci!NODDY.CM.UTEXAS.EDU!dave From: dave@NODDY.CM.UTEXAS.EDU (david w. hoffman) Newsgroups: bionet.structural-nmr Subject: (none) Date: 15 Nov 1995 06:31:21 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <9511151427.AA02882@noddy.cm.utexas.edu> NNTP-Posting-Host: net.bio.net Hi - I am trying to find a copy of a book by Ray Freeman called "A Handbook of NMR" or something like that. If anyone was this book, could you e-mail me the name of the publisher, the exact title, year published, etc. Thanks. Dave Hoffman Univ. of Texas at Austin e-mail: dave@noddy.cm.utexas.edu From owner-structural-nmr@net.bio.net Tue Nov 14 22:00:00 1995 Path: biosci!daresbury!is.bbsrc.ac.uk!news From: (Computing) Newsgroups: bionet.structural-nmr Subject: WISE-NMR Date: 15 Nov 1995 11:58:43 GMT Organization: IFR NL Lines: 11 Message-ID: <48cklj$7md@is.bbsrc.ac.uk> References: Reply-To: boetzel@bbsrc.ac.uk NNTP-Posting-Host: pc0517.ifrn.bbsrc.ac.uk X-Newsreader: WinVN 0.91.6 Hi there! Does anybody have a pulse program for running the WISE experiment on Bruker MSL machines? Ruth Ruth Boetzel IFR Norwich UK e-mail: boetzel@bbsrc.ac.uk From owner-structural-nmr@net.bio.net Tue Nov 14 22:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!sdd.hp.com!swrinde!newsfeed.internetmci.com!EU.net!news.eunet.fi!newsmaster From: piero pollesello Newsgroups: bionet.structural-nmr Subject: -S-S-cyclic 10 a.a. peptide in DTT? Date: 15 Nov 1995 07:12:42 GMT Organization: POLYbios, Area Science Park, Trieste, Italy Lines: 17 Message-ID: <48c3ta$f30@idefix.eunet.fi> NNTP-Posting-Host: mac545.espoo.orion.fi Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12(Macintosh; I; 68K) X-URL: news:bionet.structural-nmr Who could help me solving the following problem... in order to study a particular "protein-peptide" interaction by NMR, I need to work in a solution containing DTT (or my cystein containing "protein" will possibly dimerize) BUT my "peptide" is a 10 a.a. cyclic -S-S- peptide which should remain cyclic despite the DTT. Does anyone know a chemical way to modify the -S-S- bond into a non-reductable one, or does someone know an other compound (of the mercaptoethanol family) which selectively prevents the formation of new -S-S- bonds without reducing the existent ones? thanks Piero From owner-structural-nmr@net.bio.net Wed Nov 15 22:00:00 1995 Path: biosci!biophy.jussieu.fr!michel From: michel@biophy.jussieu.fr (Michel SEIGNEURET) Newsgroups: bionet.structural-nmr Subject: alpha proton exchange Date: 16 Nov 1995 10:38:38 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <9511161847.AA14942@mood.biophy.jussieu.fr> NNTP-Posting-Host: net.bio.net Hi, I was told by a collegue that in some specific deuterated organic solvent or solvent mixtures, not only peptide amide proton but also alpha and some aromatic protons can exchange to deuterium. He was unfortunately unable to remember in which solvents. Could somebody indicate to me some of these solvent and give me an idea of the exchange rates ? Thanks in advance. Michel M. Seigneuret Universite Paris 7 Lab. de Biophysique Cellulaire France From owner-structural-nmr@net.bio.net Wed Nov 15 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: son of pps Newsgroups: bionet.structural-nmr Subject: WEB Course on Protein Structure Date: 16 Nov 1995 13:07:48 -0000 Lines: 27 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <48fd34$4bh@mserv1.dl.ac.uk> X-Sender: pps2@iona.cryst.bbk.ac.uk Original-To: str-nmr@dl.ac.uk B i r k b e c k C o l l e g e Crystallography Department INTERNET COURSE IN PRINCIPLES OF PROTEIN STRUCTURE http://www.cryst.bbk.ac.uk/PPS2/ We are running a part-time London University Advanced Certificate course in Principles of Protein Structure on the Internet (a formalised version of last year's course). Units are: 1. IT and Bioinformatics 2. Protein Structure 3. Dissertation: topics in structure, function and dynamics Course runs for 1 academic year (3 terms) from 15 January to 25 October 1996. For details of course contents, administration and registration, see our Web pages at URL given above. Costs: 186 pounds sterling (EU) 500 pounds sterling (world) email: j.mcgill@mail.cryst.bbk.ac.uk Dr J Z Turner Crystallography Department Birkbeck College London WC1E 7HX Tel. (44) (0)171 631 6831/6800 Fax. 6803 email ubcg023@mail.cryst.bbk.ac.uk From owner-structural-nmr@net.bio.net Wed Nov 15 22:00:00 1995 Path: biosci!anti.irkutsk.su!krivdin From: krivdin@anti.irkutsk.su ("Leonid B. Krivdin") Newsgroups: bionet.structural-nmr Subject: Thanks Date: 15 Nov 1995 20:51:05 -0800 Organization: ANGARSK TECHNOLOGY INSTITUTE Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Thu: 16 Nov 95 Many thanks to Jens O. Duus, Morten D. Sorensen, David Cullinan, tbj (Denmark), Yuri Strelenko, Aleksei Denisov and others who helped me to get P.E.H. address. Rgds, Leonid Krivdin. From owner-structural-nmr@net.bio.net Wed Nov 15 22:00:00 1995 Path: biosci!BIOC01.UTHSCSA.EDU!raman From: raman@BIOC01.UTHSCSA.EDU (C.S.RAMAN) Newsgroups: bionet.structural-nmr Subject: NMR Processing Software - Freeware Date: 15 Nov 1995 19:15:51 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 86 Sender: daemon@net.bio.net Distribution: world Message-ID: <9511160312.AA00806@bioc01.uthscsa.edu> NNTP-Posting-Host: net.bio.net Here is something I was requested to post to the entire net. Since there was interest sometime back on data processing software availability for the Mac, I thought it would be of general interest. Cheers -raman It is a pleasure to announce that version 3.0.4 of the NMR processing program SwaN-MR is available, as three compressed-self-expanding files, (via anonymous ftp) from : sfdzuma.usc.es (193.144.75.69) directory: /pub/NMR/SwaN-MR.304 SwaN-MR is a FREEWARE program for the Macintosh and PowerMac. It processes and analyzes NMR spectra (1D to 4D, from Varian Gemini, Bruker nad TecMag spectrometers). It is also very useful in annotating, printing and presenting spectra. The program has been written by: Dr. Giuseppe Balacco MENARINI s.r.l. Via Sette Santi, 3 I-50131 Firenze ITALY In order to use SwaN-MR you need to write a SIGNED LETTER (no fax or e-mail messages) to Dr. Balacco requesting a LICENSE. With the license you will receive a password to decompress the program file. If you want to check out the program before asking for the license you can try Snail-MR (included in the demo file). It does everything that SwaN-MR does but much more slowly. The program's capabilities include: Weighting (9 different window functions) FFT (real, complex, hypercompex, etcI) Phase Correction (1 manual and 2 automatic options) Magnitude representation Baseline Correction (6 options, including 5th degree polynomials and trigonometric series) BasePlane correction Integration (manual and automatic) Least Squares Fitting (to Lorentzian or Gaussian functions) Quanto-mechanical simulations Fast Linear Prediction Digital Solvent Suppression T1 calculation (inversion recovery) Spectral Editing (algebraic addition and much more) Symmetrization What's in the files? Swan.sea contains the main application. It is protected with a password. Extra.sea contains: - instructions for the program; - the library "ObjectSupportLib"; - instructions and utilities for transferring Gemini files; - other small applications. This file is not protected (it is freely accessible). Demo.sea contains: - a few demo spectra. - Snail-MR. This file is not protected (it is freely accessible). -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ C.S.RAMAN _/ _/ Department of Biochemistry _/ _/ University of Texas Health Science Center _/ _/ 7703 Floyd Curl Drive _/ _/ San Antonio, TX 78284-7760 _/ _/ USA _/ _/ _/ _/ Tel: (210) 567-6623 _/ _/ Fax: (210) 567-6595 _/ _/ E-mail: raman@bioc01.uthscsa.edu _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ How can it be that mathematics, a product of human thought _/ _/ independent of experience, is so admirably adapted to the _/ _/ objects of reality? -Albert Einstein _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From owner-structural-nmr@net.bio.net Thu Nov 16 22:00:00 1995 Path: biosci!URANO.MIA.UV.MX!fmontes From: fmontes@URANO.MIA.UV.MX (Fernando M. Montes Gonzalez) Newsgroups: bionet.structural-nmr Subject: Positions available on protein analysis on immune recognition in Mexico Date: 17 Nov 1995 08:35:11 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 63 Sender: daemon@net.bio.net Distribution: world Message-ID: <9511171638.AA12758@urano.mia.uv.mx> NNTP-Posting-Host: net.bio.net Two positions are available for research in protein sequences and structure analysis applied to the Study of the Immune Molecular Recognition Process. Our group in Molecular Bioinformatics and Immune Recognition are opening a new laboratory in protein modeling and sequence analysis. We are seeking for two Ph.D. with experience in sequence and/or structure analysis of proteins or in the the study of the molecular mechanism of immune recognition. Our area of research is the study of the molecular basis of immune recognition. This problem is studied from a wide spectrum that goes from the analysis of the structural diversity of the germline repertoire, the comparison of the immune molecular recognition strategies in vertebrates, the construction of a 3-d specialized database of Igs, Mhc and Tcr and it analysis, molecular dynamics studies of the Fv, etc. We try to integrate these studies in the context of theoretical models and the general theory of the immune response. We are planing to extend in the future our studies to other recognition models like those of the endocrine or nervous systems. The two positions available are for a period of three years of renewal. After this period, if the work is evaluated as satisfactory the position will come permanent. The new laboratory is the result from an agreement between the National University of Mexico and the Veracruzana University. The seat of the laboratory will be the City of Xalapa at the state of Veracruz. Xalapa (1500 m. over the sea level) is a medium size city (300,000) and is the capital of the state of Veracruz. For information about the Veracruzana University please see at: http://www.coacade.uv.mx/ For information about our Molecular Biology Laboratory here in Xalapa please see at: http://uv4.invest.uv.mx/ The candidates must send their curriculum vitae with all its publications to the e-address indicated at the end of this message. You can find information about our research in: J. Mol. Evol. (1994) 38:100 J. Mol. Evol. (1995) 41:98 Biosystems (1995) 32:25 J. Mol. Biol. (1995) 246:74 Int. J. Pept. Prot. Res. (1995) 45:180 Prot. Sci. (1995) 4:1708. Immunogenenics (1995) in press. J. Mol. Biol. (1995) Nov. 24, 1995 issue. Please contact with Dr. Enrique Vargas-madrazo at: evargas@uv4.invest.uv.mx or evargas@speedy.coacade.uv.mx From owner-structural-nmr@net.bio.net Fri Nov 17 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: Sjaak.Peelen@NMR.BC.WAU.NL (sjaak peelen) Newsgroups: bionet.structural-nmr Subject: Software Date: 18 Nov 1995 13:40:10 -0000 Lines: 5 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <48knnq$s7n@mserv1.dl.ac.uk> X-Priority: 3 (Normal) Original-To: str-nmr@dl.ac.uk Does anyone know if there is software available for generating a summary of the nmr data obtained, such as noe's, HN exchange, J-couplings and chemical shifts, as a function of the primary sequence? Sjaak Peelen@nmr.bc.wau.nl From owner-structural-nmr@net.bio.net Fri Nov 17 22:00:00 1995 Path: biosci!URANO.MIA.UV.MX!fmontes From: fmontes@URANO.MIA.UV.MX (Fernando M. Montes Gonzalez) Newsgroups: bionet.structural-nmr Subject: Positions available on protein analysis on immune recognition in Mexico Date: 18 Nov 1995 06:35:41 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 63 Sender: daemon@net.bio.net Distribution: world Message-ID: <9511181440.AA13640@urano.mia.uv.mx> NNTP-Posting-Host: net.bio.net Two positions are available for research in protein sequences and structure analysis applied to the Study of the Immune Molecular Recognition Process. Our group in Molecular Bioinformatics and Immune Recognition are opening a new laboratory in protein modeling and sequence analysis. We are seeking for two Ph.D. with experience in sequence and/or structure analysis of proteins or in the the study of the molecular mechanism of immune recognition. Our area of research is the study of the molecular basis of immune recognition. This problem is studied from a wide spectrum that goes from the analysis of the structural diversity of the germline repertoire, the comparison of the immune molecular recognition strategies in vertebrates, the construction of a 3-d specialized database of Igs, Mhc and Tcr and it analysis, molecular dynamics studies of the Fv, etc. We try to integrate these studies in the context of theoretical models and the general theory of the immune response. We are planing to extend in the future our studies to other recognition models like those of the endocrine or nervous systems. The two positions available are for a period of three years of renewal. After this period, if the work is evaluated as satisfactory the position will come permanent. The new laboratory is the result from an agreement between the National University of Mexico and the Veracruzana University. The seat of the laboratory will be the City of Xalapa at the state of Veracruz. Xalapa (1500 m. over the sea level) is a medium size city (300,000) and is the capital of the state of Veracruz. For information about the Veracruzana University please see at: http://www.coacade.uv.mx/ For information about our Molecular Biology Laboratory here in Xalapa please see at: http://uv4.invest.uv.mx/ The candidates must send their curriculum vitae with all its publications to the e-address indicated at the end of this message. You can find information about our research in: J. Mol. Evol. (1994) 38:100 J. Mol. Evol. (1995) 41:98 Biosystems (1995) 32:25 J. Mol. Biol. (1995) 246:74 Int. J. Pept. Prot. Res. (1995) 45:180 Prot. Sci. (1995) 4:1708. Immunogenenics (1995) in press. J. Mol. Biol. (1995) Nov. 24, 1995 issue. Please contact with Dr. Enrique Vargas-madrazo at: evargas@uv4.invest.uv.mx or evargas@speedy.coacade.uv.mx From owner-structural-nmr@net.bio.net Sat Nov 18 22:00:00 1995 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: cholesterol 1H assignments Date: 19 Nov 1995 14:03:43 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Netters, I am looking for 1H assignments for cholesterol, preferably (but not exclusively) in aromatic solvents such as benzene-d6 or similar. Could any of you give me a reference I'll appreciate. Thanks, best regards, 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.) From owner-structural-nmr@net.bio.net Sat Nov 18 22:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!sdd.hp.com!swrinde!newsfeed.internetmci.com!in2.uu.net!news.sprintlink.net!ddi2.digital.net!usenet From: rose@digital.net Newsgroups: bionet.structural-nmr Subject: Suggestions on selling an NMR Date: 19 Nov 1995 23:39:54 GMT Organization: Florida Online Lines: 3 Message-ID: <48of8a$m4j@ddi2.digital.net> Reply-To: rose@digital.net NNTP-Posting-Host: @pm2_21.digital.net X-Newsreader: WinVN 0.92.6 We are considering selling our Bruker AC400 NMR. Any suggestions on companies who might broker this sort of equipment or any other avenues we should pursue? From owner-structural-nmr@net.bio.net Sun Nov 19 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!swrinde!news.uh.edu!mac-11178.sr-building.uh.edu!user From: chem8q@jetson.uh.edu (J.P. Germanas) Newsgroups: bionet.structural-nmr Subject: Re: alpha proton exchange Date: Mon, 20 Nov 1995 11:23:45 -0500 Organization: U of Houston Lines: 36 Distribution: world Message-ID: References: <9511161847.AA14942@mood.biophy.jussieu.fr> NNTP-Posting-Host: mac-11178.sr-building.uh.edu In article <9511161847.AA14942@mood.biophy.jussieu.fr>, michel@biophy.jussieu.fr (Michel SEIGNEURET) wrote: > Hi, > I was told by a collegue that in some specific deuterated organic solvent > or solvent mixtures, not only peptide amide proton but also alpha and > some aromatic protons can exchange to deuterium. He was unfortunately > unable to remember in which solvents. Could somebody indicate to me some > of these solvent and give me an idea of the exchange rates ? > Thanks in advance. > Michel > > M. Seigneuret > Universite Paris 7 > Lab. de Biophysique Cellulaire > France Exchange of alpha protons of peptides occurs under fairly basic conditions. We have used MeOD/MeONa to effect exchange of alpha H's in some peptides and peptidomimetics with D over a few hours (rate depends on MeONa concentration). If you are thinking of doing this to a peptide, be aware that you will probably racemize the alpha carbon atom of the amino acid and end up with a complex mixture of isomers, as well as degrade certain other amino acids (e.g. Ser, Thr, Cys). Under basic conditions you may also exchange the Ce H's of Tyr and His. For more info see "Chemical Modification of Proteins" by Means and Feeney. -- J.P. GERMANAS CHEM8Q@JETSON.UH.EDU "The more you drive, the less intelligent you are" Repo Man From owner-structural-nmr@net.bio.net Mon Nov 20 22:00:00 1995 Path: biosci!rutgers!gatech!newsfeed.internetmci.com!EU.net!news.eunet.fi!newsmaster From: piero pollesello Newsgroups: bionet.structural-nmr Subject: Re: cholesterol 1H assignments Date: 21 Nov 1995 07:53:04 GMT Organization: POLYbios, Area Science Park, Trieste, Italy Lines: 15 Message-ID: <48s0h0$n1r@idefix.eunet.fi> References: NNTP-Posting-Host: mac545.espoo.orion.fi Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12(Macintosh; I; 68K) X-URL: news:Pine.SUN.3.91.951119165740.19376A-100000@kong.syr.edu Dear Istvan try with Reich, H.J. et al. J.Am.Chem.Soc. v. 91, p. 7445 (1969) It is the reference cited by Breitmaier for the 13C assignment of cholesterol and I strongly believe it reports also the 1H assignment Ciao Piero Pollesello NMR-lab, Chem.res.dept, Orion-Farmos, Orion Corporation FIN-02101 Espoo, Finland e-mail:piero.pollesello@rd.orion.orion.mailnet.fi From owner-structural-nmr@net.bio.net Mon Nov 20 22:00:00 1995 Path: biosci!mr.unit.no!Alexej.Jerschow From: Alexej.Jerschow@mr.unit.no ("Alexej Jerschow") Newsgroups: bionet.structural-nmr Subject: Re: gamma info Date: 21 Nov 1995 07:24:03 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 33 Sender: daemon@net.bio.net Distribution: world Message-ID: <9511211622.ZM6777@samson.mr.sintef.no> NNTP-Posting-Host: net.bio.net On Nov 21, 5:31am, Athanasios Stavrakoudis wrote: > Subject: gamma info > > Dear Netters , > > does anybody know how can l get gamma program ?? > > any help is very welcome ..... > > Regards, > > Athanassios Stavrakoudis > > e-mail : astavrak@cc.uoi.gr > >-- End of excerpt from Athanasios Stavrakoudis Try http://gamma1.magnet.fsu.edu:80/~gamma/ There you can find a lot of information about GAMMA Regards -- ------------------------ Alexej Jerschow present address: MR-Center, SINTEF UNIMED N-7034 Trondheim, Norway Tel: +47-73 99 89 36 Fax: +47-73 99 77 08 From owner-structural-nmr@net.bio.net Mon Nov 20 22:00:00 1995 Path: biosci!HELIX.NIH.GOV!huang From: huang@HELIX.NIH.GOV (Xialing Huang) Newsgroups: bionet.structural-nmr Subject: subscribe Date: 21 Nov 1995 06:20:59 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: <199511211419.JAA22347@helix.nih.gov> NNTP-Posting-Host: net.bio.net subscribe str-nmr -xiaolin From owner-structural-nmr@net.bio.net Mon Nov 20 22:00:00 1995 Path: biosci!rutgers!uwm.edu!fnnews.fnal.gov!nntp-server.caltech.edu!rickert From: rickert@cco.caltech.edu (Keith Warren Rickert) Newsgroups: bionet.structural-nmr Subject: Re: alpha proton exchange Date: 21 Nov 1995 00:05:50 GMT Organization: California Institute of Technology, Pasadena Lines: 26 Message-ID: <48r54u$bq8@gap.cco.caltech.edu> References: <9511161847.AA14942@mood.biophy.jussieu.fr> NNTP-Posting-Host: accord.cco.caltech.edu X-Newsreader: NN version 6.5.0 #12 (NOV) In <9511161847.AA14942@mood.biophy.jussieu.fr> michel@biophy.jussieu.fr (Michel SEIGNEURET) writes: >Hi, >I was told by a collegue that in some specific deuterated organic solvent >or solvent mixtures, not only peptide amide proton but also alpha and >some aromatic protons can exchange to deuterium. He was unfortunately >unable to remember in which solvents. Could somebody indicate to me some >of these solvent and give me an idea of the exchange rates ? >Thanks in advance. >Michel The pyrrole-like NH protons of both histidine and tryptophan are readily exchanged for deuterium in D2O. I cannot imagine any circumstances under which you were exchanging alpha protons without racemizing your alpha carbons; Unless stereochemistry is unimportant to you, I would recommend looking for an alternate method of adressing this issue. Keith -- Keith Rickert | "The time is now. The chains of Fenric have keith@imppig.caltech.edu | shattered. The gods have lost the final battle. rickert@cco.caltech.edu | Dead men's ship has slipped its moor, and the | great ash itself trembles to its roots." From owner-structural-nmr@net.bio.net Mon Nov 20 22:00:00 1995 Path: biosci!cc.uoi.gr!astavrak From: astavrak@cc.uoi.gr (Athanasios Stavrakoudis) Newsgroups: bionet.structural-nmr Subject: gamma info Date: 21 Nov 1995 05:31:35 -0800 Organization: University of Ioannina Computer Center Ioannina, Greece 451 10 tel: +30-651-45298, fax: +30-651-45298 Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: <9511211528.AA09730@iason.cc.uoi.gr> NNTP-Posting-Host: net.bio.net Dear Netters , does anybody know how can l get gamma program ?? any help is very welcome ..... Regards, Athanassios Stavrakoudis e-mail : astavrak@cc.uoi.gr From owner-structural-nmr@net.bio.net Tue Nov 21 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!news-e1a.megaweb.com!newstf01.news.aol.com!newsbf02.news.aol.com!not-for-mail From: resourcemr@aol.com (Resourcemr) Newsgroups: bionet.structural-nmr Subject: New Home Page Date: 21 Nov 1995 19:59:29 -0500 Organization: America Online, Inc. (1-800-827-6364) Lines: 26 Sender: root@newsbf02.news.aol.com Message-ID: <48tslh$jt6@newsbf02.news.aol.com> Reply-To: resourcemr@aol.com (Resourcemr) NNTP-Posting-Host: newsbf02.mail.aol.com M R Resources is pleased to announce its new home page on the World Wide Web. The location is: www.mrr.com M R Resources is the leading supplier of high quality used and remanufactured NMR systems. We also provide a full range of engineering services for the NMR facility including applications training, system repairs, installations, system moving, magnet recommissioning and cryogen filling for all major brands of NMR instruments. The company also has a huge supply of spare parts and accessories for most models of Bruker, Varian, JEOL, and GE/Nicolet instruments. Non magnetic equipment and supplies for MRI are also available. Please have a look at our new web site, and let us hear any comments and feedback you might have. Best regards, Jon Webb M R Resources, Inc. Refurbished NMR Systems, Parts, and Services Tel: 508-632-7000 Fax: 508-630-2509 Email: resourcemr@aol.com From owner-structural-nmr@net.bio.net Wed Nov 22 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!nntp.cntfl.com!news.fsu.edu!usenet From: Sebastien Vincent Newsgroups: bionet.structural-nmr Subject: Re: Suggestions on selling an NMR Date: 22 Nov 1995 15:11:23 GMT Organization: NHMFL-FSU Lines: 5 Message-ID: <48veir$g5p@news.fsu.edu> References: <48of8a$m4j@ddi2.digital.net> NNTP-Posting-Host: bodenhausen9mac.magnet.fsu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; PPC) To: rose@digital.net X-URL: news:48of8a$m4j@ddi2.digital.net Hi, you might want to take a look at MR Resources home page (URL: http://www.mrr.com/). Sebastien From owner-structural-nmr@net.bio.net Wed Nov 22 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!nntp.cntfl.com!news.fsu.edu!usenet From: Sebastien Vincent Newsgroups: bionet.structural-nmr Subject: Re: gamma info Date: 22 Nov 1995 14:54:05 GMT Organization: NHMFL-FSU Lines: 16 Message-ID: <48vdid$g5p@news.fsu.edu> References: <9511211528.AA09730@iason.cc.uoi.gr> NNTP-Posting-Host: bodenhausen9mac.magnet.fsu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; PPC) To: astavrak@cc.uoi.gr X-URL: news:9511211528.AA09730@iason.cc.uoi.gr >does anybody know how can l get gamma program ?? >any help is very welcome ..... Hi, you can contact Scott Smith directly (ssmith@magnet.fsu.edu), but you can give a look at his homepage on the net first (URL: http://gamma1.magnet.fsu.edu/~gamma) where the program, most of the documentation and various info are available. Sebastien (-::-)(-::-)(-::-)(-::-)(-::-)(-::-)(-::-)(-::-)(-::-)(-::-)(-::-)(-::-) Sebastien Vincent vincent@magnet.fsu.edu NHMFL, 1800 E. Paul Dirac Drive, Fax: (904) 644 1366 Tallahassee, Florida 32310, USA Voice: (904) 644 1187 From owner-structural-nmr@net.bio.net Wed Nov 22 22:00:00 1995 Path: biosci!LOURIE.UND.AC.ZA!iourine From: iourine@LOURIE.UND.AC.ZA (Serge Iourine) Newsgroups: bionet.structural-nmr Subject: 1H-NMR peak assignment Date: 22 Nov 1995 04:49:10 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <199511221244.OAA14495@lourie.und.ac.za> Hi, While assigning the 1H-NMR resonances, I came across one weird peak-I wonder if somebody has met this thing before: It appears exactly under the chloroform peak (7.24, sample in CDCl3) and the corresponding carbon resonance occurs also in the chlorophorm region - at 77-78 ppm Any idea what this might be? Regards, s. From owner-structural-nmr@net.bio.net Wed Nov 22 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: son of pps Newsgroups: bionet.structural-nmr Subject: WEB course on Protein Structure Date: 23 Nov 1995 12:57:51 -0000 Lines: 17 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <491r4f$dr8@mserv1.dl.ac.uk> X-Sender: pps2@iona.cryst.bbk.ac.uk Original-To: str-nmr@dl.ac.uk B i r k b e c k C o l l e g e Crystallography Department INTERNET COURSE IN PRINCIPLES OF PROTEIN STRUCTURE http://www.cryst.bbk.ac.uk/PPS2/ We are running a part-time London University Advanced Certificate course in Principles of Protein Structure on the Internet (a formalised version of last year's course). Units are: 1. IT and Bioinformatics 2. Protein Structure 3. Dissertation: topics in structure, function and dynamics Course runs for 1 academic year (3 terms) from 15 January to 25 October 1996. For details of course contents, administration and registration, see our Web pages at URL given above. Costs: 186 pounds sterling (EU) 500 pounds sterling (world) email: j.mcgill@mail.cryst.bbk.ac.uk From owner-structural-nmr@net.bio.net Wed Nov 22 22:00:00 1995 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.structural-nmr Subject: IMPORTANT: BIOSCI miniFAQ Date: 22 Nov 1995 02:00:12 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 196 Sender: daemon@net.bio.net Distribution: world Message-ID: <199511221000.CAA12250@net.bio.net> This is a new "miniFAQ" designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. Contents: -------- 1) What to do about "spams," i.e., junk mail, ads, etc. 2) Examples of subscribing and unsubscribing to the mailing lists. 3) How to access BIOSCI/bionet newsgroup archives. 4) The BIOSCI user address and research interest directory. 1) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups) and mailing lists. The same postings are distributed on both media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the newsgroups from about 95% of the spams that are being sent to date. This means that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings. Unfortunately there are easy ways for determined spammers to override the moderation mechanism. We are working on new systems to provide access to our newsgroups over the WWW. These should be available soon, probably November 1995, and will allow you to use your Web browser to look at the news postings. While this will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. 2) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. 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For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 3) How to access BIOSCI/bionet newsgroup archives. -------------------------------------------------- Back postings of all BIOSCI/bionet newsgroups can be found on the World Wide Web at URL http://www.bio.net/. There are several searchable newsgroup indices at this site. E-mail users can search the BIOSCI archives by using our waismail e-mail server. For instructions send the message help to waismail@net.bio.net. Leave the Subject: line blank (anything entered on the Subject: line is ignored). 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-structural-nmr@net.bio.net Thu Nov 23 22:00:00 1995 Path: biosci!mr.sintef.no!Reinhard.Wimmer From: Reinhard.Wimmer@mr.sintef.no (Reinhard Wimmer) Newsgroups: bionet.structural-nmr Subject: (none) Date: 24 Nov 1995 07:18:58 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 3 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net help From owner-structural-nmr@net.bio.net Thu Nov 23 22:00:00 1995 Path: biosci!HELIX.NIH.GOV!huang From: huang@HELIX.NIH.GOV (Xialing Huang) Newsgroups: bionet.structural-nmr Subject: modeling of linear peptides Date: 24 Nov 1995 13:15:46 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: <199511242114.QAA17333@helix.nih.gov> NNTP-Posting-Host: net.bio.net I am wondering if anyone meet some problem as follows: I am studying the structure-function relationship of linear peptides (15 AA) I extracted 65 distance constraints from NOESY experiment. When generating structures using X-plor(MSI), I got 50 much different initiate structures. Then trying to do simulate annealing, I got 50 different conformations which were more folded than I expected. I am wondering why they didn't converge to one family of preferred conformation. I really appreciate if someone could give me some suggestion. Best regards. Xiaolin Huang From owner-structural-nmr@net.bio.net Fri Nov 24 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!newsfeed.internetmci.com!in2.uu.net!news00.sunet.se!sunic!news99.sunet.se!columba.udac.uu.se!rigel.bmc.uu.se!gerard From: gerard@rigel.bmc.uu.se (Gerard Kleijwegt) Newsgroups: bionet.structural-nmr Subject: Re: modeling of linear peptides Date: 25 Nov 1995 20:37:47 GMT Organization: Uppsala University Lines: 40 Distribution: world Message-ID: <497uqr$1048@columba.udac.uu.se> References: <199511242114.QAA17333@helix.nih.gov> NNTP-Posting-Host: rigel.bmc.uu.se In article <199511242114.QAA17333@helix.nih.gov>, huang@HELIX.NIH.GOV (Xialing Huang) writes: |> I am wondering if anyone meet some problem as follows: |> I am studying the structure-function relationship of linear peptides (15 AA) |> I extracted 65 distance constraints from NOESY experiment. When generating |> structures using X-plor(MSI), I got 50 much different initiate structures. |> Then trying to do simulate annealing, I got 50 different conformations which |> were more folded than I expected. I am wondering why they didn't converge |> to one family of preferred conformation. |> I really appreciate if someone could give me some suggestion. |> Best regards. |> |> Xiaolin Huang Being a protein crystallographer, I'm hardly the person to reply, but since nobody else has replied so far I'll give you my two pennies' worth: As far as I know, short peptides rarely have "innate" folds (although these can be enforced sometimes by using non- physiological solovents such as DMSO and TFA). So the fact that your models don't converge to a single conformation isn't all that surprising. You say you obtained 65 distance REstraints (I assume you mean), but how are these distributed ? If they are all intra-residue and I -> I+/-1,2,3,4, they do not contain any information about the tertiary structure (which is not surprising if the peptide doesn't assume a single tert. conf.). In that case, even if you "observe" conformations which are "more folded than expected", you have to ask yourself what you are looking at: do these conformation result from information present in your observations, or are they mere artefacts from the structure-generation method (plus force field) ? Since you find 50 different ones, my money is on the latter possibility ;-) I see you work at NIH - then you have a couple of in-house NMR gurus; why not talk to them ? --gerard From owner-structural-nmr@net.bio.net Sun Nov 26 22:00:00 1995 Newsgroups: bionet.structural-nmr Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!nih-csl!loglady.ninds.nih.gov!johnk From: johnk@spasm.niddk.nih.gov (John Kuszewski) Subject: Xccbond? Message-ID: <1995Nov27.194110.6235@alw.nih.gov> Sender: postman@alw.nih.gov (AMDS Postmaster) Nntp-Posting-Host: spasm.niddk.nih.gov Reply-To: johnk@spasm.niddk.nih.gov (John Kuszewski) Organization: National Insts. of Health Date: Mon, 27 Nov 1995 19:41:10 GMT Lines: 22 Hi, Has anyone heard of Xccbond, a program written by Reinhard Dunkel of Sitar, Inc.? What's it do? -- _____________ | ___/_ | |/ / -- /\ // /-- || || / /|| || || / / || || ||/ / || John Kuszewski || |/ /| || johnk@spasm.niddk.nih.gov || / /|| || \/ / / || \/ that's MISTER protein G to you! |/__/| | /_________| "Biophysics has driven me to an attitude of apocalyptic doom" --Frank Delaglio From owner-structural-nmr@net.bio.net Sun Nov 26 22:00:00 1995 Path: biosci!UNITY.NCSU.EDU!idshin From: idshin@UNITY.NCSU.EDU ("Dan Shin") Newsgroups: bionet.structural-nmr Subject: Re: infors about Shigemi Date: 27 Nov 1995 12:38:07 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 27 Sender: daemon@net.bio.net Distribution: world Message-ID: <9511271624.ZM18487@152.1.38.71> NNTP-Posting-Host: net.bio.net On Nov 27, 5:17am, sodano patrick wrote: > Subject: infors about Shigemi > we would like to purchase NMR tubes with flat bottom.Does anyone know the > address of Shigemi manufactory or any other sources? > > Thanks > > >-- End of excerpt from sodano patrick Here is the address and phone number for Shigemi. SHIGEMI, INC. Suite 21 4790 Route 8 Allison Park, PA 15101 (412) 444-3011 (412) 444-3020 FAX Good luck! -- Dan Shin dan_shin@ncsu.edu (919) 515-2248 From owner-structural-nmr@net.bio.net Sun Nov 26 22:00:00 1995 Path: biosci!cnrs-orleans.fr!sodano From: sodano@cnrs-orleans.fr ("sodano patrick") Newsgroups: bionet.structural-nmr Subject: infors about Shigemi Date: 27 Nov 1995 05:17:28 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 4 Sender: daemon@net.bio.net Distribution: world Message-ID: <9511271241.AA29564@admin.cnrs-orleans.fr> NNTP-Posting-Host: net.bio.net we would like to purchase NMR tubes with flat bottom.Does anyone know the address of Shigemi manufactory or any other sources? Thanks From owner-structural-nmr@net.bio.net Mon Nov 27 22:00:00 1995 Path: biosci!MAILBOX.SYR.EDU!ipelczer From: ipelczer@MAILBOX.SYR.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: address Date: 28 Nov 1995 03:52:27 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Netters, Would anybody know the Email address for Maruse Sadek from Australia? Thanks in advance, 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.) From owner-structural-nmr@net.bio.net Mon Nov 27 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!news.math.psu.edu!news.cac.psu.edu!newsserver.jvnc.net!yale.edu!news.ycc.yale.edu!proton!dcs From: dcs@proton.chem.yale.edu (Dave Schweisguth) Newsgroups: bionet.structural-nmr Subject: Re: infors about Shigemi Date: 28 Nov 1995 14:14:22 GMT Organization: Dept. of Chemistry, Yale University Lines: 11 Message-ID: <49f5fu$6nh@news.ycc.yale.edu> References: <9511271241.AA29564@admin.cnrs-orleans.fr> NNTP-Posting-Host: proton.chem.yale.edu X-Newsreader: TIN [version 1.2 PL2] sodano patrick (sodano@cnrs-orleans.fr) wrote: : we would like to purchase NMR tubes with flat bottom.Does anyone know the : address of Shigemi manufactory or any other sources? Their telephone number in the US is 412-444-3011. -- | Dave Schweisguth For purposes of complying with | | dcs@proton.chem.yale.edu (MIME OK) the New Jersey Right to Know Act: | | http://proton.chem.yale.edu/~dcs/ Contents partially unknown. | | Yale Depts. of MB&B & Chemistry Phone: 203-432-5208 Fax: 203-432-6144 | From owner-structural-nmr@net.bio.net Tue Nov 28 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!news.u.washington.edu!root From: Tom Pratum Newsgroups: bionet.structural-nmr Subject: Re: Xccbond? Date: 28 Nov 1995 22:49:28 GMT Organization: Univ of Washington Lines: 7 Message-ID: <49g3lo$spm@nntp3.u.washington.edu> References: <1995Nov27.194110.6235@alw.nih.gov> NNTP-Posting-Host: pratum-mac.chem.washington.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) To: johnk@spasm.niddk.nih.gov X-URL: news:1995Nov27.194110.6235@alw.nih.gov This is data processing program to improve the S/N of carbon detected INADEDQUATE experiments. See Anal. Chem. 64, 3133 (1992) for details. From owner-structural-nmr@net.bio.net Tue Nov 28 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!info.ucla.edu!library.ucla.edu!ihnp4.ucsd.edu!scripps.edu!usenet From: Christoph Weber Newsgroups: bionet.structural-nmr Subject: Re: modeling of linear peptides Date: Tue, 28 Nov 1995 12:23:15 -0800 Organization: The Scripps Research Institute, La Jolla, CA Lines: 45 Message-ID: <30BB6FB3.739D@scripps.edu> References: <199511242114.QAA17333@helix.nih.gov> <497uqr$1048@columba.udac.uu.se> NNTP-Posting-Host: sponsz.scripps.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0b2 (X11; I; SunOS 5.3 sun4m) In my experience there is a quite clear distinction between what I call (being a structural biologist) 'boring' and 'interesting' peptides. The former have only intraresidue and sequential NOEs and very little variation in their relative intensity as you go along the sequence. The latter display a number of medium range NOEs (i-i+2,3,4) and sometimes even longer range ones. There is an accompanying variation of sequential NOE intensities. Also, the chemical shift dispersion is much better than for your average linear peptide. Taken together, a NOESY (or ROESY) spectrum of a peptide of the 'interesting' variety is quite easy to recognize once you've seen one next to a 'boring' one. It appears that when the predominant solution conformer reaches a high enough population, structurally relevant NOE information (as detailed above) can be obtained and if that's the case, an attempt to determine the structure of this conformer is justified in the hope that it is a functionally significant one. Even then, you have to worry whether you are generating a meaningful representation due to contributions to NOE intensity from minor conformers. As a very crude check on this, I used to run a SA calculation without restraints to obtain an energy baseline for the type of protocol and system being considered. If the calculation with restraints yields a significantly higher energy, then you are definitely in trouble. Having 65 restraints of unspecified nature for 15 residues, I would guess that you cannot generate a meaningful representation of your structure wich is dictated by the experimental data and which does justice to it as well. You would want something like 6 per residue, or at the very least a few pronounced medium/long range NOEs. Taken together, I would say that peptide structure determination takes a lot of careful handling (and experience on the part of the investigator) and it is much more prone to erroneous conclusions than protein structure determinations. Bear in mind that the bulk of what determines your protein fold are vdW contacts, given enough NOEs to pull it into some sort of fold. There are precious few vdW contacts in most peptides which makes the structure determination VERY vulnerable to errors in NOE distance restraints. Cheers, Christoph -- | Christoph Weber Sen. Research Associat