June 1997 - chemweb - imperial.ac.uk

netscape bug fix progress
by Michael Barker 18 Jun '97

18 Jun '97

Hi All, Nobody seems to have mentioned the security problems recently spotted in Netscape 4 and also found in earlier versions... so here is the news as of the 16/06. *------------------------------------------------------------* | Michael H. Barker GRSC The University of Liverpool | | Department of Chemistry | | E-mail: mhbarker(a)liv.ac.uk Oxford Street | | Liverpool | | Tel: +44 151 794 2274 L69 7ZD | | Fax: +44 151 794 3588 United Kingdom | | | | http://www.liv.ac.uk/Chemistry/Links/links.html | | "WWW Links for Chemists" @ The University of Liverpool, UK | *------------------------------------------------------------* http://home.netscape.com/flash3/misc/security_update.html SECURITY UPDATE June 16, 1997 ------------------------------------------------------------------------- The reported privacy bug affecting Netscape Navigator has been identified and fixed. It is now being thoroughly tested by Netscape, and a fix will be released by Wednesday, June 18. The bug, reported by an Internet consultant, affects Netscape Navigator 2.0 and 3.0, and Netscape Communicator 4.0 on all platforms (Windows, Macintosh, and Unix). Netscape will test the fix extensively before releasing it in an updated version of Communicator 4.0 during the week of June 16. A fix for Navigator 3.0 will follow shortly after the Communicator fix. Netscape knows of no reports of successful exploitation of this privacy bug, and no customer incidents have been reported. The privacy bug can allow malicious Web site operators to retrieve known files from the hard disks of visiting users by mimicking the submission of a form. Under ordinary circumstances, users browsing on known, trusted sites are not at risk. However, if a user visits an unknown, untrusted site, the operator of that site can potentially retrieve files from a user's hard disk through an obscure series of steps. For this attack to work, the hacker must know the exact name and path of the file. To completely remove any risk of this bug, Navigator users should download the updated version of Communicator (or Navigator), which includes the fix. In the interim, users of Navigator 3.0 and Communicator 4.0 can take the following steps to enable warning dialog boxes to detect and cancel form submissions: * In Navigator 3.0: Go to the Options menu and select Security Preferences. Select the "Submitting a Form Insecurely" preference to enable that warning dialog box. * In Navigator 4.0: Select the lock in the toolbar to open the Security Advisor. Select Navigator, then select the "Sending Unencrypted Information to a Site" preference to enable that warning dialog box. Although the Internet consultant was unwilling to release the technical details of the bug, he has subsequently released them to Netscape. The information that he provided matches what Netscape determined independently. Netscape will post a fix by June 18. Customers and partners will find download details and updates on the Netscape home page when the fix is available. ------------------------------------------------------------------------- [Navigation bar] Corporate Sales: 415/937-2555; Personal Sales: 415/937-3777; Government Sales: 415/937-3678 If you have any questions, please visit Customer Service, or contact your nearest sales office. Copyright ) 1997 Netscape Communications Corporation chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to majordomo(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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ChemStarter - Online Discussion Forum
by Rolf Claessen 16 Jun '97

16 Jun '97

ChemStarter - Online Discussion Forum I added an online discussion forum to the ChemStarter at http://destille.chemie.de/HyperNews/get/forums/chemstarter.html It is possible to use html. So you can include images, vrml, chime, ... into your messages to illustrate the discussion about chemistry problems. Yours Rolf Claessen claessen(a)chemie.de chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to majordomo(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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RSC CIG/CSA Autumn Meeting - Chemical structures and networking
by john blackmore 13 Jun '97

13 Jun '97

(apologies for multiple list postings) This is the first announcement of a Joint Royal Society of Chemistry Chemical Information Group (RSC CIG) and the Chemical Structure Association (CSA) meeting The all-day meeting entitled: Chemical structures and networking - an overview of recent developments and trends is to be held on Thursday, October 16th 1997, Burlington House, Piccadilly, London. Rapid development continues in the application of increasingly sophisticated computer technology, both hardware and software, to the location, retrieval, registration, manipulation and exploitation of chemical structure and related data. These developments are helping users cope with the new demands arising from the continuing growth in the volumes and complexity of data, especially from such techniques as combinatorial chemistry and high-throughput screening. All of this is taking place alongside the continuing growth in the use of Internet/Intranet technology. Most of the new developments allow the use of a browser interface, and many of them are accessible via the Internet. This meeting will review recent developments and trends in the availability of tools for manipulating chemical structure and related data. Key presentations will provide overviews which will be supplemented by presentations and demonstrations from major systems suppliers. After the presentations, there will be a (free) wine and cheese reception, which will provide a further opportunity to network and to view the various demonstrations. This one-day meeting presents a highly cost-effective way of keeping up to date with this fast-moving field. The cost is 20 to members of the RSC CIG or CSA and 25 to non-members. The number of attendees will be be limited to 50, so early booking is advisable. Further details and registration forms are available from: Doug Veal Doverton Ltd 46 The Knoll Hayes Bromley Kent BR2 7DHP Phone/fax 0181-325-7608 e-mail: doverton(a)compuserve.com announcement posted by john blackmore, RSC CIG johnb(a)infonol.demon.co.uk chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to majordomo(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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Babel and XCART
by Trevor Gilson 11 Jun '97

11 Jun '97

I don't recall the Babel molecular structure file format conversion utility referred to recently - might be a good time to remind folk that it may be obtained from: http://mercury.aichem.arizona.edu/babel.html - and while we are on the subject, I wrote to Arizona recently about an ambiguity over Cambridge cssr files. This format is used by Desk Top Molecular Modeler for PC, but it chooses to allow the atom 'label' (usually an integer) (columns 7-10) to be seperated by a space from its atom (symbol), so long as it is in its correct column. BABEL, by contrast, seems to interpret the label as the x-coordinate when it occurs. I suspect that BABEL is going on columns encountered rather than on the old-fashioned (and horrible) rigid FORTRAN-type format? It is not particularly difficult to edit the DTMM file into BABEL compliance, just a nuisance to do it every time! I recommend the DOS technical editor Tech-Edit 2.61 which processes or removes columns with dexterity. I also have a DOS based molecular coordinate/structure constructor/viewer utility, xcart with xtick - see http://www.soton.ac.uk/~trg/acad/xcart.html (Requires chime to view). I don't recommend this as user-friendly, but it can be useful for smallish difficult molecules particularly in inorganic chemistry and it outputs pdb files, one of the main chemical mime specified formats. It can also be used to add connectivity information to any raw list of atom coordinates (up to 255 atoms). I have used a development of the package (not yet online) for the production of raytraced vibrational animations, as used to generate the animated gifs on my home page. Trevor Gilson chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to majordomo(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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xyz2rgb molecular animations
by Paul May 11 Jun '97

11 Jun '97

Hi, I was recently sent this, which might be of interest here: > > > xyz2rgb makes pretty pictures and movies of molecules. It expects input > in the form of an XYZ file, one of the file formats frequently used by > computational chemists. As output, it produces one or more line-interlaced RGB > files. These can be converted to other formats using the ImageMagick image > processing toolkit. Conversion between a wide variety of molecule file formats > can be accomplished using a program called Babel. > > Information on xyz2rgb (including source code) is available at > http://world.std.com/~wware/xyz2rgb.html > xyz2rgb is GPL-ware. > - ------------------------------------------------------------- > Will Ware email: wware[at]world[dot]std[dot]com Regards, ------------------------------------------------------------------------- Dr Paul May, School of Chemistry, University of Bristol, UK tel: +44 (0)117 9287667, fax: +44 (0)117 9251295 <mailto:paul.may@bris.ac.uk> <http://www.bris.ac.uk/Depts/Chemistry/staff/pwm.htm> "Why don't you just leave me alone with my thought" Homer Simpson ------------------------------------------------------------------------- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to majordomo(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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Register now for Chemistry Webmasters 3
by ALLENB＠rsc.org 10 Jun '97

10 Jun '97

If you have not yet done so, NOW IS THE TIME TO REGISTER for CHEMISTRY WEBMASTERS 3 - Future Technologies for Chemistry on the Internet on Thursday 10 July 1997, at the University of Oxford Chemistry Sub-Faculty Organised by The Royal Society of Chemistry and the University of Oxford on behalf of the CLIC consortium, this FREE meeting will be a mixture of presentations, posters and workshops. Speakers include Dr Henry Rzepa on 'Publishing CD-ROMs of Internet Sites and Electronic Conferences', Dr Mark Winter on 'Stylish chemistry web pages and how to plug them', Dr Peter Murray-Rust on 'Chemical Data on the Internet - CML and XML' and Omer Casher on 'Programming web sites - Hyperwave and Netscape 4'. Workshops will include Dr Karl Harrison's Virtual Chemistry Lab, to be used in teaching for the first time this autumn, and Dr Mark Winter will chair what is sure to be a lively discussion on future directions and funding issues. Full details of the programme are at http://chemistry.rsc.org/rsc/chemwebm.htm To register email Becky Allen at allenb(a)rsc.org chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to majordomo(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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Problem with using Chime in Netscape
by Jonathan W. Steed 09 Jun '97

09 Jun '97

Dear all, I was hoping for some advice on getting a .PDB file to run using Netscape3/Chime. I have set up the HTML using the excellent guide at Imperial and my molecule looks great when I load my HTML file into my browser from my local drive. BUT when I mount the page (see URL below) I just get a 'broken image' symbol and nothing works even though the .PDB file is in the right directory (all other images work fine). Oddly in Internet Explorer on the other hand it recognises that it has a .PDB but displays a blank image!!! Does anybody have any ideas on this problem? Many thanks, Jon. Dr. Jonathan W. Steed Department of Chemistry, King's College London, Strand, London WC2R 2LS, UK. Tel: +44 (0)171 873 2117, Fax: +44 (0)171 873 2810 e-mail: jon.steed(a)kcl.ac.uk Web site: HTTP://CRAC3.CH.KCL.AC.UK/KCLCHEM/SUPRAMOL.HTM chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to majordomo(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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Microsoft XML Parser in Java is Av (fwd)
by Peter＠ursus.demon.co.uk 07 Jun '97

07 Jun '97

I am forwarding this announcement from the XML-DEV list. It announces an XML parser from Microsoft, provided as an open tool including source. This has important and exciting implications for the future of WWW-based chemistry as it implies that Microsoft will be a fully compliant open supporter of XML. I shall be exploring it over the w/e but assume that it will be simple to interface it with CML and JUMBO. Assuming that the Microsoft browsers in the future contain open XML-compliant software (XML-support had already been announced, but it was not clear whether there would be an API.), it should be straightforward to add CML on top. The use of the DOM should interoperate directly with CML. P. Forwarded message follows: [...] > From: Jean Paoli <jeanpa(a)microsoft.com> > To: "'xml-dev(a)ic.ac.uk'" <xml-dev(a)ic.ac.uk> > Cc: Istvan Cseri <istvanc(a)microsoft.com>, Chris Lovett > <clovett(a)microsoft.com> > Subject: Microsoft XML Parser in Java is Available > Date: Fri, 6 Jun 1997 20:50:02 -0700 > X-Priority: 3 > X-Mailer: Internet Mail Service (5.0.1458.30) > Sender: owner-xml-dev(a)ic.ac.uk > Precedence: bulk > Reply-To: Jean Paoli <jeanpa(a)microsoft.com> > Status: R > > ANNOUNCEMENT: Microsoft XML Parser in Java is Available > > I am *really* pleased to announce : > > The XML Parser in Java (MSXML) from Microsoft Corporation is now > available for download from: > http://www.microsoft.com/standards/xml/xmlparse.htm > > This is the second piece of XML technology from Microsoft, the first > being > the Channel Definition Format support in Internet Explorer 4.0. > > The Microsoft XML Parser is a validating XML parser written in Java. > Once parsed, the XML document is exposed as a tree through a simple set > of Java methods. > We are actively working with the W3C to standardize an XML API > (See the W3C overview page for the Document Object Model > http://www.w3.org/MarkUp/DOM/. > The DSSSL/grove Object Model is carefully studied by the DOM group). > > These methods support reading and/or writing XML structures, such as the > Channel Definition Format (CDF) or other text formats based on XML. > > This version (Alpha 1.0) of the parser implements the W3C working draft > of the XML specification dated March 31, 1997 > (http://www.w3.org/TR/WD-xml-961114.html) and will be revised to reflect > future W3C changes to the specifications. > > The following components of the XML spec have not yet been implemented > (but will be soon) : > > * XML-SPACE (for control over white space > handling) > * XML encoding declaration (<?XML > ENCODING='EUC-JIS' ?>) > * Conditional sections in the DTD (INCLUDE & > IGNORE keywords) > * Required Markup Declaration 'RMD' > > Full source code is provided, royalty free, and will be updated > frequently to fix bugs > and to reflect future W3C changes to the specifications.(read the > Microsoft XML Parser in Java license agreement > http://www.microsoft.com/standards/xml/xmllic.htm) > > Bugs should be sent to Istvan Cseri (istvanc(a)microsoft.com) or Chris > Lovett (clovett(a)microsoft.com) > > Enjoy, and let us make XML a success story! > > -Jean Paoli > jeanpa(a)microsoft.com > > > xml-dev: A list for W3C XML Developers > Archived as: http://www.lists.ic.ac.uk/hypermail/xml-dev/ > To unsubscribe, send to majordomo(a)ic.ac.uk the following message; > unsubscribe xml-dev > List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk) > > -- Peter Murray-Rust, domestic net connection Virtual School of Molecular Sciences http://www.vsms.nottingham.ac.uk/ chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to majordomo(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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Screen vs Paper for E-journals
by Rzepa, Henry 03 Jun '97

03 Jun '97

I have just returned from a "multimedia publishing" conference in Finland. Amongst the talks was one about the "NewJour" project, which tracks all new electronic journals. It has about 11 entries only for chemistry. Ann Okerson gave a talk in Finland about the project, and estimated perhaps 6000 journals would be electronic by the end of this year. http://gort.ucsd.edu/newjour/ Of these 6000, it seems the very large majority are in fact "journals delivered electronically" rather than "2nd generation true electronic journals". In turn, electronic delivery of journals seems to correspond to delivery of "printable" documents, eg predominantly in PDF format. Few journals can be described as "multimedia" or offering features not possible with paper. Those that do seem to concentrate on e.g. MPEG animation. Several speakers presented e-journals where the boundary condition was that an Acrobat PDF version was being provided so that "people could print any article they were interested in". The widespread assumption still is that pretty much everyone will hit the "print" button the moment they find something sufficiently interesting that they want to study it in depth. Is this assumption justified? Does the chemistry community want more from its e-journals, or will PDF suffice over the next few years? Certainly, it is much favoured in the more mathematical areas of chemistry, for well justified reasons. Jessie Hey from the Open Journal project at Southampton started from Vannevar Bush and Eugene Garfield, and described e-journals as pre-eminently offering (hyper)links as THE additional value that an e-journal can offer. Such link databases can be constructed between different e-journal articles (interesting, a process the author themself is NOT involved in), and its this LINKING that according to this model of the e-journal, is what readers really want (I note that we actually did this as part of ECHET96; see Earlier this year, we spent some time producing and testing the CD corresponding to the proceedings of the ECHET96 conference, but one of the areas we did not concentrate on was to ensure its "printability". I gather that the subsequent abstracting of this CD by CAS was delayed because this mandated printing the entire product prior to its abstracting. Both these observations lead me to ask what the fate of any non-printable representation of chemistry that imparts knowledge or undertanding to new scientific results might be? So, is the near future of electronic chemistry journals destined to be simply a delivery mechanism for documents that if destined to be read by the reader, have to be printed? Or should the chemistry community be pressing learned society and commercial publishers for e-journals that can deliver "models" encoded via software rather than words, and to develop non-printable ways of archiving such information? Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; mailto:rzepa@ic.ac.uk; Tel (44) 171 594 5774; Fax: (44) 171 594 5804. URL: http://www.ch.ic.ac.uk/rzepa/ chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to majordomo(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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Re: Screen vs Paper for E-journals
by Mark Griskey 03 Jun '97

03 Jun '97

The National Academy Press, http://www.nap.edu (NAP), the publisher for the U.S. National Academy of Sciences, National Academy of Engineering, Institute of Medicine, and National Research Council, is putting all of the Academy's books and reports on-line in their entirety (also free for the reading). Right now, there are about 1,200 on-line, with a few thousand more planned to go on-line. The books are served using a software the NAP developed called the "Bookobject". This allows a reader to navigate through the book on-line as easy as the printed version. There are also plans to include searching and print on demand options to a local printer. The disadvantage is speed, which is still restricted because of bandwidth and network traffic. The on-line book is not a replacement for the printed version, but simply another way to disseminate the information with more options such as full text searching. It also has the advantage that it is always available after the printed supply is long gone. Mark Griskey National Academy Press chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to majordomo(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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