From owner-structural-nmr@net.bio.net Sat Aug 08 23:00:00 1998 Path: biosci!biosci!not-for-mail From: Lawrence McIntosh Newsgroups: bionet.structural-nmr Subject: postdoctoral position in Vancouver Date: 9 Aug 1998 11:47:33 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 36 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net POSTDOCTORAL POSITION in BIOLOGICAL NMR at UBC A postdoctoral position is available for NMR studies of proteins involved in signal transduction and the regulation of gene expression. The successful candidate should have a solid background in biological NMR spectroscopy, including the determination of macromolecular structures using multi-dimensional heteronuclear methods. Experience in basic biophysics, molecular biology, and/or protein chemistry is also advantageous. The University of British Columbia offers an excellent academic environment, as well as unlimited opportunities for outdoor persuits in and around the city of Vancouver. Additional information on my research program, and involvment in the Protein Engineering Network of Centres of Excellence, can be found via http://www.science.ubc.ca/~chem/brochure/mcintosh.html. Interested applicants should send a CV, along with the phone numbers/ email addresses of two or more people familar with their work. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Lawrence McIntosh 2146 Health Sciences Mall Departments of Biochemistry and Chemistry University of British Columbia Vancouver, BC, Canada V6T 1Z3 mcintosh@otter.biochem.ubc.ca ph: (604) 822-3341 fax: (604) 822-5227 http://www.biochem.ubc.ca/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-structural-nmr@net.bio.net Mon Aug 17 23:00:00 1998 Path: biosci!biosci!not-for-mail From: "Graham E Jackson" Newsgroups: bionet.structural-nmr Subject: Pentagastrin stuff Date: 18 Aug 1998 12:01:54 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 39 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <6qutnf$g1l@mserv1.dl.ac.uk> NNTP-Posting-Host: net.bio.net The following problem comes from Shane Stone: Shane@psipsy.uct.ac.za The Pentagastrin assignment nightmare: Pentagastrin: beta-Ala-Trp-Met-Asp-Phe Amide (Acetate Salt) Sigma product: des-BOC-Pentagastrin (Lot 128F58351) The problem at hand: In the 1H NMR cannot find the alpha-CH or beta-CH3 of Ala, nor are these visible in COSY or TOCSY. 13C carbon count is correct, however, DEPT shows 1 CH3 for Met but no Ala or acetate CH3. HMQC and DEPT show 4 extraneous CH2's. Also, HMQC shows the alpha-C's of Trp and Phe to be on top of each other. Does anyone have reference to the 13C and 1H spectra of Pentagastrin? Also, is there a possible explanation for the absence of the Ala C and H peaks? Thanks Shane Graham E Jackson Associate Professor Department of Chemistry University of Cape Town Cape Town South Africa Fax: (027 21) 6897499 Tel: (027 21) 6502531 E-mail: jackson@psipsy.uct.ac.za http://www.uct.ac.za/depts/cem/academic/gjackson.htm From owner-structural-nmr@net.bio.net Fri Aug 21 23:00:00 1998 Path: biosci!biosci!not-for-mail From: BIOSCI Administrator Newsgroups: bionet.structural-nmr Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 22 Aug 1998 10:40:00 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <199808220900.CAA09071@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is 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/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all 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 USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, 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 on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface 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. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) 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. 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. From owner-structural-nmr@net.bio.net Mon Aug 24 23:00:00 1998 Path: biosci!biosci!not-for-mail From: "Tonny Johnson" Newsgroups: bionet.structural-nmr Subject: Postdoctoral Position in Protein Expression and Purification Date: 25 Aug 1998 16:28:32 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 26 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <9808251903.ZM15964@MOZART.nmrcore.uab.edu> NNTP-Posting-Host: net.bio.net Postdoctoral Position in Protein Expression and Purification A postdoctoral position is available in the expression and purification of proteins for studies by NMR. Experience in cloning and expression of recombinant proteins in both prokaryotic and eukaryotic expression system is highly desirable.Applicants should also have experience in large scale purification of recombinant proteins using various chromatographic techniques. Working knowledge of basic bioinformatic tools such as GCG or related Internet based application programs for the analysis of DNA and protein sequences is highly recommended. Interested persons should send their CV along with names, addresses and telephone numbers of two academic referees to the following address: Dr. N. Rama Krishna Professor of Biochemistry Director, NMR Core Facility CHSB-19 B-31, 933 19 th Street South University of Alabama at Birmingham Birmingham, AL 35294 Telephone: (205)-934-5695 Fax: (205)-934-6475 E-mail: nrkrishna@bmg.bhs.uab.edu From owner-structural-nmr@net.bio.net Mon Aug 24 23:00:00 1998 Path: biosci!biosci!not-for-mail From: romano@bellatrix.pcl.ox.ac.uk (Romano Kroemer) Newsgroups: bionet.structural-nmr Subject: Q: structure of protein complex + alanine scan Date: 25 Aug 1998 09:35:08 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 24 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <6rukqn$hvg@mserv1.dl.ac.uk> NNTP-Posting-Host: net.bio.net Hi all, can anyone point me to references concerning the following topic: Systematic "alanine scanning" studies on protein complexes for which the (wild type)structure is known (by NMR/X-ray). I am aware of two examples: human growth hormone + receptor anti-hen egg white lysozyme (HEL) antibody + HEL Thanks! Romano Kroemer -- =============================================================================== Dr. Romano T. Kroemer Phys. & Theoret. Chem. Lab. University of Oxford South Parks Rd. | Tel: ++44-1865-275475 Oxford OX1 3QZ | Fax: ++44-1865-275410 England, U.K. | Email: romano@bellatrix.pcl.ox.ac.uk =============================================================================== From owner-structural-nmr@net.bio.net Mon Aug 24 23:00:00 1998 Path: biosci!biosci!not-for-mail From: Izumi Newsgroups: bionet.structural-nmr Subject: Linux Date: 25 Aug 1998 12:31:08 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 3 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <35E31024.141FC35C@siegfried.utmb.edu> NNTP-Posting-Host: net.bio.net Can we use "midas", "molscript", etc in Linux system? Thanks From owner-structural-nmr@net.bio.net Wed Aug 26 23:00:00 1998 Path: biosci!biosci!not-for-mail From: Brian Smith Newsgroups: bionet.structural-nmr Subject: Processing - Azara on Linux Date: 27 Aug 1998 08:50:44 -0700 Organization: Edinburgh University Lines: 40 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net AZARA works on LINUX Dear All, Just to let anyone who uses AZARA currently or is looking for academic software for multidimensional NMR processing on LINUX. For the uninitiated, AZARA is academic software for NMR processing written by Wayne Boucher as part of Ernest Laue's group in Cambridge University and still maintained by him. It is a fully functional 1D and multidimensional processing package with a robust implementation of maximum entropy processing and all the usual window function, baseline correction, convolution & linear prediction tools you would expect. It is able to process data from any spectrometer in principle and can directly process from the major spectrometer manufacturers' formats. It uses the same format as Per Kraulis's ANSIG assignment program and as such forms the obvious processing route for ANSIG users but conversion programs exist to provide routes to NMRview for example. See http://www-ccmr-nmr.bioc.cam.ac.uk for the Azara web site. I made this post to let people know that Azara can now be used free of any commercial software ties (in it's normal incarnation it uses the Motif toolkit for the graphical parts). I have just successfully compiled it under Red Hat LINUX using the Motif replacement LessTif (see http://www.lesstif.org) requiring only minor modifications to the makefiles (feel free to contact me if you need help). Everything seems to work if you pay attention to the opposite byte order on LINUX machines compared with SGI/Sun by using the "swap" keyword appropriately. Hope everyone's having fun in Japan. Brian Smith Brian O. Smith Room 209 ICMB/Chemistry Dept. of Chemistry email: brian@chem.ed.ac.uk Joseph Black Building Tel: 0131 650 4704 West Mains Road Fax: 0131 650 4743 (probably) Edinburgh EH9 3JJ From owner-structural-nmr@net.bio.net Fri Aug 28 23:00:00 1998 Path: biosci!biosci!not-for-mail From: Michael Overduin Newsgroups: bionet.structural-nmr Subject: employment in NMR Date: 29 Aug 1998 16:48:38 -0700 Organization: UCHSC Lines: 66 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <35E87769.175103EC@UCHSC.edu> NNTP-Posting-Host: net.bio.net Postdoctoral Fellows and Research Assistants in NMR WHAT? Positions for two postdoctoral fellows and a research assistant interested in the structure & function of protein domains are available. Projects include studies of domains involved in cell growth, cancer, signal transduction, endocytosis, neurotransmitter signaling, eukaryotic mRNA frameshifting, and viral DNA packaging. Several projects involve NMR-assisted design of peptidic and peptidomimetic inhibitors, kinetic characterization by surface plasmon resonance detection, and mutagenesis. WHERE? The University of Colorado Health Sciences Center in Denver, Colorado has built a high-field NMR Center as a part of its Biomolecular Structure Program (see http://biomol.uchsc.edu). The 2500 square foot NMR Center is geared for solution studies of biomolecules. It includes 4-channel 600 and 500 MHz Varian INOVA spectrometers, and seven Sun Ultra and SGI O2 workstations. The campus is located in a residential area a few miles east of downtown Denver, and is an hour's drive from several ski resorts and National Parks in the Rocky Mountains. WHO? You would be joining Michael Overduin's research group in the Department of Pharmacology of the University of Colorado Health Sciences Center. The projects all involve collaborative arrangements with molecular or cellular biologists, biochemists, and/or drug discovery groups. One of the postdoctoral positions is being offered jointly with Dr. Carlos Catalano, an expert in viral packaging. WHEN? The positions are available starting in the fall of 1998. Applications will be accepted until all positions are filled. Competitive salaries and benefit packages are provided. Funding is provided from the National Institutes of Health, March of Dimes, Howard Hughes Medical Institute, and Pew Charitable Trusts. HOW? Please submit a curriculum vitae including a brief description of research interests, and names, e-mail addresses and phone numbers of three references by mail, e-mail or fax. Candidates must be highly motivated. Recommended qualifications include a recent Ph.D. (or similar degree) in chemistry, biochemistry or a related field, and training in multidimensional NMR, protein structure and/or stability, or molecular biology and protein biochemistry. Contact Information: Michael Overduin, Ph. D. Department of Pharmacology Campus Box C-236 University of Colorado Health Sciences Center 4200 East Ninth Avenue Denver, Colorado 80262, USA Phone: (303) 315-8774 Fax: (303) 315-7097 e-mail: Michael.Overduin@UCHSC.edu