May 1998 - chemweb - imperial.ac.uk

Molecule Editor in Java
by Denis M. Bayada 18 Feb '99

18 Feb '99

Dear all, I have just finished writing a molecule editor in JAVA. If anyone is interested, it is available at : http://www.chem.leeds.ac.uk/ICAMS/people/denis/moledit.html You may freely download the Java source code and modify it. Any comments are indeed welcome. Thank you Denis --------------------------------------------------------------------- Denis M. Bayada e-mail: denis(a)mi.leeds.ac.uk ICAMS voice: (44) (0)113 233 65 95 School of Chemistry fax: (44) (0)113 233 65 63 University of Leeds http://www.chem.leeds.ac.uk/ICAMS/people/denis Leeds LS2 9JT ENGLAND ... but as I proceeded in my labour, it became every day more horrible and irksome to me. Sometimes I could not prevail on myself to enter my laboratory for several days, and at other times I toiled day and night in order to complete my work. It was, indeed, a filthy process in which I was engaged. Frankenstein (Mary Shelley) --------------------------------------------------------------------- ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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INFORMATION
by Novena Chemicals 29 May '98

29 May '98

DEAR SIR, I HAVE CONTECT YOU FOR INFORMATION- I REREIVE ATTACHED FILE I WANTED TO KNOW REGARDING YOUR CHARGES TO PROVIDE SERVICE ONE GOOD NEWS WE HAVE HOSTED OUR WEBSITE ON INTERNET http://www.novenachem.com PLEASE VISIT OUR SITE AND ADVISE SPECIFICALY HOW YOUR SERVICE BENEFITED US I HAVE GOT WINDOW-95, AND EUDORA ONLY PLEASE SEND READABLE FILE BEST REGARDS ASHWIN THAKER chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)

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Need feedback from ejournal users
by Carmen I Nitsche 28 May '98

28 May '98

Dear list members-- I am working on my talk for the 1998 International Chemical Information Conference and am looking for additional feedback. My topic is "ejournals: what end-users need, want and expect from them." If you are an actual user of ejournals could you spare 5 minutes to respond to the following questions? Please direct your responses to me personally and I will summarize for the respondents (and the list, if there is interest) in due course. Do you work in: academia __ government __ industry __ other (describe) __ In what country? What ejournals do you currently read (list titles)? Do you use (mark all that apply): personal subscription __ institutional subscription __ free trial __ What ejournal features are most useful to you? What ejournal features are least useful to you? What features would you like to see? Is printing (ease and quality) important to you? Are you willing to pay more, the same, or less for an electronic version? If you could only pick one format, would you pick paper or electronic? Thank you for your time. Sincerely, --Carmen Carmen I. Nitsche Staff Scientist Global Research Resources Nalco Chemical Company 1 Nalco Center Naperville, IL 60563-1198 cnitsche(a)nalco.com Phone: 630-305-2404 FAX: 630-305-2876 chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)

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HTML 4 and Chemistry
by Adam Hodgkin 28 May '98

28 May '98

Dear Netters in relation to Henry Rzepa's interesting post, I have more questions than answers. Why should we explicitly exclude XML and CML? Surely if they have a role to play it is a mistake to try and cover the same ground in HTML 4? Is HTML 4 coming from a different set of concerns than is served by XML? How many Chemistry Robots are there which can process Henry's SMILES string or the HTML 4 form of the viagra molecule? There is a difference between chemistry on the page (explicitly encoded in HTML) and chemistry available through the www (in databases which may be accessed through the www) -- a suitably designed robot could rely on the search capabilities of the databases it was pointed at. Should a chemistry robot trawl for chemically interesting HTML or offer multiple searches of www sites with publicly available databases? Or both? If both, there is likely to be a trade-off between consistency and completeness. Well it wont be the first time. Seems as though it would be a good idea if HTML evolves to support some explicit tagging of Molecular Structures (cf the provision of key terms for abstracts with conventional publications). But what about the differences/non-equivalence between different encoding systems? Does it matter? ChemSymphony does have ways of allowing the author/publisher to decide whether or not and how much presentational autonomy to give the user. In effect the publisher can give the user a control applet which allows the user to over-ride the default html. But there is a big difference between Java applets and programs which require installation of helper applications on the browser side. The publisher who writes HTML 4 is going to invoke his applets with different code (using the Object tags), but it is pretty clear how to use the 'object' tags in place of the applet tags and the users will then get the benefit of HTML4. See http://www.w3.org/TR/WD-html40-970708/appendix/changes.html Admitted, there may be more of a problem for the client who uses plug-ins or applications to read html. On the issue of 'backwards compatibility': the browsers which support HTML4 will have to be backwards compatible -- otherwise they will never win acceptance. We should avoid 'applet' and 'font' tags when we start producing HTML 4 but surely the browsers will support these 'deprecated' tags for a long time to come. Provided they can handle Java applets they should be able to handle Chemistry pages which use ChemSymphony. Users may not get all the benefits of HTML4 in the way that HTML4 provides it, but maybe they will get enought of what they need. Adam --- --- Adam Hodgkin | e-mail: adam(a)cherwell.com Chairman | Phone: +44 (0)1865 784810 Cherwell Scientific Publishing | Fax: +44 (0)1865 784801 Oxford OX4 4GA, UK | URL: http://www.cherwell.com --- --- chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)

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SDPD Round Robin news
by L.M.D.Cranswick＠dl.ac.uk 27 May '98

27 May '98

Present statistics for the Structure Determination by Powder Diffractometry Round Robin (SDPDRR). http://fluo.univ-lemans.fr:8001/SDPDRR/ - 28 data sets downloaded - One questionnaire returned. Deadline is June 30, 1998. All submissions welcome. Armel Le Bail (E-mail: armel(a)fluo.univ-lemans.fr) Lachlan Cranswick (E-mail: l.cranswick(a)dl.ac.uk) -- Lachlan M. D. Cranswick Collaborative Computational Project No 14 (CCP14) for Single Crystal and Powder Diffraction Daresbury Laboratory, Warrington, WA4 4AD U.K Tel: +44-1925-603703 Fax: +44-1925-603124 E-mail: l.cranswick(a)dl.ac.uk Ext: 3703 Room C14 CCP14 Webpage (Under heavy reconstruction): http://www.dl.ac.uk/CCP/CCP14/ chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)

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[Fwd: Chance to win $1000]
by Antonio Lopes 27 May '98

27 May '98

Dear netters Do you believe? A "free lunch" from GATES? It is not hard to try... Best from Antsnio

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Chemistry Webmasters 4 - call for posters
by Becky Allen 27 May '98

27 May '98

CHEMISTRY WEBMASTERS 4 - Teaching tools and the internet CALL FOR POSTERS Submission of posters (virtual or otherwise) are invited for Chemistry Webmasters 4, which is being organised by The Royal Society of Chemistry at the University of Bristol on Friday 3 July 1998. We wish to attract a wide variety of material from chemists using the Internet in their teaching. If you are interested in submitting a poster, please email its title, URL or abstract plus contact details to Becky Allen email: beckyallen(a)compuserve.com as soon as possible. Full details of the programme are at http://www.chemsoc.org/web4; those wishing to register for the event, which is once again FREE, should also email Becky Allen at beckyallen(a)compuserve.com chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)

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HTML 4 and Chemistry
by Shu-Kun Lin 27 May '98

27 May '98

Dear colleagues: I would like to invite you to contribute your ideas regarding "HTML 4 and Chemistry" for presentation at the upcoming electronic conference ecsoc-2 http://www.mdpi.org/ecsoc-2.htm Section E. Shu-Kun Lin --------------------------------------------------------- Dr. Shu-Kun Lin Molecular Diversity Preservation International (MDPI) Saengergasse 25, CH-4054 Basel, Switzerland http://www.mdpi.org/ MOLECULES http://www.mdpi.org/molecules/ ECSOC-2 http://www.mdpi.org/ecsoc-2.htm E-mail lin(a)mdpi.org Tel. +41 79 322 3379, Fax +41 61 302 8918 -------------------------------------------------------- chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)

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Re: Will HTML 4 break most chemistry web pages?
by thomas＠chem.uni-potsdam.de 26 May '98

26 May '98

Hallo, It is right, the netscape will not support HTML 4.0. I hope, that this support is installed with the next generation of netscape communicator Version 5). Microsoft's IE 4.0 has implemented some core feature s of HTML 4.0. For example, the <iframe>- Tag works excellent and give more power. The support for CSS Level 2 is also better as for netscape. Not so good is the implementation of the object - tag. This Tag will not work with IE 4.0, but I think in the next generation the problem is fixed. ************************************************************************ Dr. St. Thomas Universität Potsdam http://www.chem.uni-potsdam.de/~thomas ************************************************************************* Lächele und sei froh, denn es könnte viel schlimmer kommen! Ich lächelte und war froh, und siehe da, es kam schlimmer! -------------- Nach Paragraph 28 Abs. 3 Bundesdatenschutzgesetz widerspreche ich der Nutzung oder Übermittlung meiner Daten für Werbezwecke oder für die Markt- und Meinungsforschung.

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Will HTML 4 break most chemistry web pages?
by Rzepa, Henry 26 May '98

26 May '98

It is now quite common for chemists to author web pages in HTML (leaving aside whether its better to use XML/CML etc) using entries such as e.g. Chime: <embed src=viagra.mol width=300 height=200 name=viagra BGCOLOR="white" spinx=10 spinz=10 spiny=10 startspin=true options3d=specular display3D=ball&stick alt="O=S(C1=C([H])C([H])=C(OCC)C(C(N2[H])=NC(C(CCC)=NN3C)=C3C2=O)=C1[H])(N4CCN(C )CC4)=O"> (the alt field is my own invention, but as its ignored by e.g. Chime, it does no damage, and might conceivably help some poor chemical robot index my content!) OR e.g. ChemSymphony; <APPLET archive=chemsymphony.zip code=RenderBasic.class width=200 height=200 name=model> <PARAM name=model value=models/spiro.mol> <param name=displaytype value=1> <param name=atomtype value=0> <param name=hydrogen value=1> <param name=bonds value=0> <param name=atomsradius value=0.75> <param name=bgcolor value="#000000"> <param name=scale value=1.0> OR an external Viewer (e.g Weblab Viewer from MSI) <A HREF=viagra.mol >click here to see molecule</a> The trouble is that these three ways of displaying a molecule do not "cascade", ie the user has no simple way of deciding how THEY want the molecule displayed, and if the author wants to provide that, they would have to generate the HTML dynamically (even more complicated). HTML 4 strongly deprecates these mechanisms, and instead provides a nicely cascading process (If I have read the spec correctly) <object data="viagra.mol" width="300" height="200" id="viagra" title="Viagra" style="spinx: 10; display3D: ball&stick" type="chemical/x-mdl-molfile"> <OBJECT title="Sildenafil (Viagra), C22H30N6O4S" data="sildenafil.gif" type="image/gif" width="500" height="490"> </OBJECT> 5-[2-ethoxy-5-(4-methylpiperazin-1-ylsulfonyl)phenyl]-1-methyl-3-n-propyl-1,6-di hydro-7H-pyrazolo[4,3-d]pyrimidin-7-one </object> If the browser can internally resolve chemical/x-mdl-molfile, it will display the first object; if not then the image will appear, and if you have images switched off then the molecule name will appear. Certainly makes for far more robust behaviour, and provides an abundance of chemical information about the object for index/search engines to cogitate about. BUT It does mean that much of the chemical content of the Web will be unavailable to browsers supporting HTML 4, unless they also are backwards compatible. In this regard, I have no idea if Netscape 5+ will ever support HTML 4. Does anyone know what Microsoft's policy with Internet Explorer might be? 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. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)

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