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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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Re: Screen vs Paper for E-journals
by ryanmd＠mms.sbphrd.com 03 Jun '97

03 Jun '97

On Jun 3, 10:17am, citroen(a)library.tudelft.nl wrote: > Subject: Re: Screen vs Paper for E-journals > One simple tool that already helps (a little) is to install the > (Netscape) browser so as to take up as little space as possible on the > screen. I notice many people have too many buttons+text displayed that > take away space for more useful reading data. While efficient use of screen real estate is always good advise, it is useful for anyone putting up a page to remember that different people might use different devices. I run netscape on my SGI Indigo2 Extreme and generally I find I have a much bigger page size than anyone using a PC (or Mac). I sometimes pull in a page that has internal links from a 'menu' to places lower down on the same page, yet the whole page is up in my browser. -- M. Dominic Ryan (610)-270-6529 SmithKline Beecham Pharmaceuticals ryanmd(a)mms.sbphrd.com King of Prussia, PA 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 ryanmd＠mms.sbphrd.com 03 Jun '97

03 Jun '97

On Jun 2, 6:22pm, Rzepa, Henry wrote: > Subject: Screen vs Paper for E-journals <snip> > 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? When I ask colleagues about this I see an almost generational split. Chemists of all flavors older than some unquantified number seem to prefer paper. Even in the younger crowd (under 50?) many prefer paper. It might be tempting to ascribe this to an age-related issue, but I think the reasons lie elsewhere. In my opinion electronic representations still suffer from poor scanning and page flipping capabilities. If you happen to be very focussed on a particular paragraph or two then you don't need this and it is less of an issue. If the item you are focussing on also contains value-added VRML then you would welcome the new capability perhaps even at the expense of the loss of scannability. The trouble comes from the fact that one very often needs to scan prior to digging into the details and even PDF docs are not very good for this, performance is just not there, one has to zoom in and out, pages take to long to draw, the viewer takes too long to start up. Some of this will no doubt improve as both depiction code and hardware speed up. But the standard monitors/resolution/page sizes will take longer to address. I beleive that the 'older' folks are often people in a position that requires them to be able to scan larger numbers of documents quickly rather than digest fewer in depth. This is particularly bad for electronic presentations at this time. Thus it is not so much age as it is function (manager) and that function and age are often correlated. The sort-term strategy might be to keep published electronic documents very short, only one idea per document. To make this valuable there needs to be a longer term plan to allow for integration of these documents into a more comprehensive work. I think this is where the real challenge lies. To build a meta-document 'integrator'. Think of it as a dynamic page generator that takes the underlying elements as targets that it must build links for. This is a bottom-up outlining tool, rather than top-down. I imagine a browser-like interface that allows you to tag element pages with properties such as "Background", "Data evidence", "hypothesis", "flame-bait" together with a unique project (publication?) code. Given document elements could have multiple project codes attached to facilitate zillion part articles. Then a standardized chemistry (science?) journal article browser would know how to assemble the parts. With standardized elements there could be greater transparent hyperlinking between elements. This would be my suggestion to address the scannability issue. Make it more scannable by having more dynamic outline/in-depth control. Find a way to make existing monitor sizes fit the data to them, rather than trying to reproduce the printed page more accurately. Today's web browsers already do this with a standard web-page. We just need it to happen transparently in a chemistry article. We need to make the article inherently scannable, not the depiction. To do this requires thinking do define the elements and not just technology. -- M. Dominic Ryan (610)-270-6529 SmithKline Beecham Pharmaceuticals ryanmd(a)mms.sbphrd.com King of Prussia, PA 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 Jeffrey.Nauss＠UC.Edu 03 Jun '97

03 Jun '97

On Jun 2, 6:22pm, Rzepa, Henry wrote: > http://gort.ucsd.edu/newjour/ Thanks for the URL! It saves people some work. > Of these 6000, it seems the very large majority are in fact > "journals delivered electronically"... I think you are being lenient. Many seem to be journals that have just advertised themselves on the Web. Many only have abstracts. Very few delivery of "printable" documents, as you say. > 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"... > Is this assumption justified? Yes, I think it is. As Joe Leonard pointed out in another post, hardcopy is portable. It can stuffed in a folder or a briefcase. And it can be annotated by the user. HTML versions of documents do not offer those capabilities. Furthermore, the questions in my mind is how long will the full-fledged HTML documents with animation and Java scripts and all the gee-whiz features remain available on the Web. Where is the "library" that will allow the user to access these documents in later years? A hardcopy can reside in my file cabinet until needed. Can we say the same about all the WWW documents available today? > 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. I don't agree with this statement. IMHO, e-journals offer me in this order of impact or importance: (1) Easy access from my desk to review abstracts and to scan interesting articles. (2) A means to print these articles from my desk (and in the case of PDF files, with better quality print) (3) Ready access to supplementary material (4) Multimedia presentations Other folks have different opinions but this is how I see e-journals being useful right now. > 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? Both. Printable media (and I would say PDF is the best standard followed by Postscript) will have it's uses for the immediate future. But e-journals could provide so much more to the reader with multimedia presentations. Until these multimedia aspects of journals can be made portable and easily stored locally, printable documents will still be required. -- Jeffrey L. Nauss, PhD Telephone: 513-556-0148 Dir. Molec. Model. Serv. Fax: 513-556-9239 Department of Chemistry e-mail: Jeffrey.Nauss(a)UC.Edu University of Cincinnati URL http://www.che.uc.edu/~nauss 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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Winners of "Top 5% Chemistry Site" Award
by Rolf Claessen 03 Jun '97

03 Jun '97

Winners of "Top 5% Chemistry Site" Award given by The Homepage for Chemists http://www-public.rz.uni-duesseldorf.de/~knecht/chempage.htm und Rolf Claessen's Chemistry Index http://www.geocities.com/Tokyo/5243/home_en.htm This time 11 applicants (the top 5% of all applicants this month) received the award. Check lists of the award winners of may and april at the URLs given above. Yours sincerely, Rolf Claessen Rolf Claessen's Chemistry Index http://www.geocities.com/Tokyo/5243/index.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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Re: Screen vs Paper for E-journals
by Rzepa, Henry 02 Jun '97

02 Jun '97

Dominic Ryan wrote, >The abandoning of that mode is part of the thought that must go into it that I >was alluding to. But, I would like to see a smarter browser (or perhaps >composition tool) that would make it easy to assemble the main point as the >main page, with all the supporting information as links that could be tailored >to a customizable level of desired detail. ... >intro.historcal > .controversial Such divisions are likely to be contentious, and probably undefinable. But it does emphasize that as authors, we all will have to learn how to structure an article. This, in many ways, is what the XML initiative currently under way is all about. XML would in principle at least allow a framework for such divisions. More interestingly, once a chemistry article is marked up, it can be re-displayed using smart browsers to whatever level of detail is desired, and maybe even beyond the level to which the author has marked it up, if one includes heuristics in the browser. For example, if one is looking at the molecule, one could automatically generate links to "similar" molecules in the document collection. A lot of what Dominic describes is actually already present in the CML examples produced by Peter Murray-Rust, and is browsable in the way Dominic suggests using his JUMBO (Java Universal Molecular Browser). You can try this out from the ECHET96 CD-ROM (available in issue 6 of ChemComm). A much more complete release of CML/XML/JUMBO is currently in preparation from the Open Molecule Foundation, and is expected to become available during the summer. The point I would make is that if we learn to think in terms of the structure of a collection of ideas and data, we can achieve much more than if we accept e.g. PDF files as the paradigm. PDF as I see it, does nothing to encourage people to think about such structures, it only encourages them to print in the traditional linear style. Where in this, I ask, is the "added-value" a publisher is supposed to impart? Henry Rzepa. +44 171 594 5774 (Office) +44 594 5804 (Fax) 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 ryanmd＠mms.sbphrd.com 02 Jun '97

02 Jun '97

On Jun 2, 3:49pm, Robert_L_Swofford(a)mta.wfu.edu wrote: > Subject: Re: Screen vs Paper for E-journals > > If we think of e-journals as just electronic renditions of their linear > paper cousins, then we are missing an important opportunity. We need an > outlining format that is a radical departure from the one we learned in > high school (and rarely used). Dominic hints at such a tool in his > comments about tagging elements in the document. If we could represent the Indeed, that is precisely what I was trying to get at, though I stressed the need for it being the ability to scan a document quickly and flexibly. > e-document at varying levels of detail (i.e., varying levels of outline), > with non-linear links to other sections or to more detail, then I think we > would have an important new resource. But until we are comfortable with > abandoning the linear mode of presentation, then anything we do will suffer The abandoning of that mode is part of the thought that must go into it that I was alluding to. But, I would like to see a smarter browser (or perhaps composition tool) that would make it easy to assemble the main point as the main page, with all the supporting information as links that could be tailored to a customizable level of desired detail. Then it is the single overhead talk for those familiar with the subject, and inlined expanded links for those not. It puts some of the composition effort in the hands of the reader. <snip> Just for sake of discussion, how many low-level information nuggets could be come up with? These would be the new chemistry-journal tags in an expanded html-like vocabulary. Off the top of my head I would see the following, with some or all having numeric attributes for outline level or grouping Finally, web-permanence might be addressed by a top-level tag constituted by an author's registered public encryption key/electronic signature which would be unique, traceable, and provide a pointer for linking other documents. intro.historcal .controversial .reviews .current .problem_statement.1 .problem_statement.n... main.table.1... .graph .structure conclusions.explaination .new_work .challenge .litt_comp.1.. experiment.synthesis .supplies .methods.named_reactions.1... -- M. Dominic Ryan (610)-270-6529 SmithKline Beecham Pharmaceuticals ryanmd(a)mms.sbphrd.com King of Prussia, PA 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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