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From owner-molec-model@net.bio.net Wed Nov 11 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed.tli.de!newsfeed.wirehub.nl!oleane!jussieu.fr!univ-lille1.fr!not-for-mail From: "Philippe CHAVATTE" Newsgroups: bionet.molec-model Subject: Bay-12-9566 Date: Thu, 12 Nov 1998 17:57:24 +0100 Organization: Universite des Sciences et Technologies de LILLE, France Lines: 18 Message-ID: <72f422$vs3$1@netserv.univ-lille1.fr> NNTP-Posting-Host: icp16.univ-lille2.fr X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Where can I find chemical structure of Bay-12-9566 ? Thanks in advance P. CHAVATTE ----------------- Philippe CHAVATTE Institut de Chimie Pharmaceutique de Lille BP 83 59006 LILLE CEDEX FRANCE E-Mail : pchavatt@phare.univ-lille2.fr From owner-molec-model@net.bio.net Thu Nov 19 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!pln-w!spln!extra.newsguy.com!newsp.newsguy.com!mryan From: mryan@worthpub.com (Mo) Newsgroups: bionet.molec-model Subject: Structure for ATP:hexokinase? Date: Thu, 19 Nov 1998 23:49:01 -0500 Organization: http://extra.newsguy.com Lines: 8 Message-ID: NNTP-Posting-Host: p-677.newsdawg.com X-Newsreader: MT-NewsWatcher 2.4.4 I'm trying to inspect the surface contacts of ATP binding to hexokinase for a detailed illustration. The released pdb structures have glucose bound, but no ATP. How can I get detailed visual information about this? Would comparing to an ATP-binding family homolog be accurate enough? Is that the best technique? I'm hoping there is another option, because I'm not sure how to manage the superposition--but maybe this is the project where I learn how. Any help appreciated. Does a pdb of hexokinase:ATP exist? Morgan From owner-molec-model@net.bio.net Sun Nov 22 22:00:00 1998 Newsgroups: bionet.molec-model Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.gtei.net!newsfeed.cwix.com!194.72.7.126!btnet-peer!btnet!nntp.news.xara.net!xara.net!server6.netnews.ja.net!leeds.ac.uk!news From: bmbjmm@bmb.leeds.ac.uk (Jeremy Murray) Subject: Re: PDB files & CHIME X-Accept-Language: en Message-ID: <3659E5C6.CF925034@bmb.leeds.ac.uk> NNTP-Posting-Host: bmbsgi15.leeds.ac.uk X-Mailer: Mozilla 4.5 [en] (X11; I; IRIX 6.2 IP22) Content-Type: text/plain; charset=us-ascii Organization: University of Leeds MIME-Version: 1.0 Date: Mon, 23 Nov 1998 22:56:55 +0000 (GMT) References: To: "A.J.Cann" Lines: 48 Content-Transfer-Encoding: 7bit i guess your first port of call is the cam cryst database http://www.ccdc.cam.ac.uk/ and then maybe HICUP http://alpha2.bmc.uu.se/hicup/ happy hunting "A.J.Cann" wrote: > I have been trying to find PDB files of several molecules for use with the > CHIME plugin in a new online tutorial: > > http://www-micro.msb.le.ac.uk/Tutorials/dfwt/dfwt1.html > > I would like to find information for: > > sulphonamide > p-aminobenzoic acid > folic acid > > Can anyone tell me where to find thes files or how to construct them? > > TIA, > > -- > Dr Alan J. Cann PhD, Department of Microbiology & Immunology, > University of Leicester, P.O. Box 138, Medical Sciences Building, > University Road, Leicester LE1 9HN, UK. -- . .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .- |\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|| ||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \| -' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' ` Jeremy Murray MAIL: bmbjmm@bmb.leeds.ac.uk Biochemistry & Molecular Biology TEL: +44 113 233 2591 Leeds University, LEEDS LS2 9JT FAX: +44 113 233 3167 http://www.smb.leeds.ac.uk/wwwsb/jez.html . .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .- |\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|| ||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \| -' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' ` From owner-molec-model@net.bio.net Sun Nov 22 22:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!nntp.abs.net!cyclone.i1.net!uunet!in5.uu.net!news1-gui.server.ntli.net!news-feed.ntli.net!news5-gui.server.ntli.net!news-feed.ntli.net!server4.netnews.ja.net!server2.netnews.ja.net!leicester!nna From: nna@le.ac.uk (A.J.Cann) Newsgroups: bionet.molec-model Subject: PDB files & CHIME Date: Mon, 23 Nov 1998 11:57:15 +0000 Organization: University of Leicester, UK Lines: 19 Message-ID: NNTP-Posting-Host: mac47.msb.le.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.4.0 I have been trying to find PDB files of several molecules for use with the CHIME plugin in a new online tutorial: http://www-micro.msb.le.ac.uk/Tutorials/dfwt/dfwt1.html I would like to find information for: sulphonamide p-aminobenzoic acid folic acid Can anyone tell me where to find thes files or how to construct them? TIA, -- Dr Alan J. Cann PhD, Department of Microbiology & Immunology, University of Leicester, P.O. Box 138, Medical Sciences Building, University Road, Leicester LE1 9HN, UK. From owner-molec-model@net.bio.net Mon Nov 23 22:00:00 1998 Path: biosci!AOL.COM!GIDGE1026 From: GIDGE1026@AOL.COM Newsgroups: bionet.molec-model Subject: Photo Mouse Pads ......... Great Christmas Gifts ! Date: 24 Nov 1998 00:25:42 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 149 Sender: daemon@net.bio.net Distribution: world Message-ID: <901733a5.365a5b33@aol.com> NNTP-Posting-Host: net.bio.net GREAT CHRISTMAS GIFT IDEA! PHOTO TRANSFER SPECIALTIES! MOUSEPADS WITH YOUR FAVORITE PHOTOS! Now you can have your favorite photos printed onto mousepads! Photo mousepads are our most popular gift year after year! In the past we have provided our HIGH QUALITY mousepads to thousands of customers. Most are so pleased they reorder each year! Photo mousepads make a PERFECT GIFT for ANYONE! Replace boring, dirty, frayed mousepads! Instead of plain, generic, boring corporate logos you can have PERSONALIZED photo mousepads brighten your desktop! PHOTO Mousepads are DAILY REMINDERS of your favorite: CHILDREN, PETS, EVENTS....... WEDDING PHOTOS, FAMILY, GRADUATION..... LOVED ONES,HOLIDAY PHOTOS,GRANDCHILDREN..... Anything you choose! Use your imagination! These HIGH QUALITY,LONG LASTING mousepads are non-skid 1/4" rubber bottoms with comfortable, washable cloth tops. PHOTO TRANSFER SPECIALTIES uses the latest technology available to transfer your favorite 3x5,4x6,5x7,and 8x10 photos onto mousepads. Your photos will be safely RETURNED with your order! This year we are offering a great new LOW PRICE and we are accepting CONVENIENT credit card payment as well as checks and money orders! ORDERS filled FAST and at a great new LOW PRICE! EASY ORDER FORM Please complete and PRINT this form. Mail your photograph(s), payment, and completed order form to the address below along with: ______Check or _____ Money Order Payable to: PHOTO TRANSFER SPECIALTIES Or pay by VISA or MASTERCARD by filling out this CONVENIENT order form! ____ VISA ____ MASTERCARD Card number: __________________________________ (16 Digits) Expiration Date: ______________________________ Name on card: _________________________________ Billing Address: ________________________________ ________________________________ Indicate amount: _______________________________ Signature : ___________________________________ Date: __________________________________________ Email address (optional):__________________________ CREDIT CARDS : All information must be accurate and complete for proper verification. Incomplete orders cannot be processed and will be returned. Charges on your statement will appear as Pacific Coast Mail Order. $ 10.99 EACH Photo Mousepads $ 9.99 EACH Additional Pads $ 2.50 EACH Shipping and Handling EACH MOUSEPAD $ 1.05 EACH California residents (sales tax) ************ International EXTRA $5.00 EACH MOUSEPAD for shipping ********* Address Mousepads to be shipped to: Name: ____________________________________ Address: ____________________________________ Phone # ____________________________________ City,State,Zip_________________________________ Mail Payment, Photographs, and completed order form to: PHOTO TRANSFER SPECIALTIES P.O. BOX #782 ROSS, CA 94957 * Please allow 2 weeks for delivery. * All orders postmarked by December 10th are guaranteed Christmas delivery! * Please feel free to copy and distribute this order form as you like. Combine your order with friends and coworkers and save $1.00 on each additional mousepad. This is a one time only mailing! You have already been placed on our remove list and will not receive another offer from us! Thank You! From owner-molec-model@net.bio.net Mon Nov 23 22:00:00 1998 Date: Tue, 24 Nov 1998 01:37:51 +0100 From: dumbo@xray.bmc.uu.se (Dombo Journal (Est. 1893)) Newsgroups: bionet.molec-model Subject: Re: PDB files & CHIME Message-ID: References: Organization: Molecular Biology, Uppsala University X-Newsreader: Value-Added NewsWatcher 2.1d3+ NNTP-Posting-Host: nostromo.bmc.uu.se X-Trace: 24 Nov 1998 01:38:23 +0100, nostromo.bmc.uu.se Lines: 24 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!newsfeed1.telenordia.se!newsfeed.sunet.se!news01.sunet.se!news99.sunet.se!newsfeed.uu.se!nostromo.bmc.uu.se!user In article , nna@le.ac.uk (A.J.Cann) wrote: ;->I have been trying to find PDB files of several molecules for use with the ;->CHIME plugin in a new online tutorial: ;-> ;->http://www-micro.msb.le.ac.uk/Tutorials/dfwt/dfwt1.html ;-> ;->I would like to find information for: ;-> ;->sulphonamide ;->p-aminobenzoic acid ;->folic acid ;-> ;->Can anyone tell me where to find thes files or how to construct them? try the HIC-Up site at: http://alpha2.bmc.uu.se/hicup/ --cd ----------------------------------------------------------- Gerard J. Kleywegt Department of Molecular Biology, Biomedical Centre, Uppsala University, Uppsala, SWEDEN mailto:gerard@xray.bmc.uu.se *** http://alpha2.bmc.uu.se/usf/ From owner-molec-model@net.bio.net Mon Nov 23 22:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!nntp-out.monmouth.com!newspeer.monmouth.com!rill.news.pipex.net!pipex!server1.netnews.ja.net!leicester!nna From: nna@le.ac.uk (A.J.Cann) Newsgroups: bionet.molec-model Subject: Re: PDB files & CHIME Date: Tue, 24 Nov 1998 12:34:35 +0000 Organization: University of Leicester, UK Lines: 68 Message-ID: References: NNTP-Posting-Host: mac47.msb.le.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.4.0 In article , nna@le.ac.uk (A.J.Cann) wrote: >I have been trying to find PDB files of several molecules for use with the >CHIME plugin in a new online tutorial: >http://www-micro.msb.le.ac.uk/Tutorials/dfwt/dfwt1.html >I would like to find information for: >sulphonamide >p-aminobenzoic acid >folic acid >Can anyone tell me where to find thes files or how to construct them? Many thanks to all those who replied. Summary of responses: Jeffrey Atkinson Try the Klotho database at http://www.ibc.wustl.edu/klotho/. All kinds of stuff here including the thing at least the folate that you are looking for. They don't have sulphonamide or PABA, but these can be easily drawn with one of the structure packages such as ChemDraw or IsisDraw, Spartan or Hyperchem. The 2D IsisDraw is free on the net but does not have 3D capability. John Osborn If the crystal structures of these compounds have been published they will almost certainly be in the Cambridge Crystallographic Database. Since you are at a British university you are entitled to register to use this database free of charge through the Daresbury Chemical Database Service. For details see http://www.dl.ac.uk/CDS/cds.html The structure files you can download from the database will not be in PDB format, but if you need this format you can probably convert them using the free molecular data format conversion program called BABEL, available from ftp://ccl.osc.edu/pub/chemistry/software/MAC/babel/ There may also be data format conversion software available on the Daresbury Chemical Database Service - I am not sure about this. Kenward Vaughan Have you visited the following? http://www.sci.ouc.bc.ca/chem//molecule/molecule.html http://www.ibc.wustl.edu/moirai/klotho/ http://ourworld.compuserve.com/homepages/JDebord/models.htm (last one has some other links, too) and a place of links I just ran across, but don't know about currency: http://sch-www.uia.ac.be/u/thys/chem.html Jeremy Murray I guess your first port of call is the cam cryst database http://www.ccdc.cam.ac.uk/ and then maybe HICUP http://alpha2.bmc.uu.se/hicup/ Lynda Ellis I enjoyed looking at your tutorial. One place to look for pdb files would be the ChemFinder Webserver, http://chemfinder.camsoft.com/ I did not find a pbd file for sulphonamide when I looked there, but there was a link to the ChemSymphony site, where the chemical was the molecule of the month for February 1998. http://www.chemsymphony.com/gallery/html/sulfanil.html If you have the SMILES string for a compound or draw it using their editor, CORINA will produce a pdb file for you on the web (for at least the first 1000 compounds): http://www2.ccc.uni-erlangen.de/software/corina/index.html -- Dr Alan J. Cann PhD, Department of Microbiology & Immunology, University of Leicester, P.O. Box 138, Medical Sciences Building, University Road, Leicester LE1 9HN, UK. From owner-molec-model@net.bio.net Thu Nov 26 22:00:00 1998 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molec-model Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 27 Nov 1998 02:00:14 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199811271000.CAA15989@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. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. 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-molec-model@net.bio.net Sat Nov 28 22:00:00 1998 Path: biosci!rutgers!rockyd.rockefeller.edu!news-nysernet-5.sprintlink.net!news-dc-2.sprintlink.net!news-east1.sprintlink.net!news-peer1.sprintlink.net!news.sprintlink.net!howland.erols.net!dca1-hub1.news.digex.net!digex!hub1.ispnews.com!news14.ispnews.com.POSTED!not-for-mail From: tfwwco@YAHOO.COM Newsgroups: bionet.molec-model Subject: LOWEST PRICES ON MAGAZINES 4661 Lines: 63 Message-ID: NNTP-Posting-Host: 207.240.233.44 X-Trace: news14.ispnews.com 912376727 207.240.233.44 (Sun, 29 Nov 1998 16:58:47 EDT) NNTP-Posting-Date: Sun, 29 Nov 1998 16:58:47 EDT Organization: ISPNews http://ispnews.com Date: Sun, 29 Nov 1998 21:58:47 GMT For a complete magazine discount list (175 magazines) click on http://ourworld.compuserve.com/homepages/magazine_man COMPUTER MAGAZINES AT HUGE DISCOUNTS //////////////////////////////////// Magazine Reg. Price. One Year Three Years Byte $35 sale $10.00 sale $15.00 (2 yr.) 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CALL 800-958-2650 ext. 300 to order with your credit card For a complete magazine discount list (175 magazines) click on http://ourworld.compuserve.com/homepages/magazine_man Best Deal Magazines 217 E. 86th Street New York, NY 10028 voice or fax 212-426-7492 *** These prices are good for 30 days only. Order today. For my complete list of more than 175 magazines at huge discounts see above. qjkvfrrmdxetmlzcyuynietrgbekjgeykccfutokmfgst From owner-molec-model@net.bio.net Sun Nov 29 22:00:00 1998 Path: biosci!SYR.EDU!desingh From: desingh@SYR.EDU (Deepak Singh) Newsgroups: bionet.molec-model Subject: Subscription Date: 30 Nov 1998 07:43:28 -0800 Organization: Dept. of Chemistry, Syracuse Univ. Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: <3662BD09.884BA84B@syr.edu> NNTP-Posting-Host: net.bio.net I just sent a similar message to the computational biology newsgroup. Ho wdo I subscribe? Deepak. -- ********************************************************************** Deepak Singh Email: desingh@syr.edu Graduate Fellow URL: http://web.syr.edu/~desingh Department of Chemistry and Biochemistry, Tel: (315) 443 1739 -- work Syracuse University (315) 472 9659 -- home 1-014 Scitech Syracuse NY 13244 Fax: (315) 443 4070 "Violence is the last resort of the incompetent". -- Salvor Hardin ********************************************************************** From owner-molec-model@net.bio.net Mon Nov 30 22:00:00 1998 From: "clive delmonte" Newsgroups: bionet.biophysics,bionet.molec-model,bionet.xtallography Subject: DNA Structure: Puzzle Number 2 Date: Tue, 1 Dec 1998 10:19:15 -0000 Lines: 32 X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 NNTP-Posting-Host: 195.7.227.184 Message-ID: <36643fd2.0@news.netdirect.net.uk> X-Trace: 1 Dec 1998 19:13:22 GMT, 195.7.227.184 Path: biosci!agate!newsfeed.berkeley.edu!btnet-peer!btnet!news-lond.gip.net!news.gsl.net!gip.net!demeter.clara.net!news.clara.net!peer.news.nildram.co.uk!news-peer.netdirect.net.uk!news.netdirect.net.uk!195.7.227.184 Xref: biosci bionet.biophysics:4608 bionet.molec-model:2334 bionet.xtallography:4500 It was Franklin's famous diffraction photograph of B-DNA (2), shown to him by Wilkins, that Watson sketched on the train back to Cambridge to rejoin Crick. One of Wilkins' collaborators, A R Stokes (3), working on the Fourier transform for a helix, showed that, defining as "delta" the angle between an arm of the "helical cross" and the Y-axis (meridian), tan delta = helical pitch / helical circumference Applying this result to Franklin's photograph of B-DNA, delta is measured as 40 degrees, and, with a pitch of 3.34 nm, the helical diameter is found to be some 1.3 nm. For a supposed double helical diameter of 2 to 2.2 nm, delta should be 28 - 26 degrees respectively, far removed from the actual value of 40. Interestingly, the helical diameter of 1.3 nm, found from Stokes equation applied to Franklin's photograph, coincides with the STM value of 1.3 nm measured by Lee et al. (Puzzle 1, ref. 1) and recorded in their Figure 3(D). 2 Molecular Configuration in Sodium Thymonucleate; R.E. Franklin & R.G. Gosling; Nature Vol 171 (1953) 740 - 741 3 The Theory of X-ray Fibre Diagrams; A.R. Stokes; Prog. Biophys. & Biophys. Chem. Vol 5 (1955) 140 - 167 -------------------------------------------------------------- Clive Delmonte From owner-molec-model@net.bio.net Mon Nov 30 22:00:00 1998 From: "clive delmonte" Newsgroups: bionet.biophysics,bionet.molec-model,bionet.xtallography Subject: DNA Structure: Puzzle Number 3 Date: Tue, 1 Dec 1998 10:33:37 -0000 Lines: 28 X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 NNTP-Posting-Host: 195.7.225.160 Message-ID: <36644332.0@news.netdirect.net.uk> X-Trace: 1 Dec 1998 19:27:46 GMT, 195.7.225.160 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!btnet-peer!btnet!news.freedom2surf.net!peer.news.nildram.co.uk!news-peer.netdirect.net.uk!news.netdirect.net.uk!195.7.225.160 Xref: biosci bionet.biophysics:4609 bionet.molec-model:2335 bionet.xtallography:4501 In 1953, James & Mazia (4) reported that 1 mg of dry calf thymus DNA could be spread in a monolayer to cover 0.28 sq. m. From this measurement, it is possible to calculate the diameter of the DNA as it lies across the film surface. Calf thymus DNA, with 40% C+G base pairs, has an average mass of 330 daltons per base unit, and a base repeat distance of 0.334 nm, giving a helical diameter. measured across the surface film, of 1.2 nm. James & Mazia measured the film height as 2.16 nm using an ellipsometer. So there are two independent determinations of the height and width of the duplex DNA as 1.2 nm x 2.1 nm, that is, DNA would have an elliptical cross section. The DNA molecular width in the film of 1.2 nm is close to that of 1.3 nm found by Lee et al. (Puzzle 1, ref 1) using STM on duplexes not under lateral compression, and to the value found by applying Stokes' equation (Puzzle 2, ref. 3) to Franklin's B-DNA photograph. 4 Surface Films of Desoxyribonucleic Acid; T.W. James & D. Mazia; Biochim. Biophys. Acta Vol 10 (1953) 367 - 370 ------------------------------------------------------------------ Clive Delmonte From owner-molec-model@net.bio.net Mon Nov 30 22:00:00 1998 From: "clive delmonte" Newsgroups: bionet.biophysics,bionet.molec-model,bionet.xtallography Subject: DNA Structure: Puzzle Number 1 Date: Tue, 1 Dec 1998 10:01:47 -0000 Lines: 24 X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 NNTP-Posting-Host: 195.7.225.154 Message-ID: <36643bb9.0@news.netdirect.net.uk> X-Trace: 1 Dec 1998 18:55:53 GMT, 195.7.225.154 Path: biosci!agate!newsfeed.berkeley.edu!btnet-peer!btnet!news.netkonect.net!peer.news.nildram.co.uk!news-peer.netdirect.net.uk!news.netdirect.net.uk!195.7.225.154 Xref: biosci bionet.biophysics:4606 bionet.molec-model:2333 bionet.xtallography:4499 In their STM study of nucleic acids (1), Lee et al. recorded in Figure 3(b) lengthy stretches of at least four well-resolved linear DNA duplexes. The vital feature of this image of DNA molecules is that no plectonaemic winding can be discerned. That is, they show no sign of being double-helical. The duplexes consist of long, paired, helices with a consistent, uninterrupted parallel (or antiparallel) contour running between the two strands of each of the four duplexes, whose highlighted features remain exactly in phase with each other over their whole lengths, extending to some 17 - 20 full helical turns. 1 Scanning Tunnelling Microscopy of Nucleic Acids; G. Lee, P.G. Arscott, V.A. Bloomfield & D. Fennell Evans; SCIENCE Vol 244 (1989) 475 - 477 ---------------------------------------------------------------------------- Clive Delmonte