- chemweb - imperial.ac.uk

Digital Signatures
by Rzepa, Henry 27 Apr '02

27 Apr '02

Slightly off beat this one, but you might be interested in the increasing use/acceptability of digital signatures to sign legal documents. Thus I have a) Digitally signed RSC copyright forms with submission of manuscripts, which has been accepted by them b) Digitally signed the Cambridge CSD renewal form, which has just been accepted by them c) I note that the NSF in the USA will REQUIRE all grant applications made to them from June of this year to be so signed d) Noted that the ACS do not so accept copyright transfers, insisting instead on a fax. The technicalities are simple. Firstly you acquire a digital certificate from Verisign (about $150 and install it into your email program or into eg the your profile of the Windows operating system. Using it you can sign email (using so called S/MIME email programs, which include Outlook, and the various Netscape messenger programs), Acrobat files or Word XP documents. These certificates are used for two quite distinct reasons a) To date stamp as authentic a document. This requires only your certificate, and shows any recipient that the document is yours, and has not been tampered with since it was created b) To encrypte a document. This requires not only your certificate, but the so called public portion of the recipients certificate, which you must first have been sent by them. This means only they can read the document. In most case, the document is both signed AND encrypted, and either can be done independent of the other. In future, one could also use one's certificate as an authentication for access to protected sites instead of a regular password. Thus entering a web site, the browser would probe for your certificate, and it it maches its own access control list, let you in. Certificates of course can be installed not just on computers, but into eg smart cards etc etc. I would be interested to hear if indeed their use has now become common (they have been around for more than 3 years) or whether indeed their use is still very rare indeed. -- Henry Rzepa. +44 (0870) 132 3747 (eFax) +44 0778 6268 220 (Mobile) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College, London, SW7 2AY, UK. 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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Case sensitivity
by Steven Abbott 22 Apr '02

22 Apr '02

It's always astonished me that anything be it C, Java, or Web addresses should be case sensitive. That anyone should want the 'luxury' of having two variables or sites or folders called 'ThisExampl'e and 'thisexample' has always seemed to me to be bizarre and a guarantee of trouble ahead. In the early stone age it was easier for a compiler (etc.) to be case insensitive but as we all have vast excesses of processing power for parsing stuff, this excuse no longer holds. I was pleased to read Wendy's New Scientist article and Henry's comment that all this has been lurking around for ages. It's time that the CamPaign for ErradiCation of cAse sEnsitivitY got under way. Steve Abbott 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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Sourceforge, XML, CML and others
by Rzepa, Henry 18 Apr '02

18 Apr '02

I am sure many of you will be familiar with the phenomenon that is sourceforge. Some 37,000 openSource projects are registered there (!), and it is where information about them, software downloads etc can be found. Its difficult to be certain how many chemical-related projects are on the site (since "chemistry" or "molecular science" is not one of the categories they are sorted by; bio-informatics comes closest) but we think around 10 or so ar active. We have just started up one such site for XML and CML information and tools. Do please visit at http://cml.sourceforge.net/ (although we are still building many of the features). These will include eg XML libraries, including XSD (schemas), XSLT (filters and transformations) and various Java-based tools. If you wish to learn, ask FAQs, or make contributions, do please consider joining the mailing list at the site. -- Henry Rzepa. +44 (0870) 132 3747 (eFax) +44 0778 6268 220 (Mobile) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College, London, SW7 2AY, UK. 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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Buy ArgusLab and get a second license free
by Mark Thompson 16 Apr '02

16 Apr '02

BUY ONE ARGUSLAB 3.0 LICENSE AND GET A SECOND LICENSE FREE. For a limited time, we are offering 2-for-1 on ArgusLab single-purchase licenses. If you purchase an ArgusLab license, you will get a second license for free. Split the cost with a friend or colleague. For academic licenses, this means you now get 2 licenses for only $79.95 ArgusLab can be downloaded from http://www.planaria-software.com/download_3_0.htm Visit us at Planaria Software to learn more about ArgusLab. http://www.planaria-software.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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Release of Jmol Applet 2
by E.L. Willighagen 15 Apr '02

15 Apr '02

Dear colleagues, we are glad to announce the release of Jmol Applet 2 for viewing chemical animations on webpages. It supports these input formats: Gaussian9X, MDL molfile, CML, PDB, XYZ, ACES II, ADF, Dalton, GAMESS, Jaguar, and MOPAC. The applet has been tested in MS InternetExplorer 5.x, Netscape Navigator 4.5/4.7x, Mozilla/Galeon and Konqueror (KDE 2.2 and 3.0). More information can be found at http://jmol.sf.net/. regards, Egon Willighagen 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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Final release of VEGA1.4.0
by Giulio Vistoli 15 Apr '02

15 Apr '02

Dear colleagues, we are glad to announce the new final release of VEGA1.4.0 (http://users.unimi.it/~ddl) our well known program to convert, manage and visualize of 3D structures for several platforms (Win32, Linux, Irix, AmigaOs). New features of VEGA1.4.0: - MDL Mol file loader. - Improved IFF file format (new chunks). - Extended command line interface for language scripting. - Return code handler. - Fix: Biosym archive 3 (.car) loader now reads the element column. - Fix: mol2 hack for Insight generated mol2 files. - Fix: mol2 saver. - Manual: added Frequently Asked Question (FAQ) page. - Win32: atom picking and interactive measures/selection (atom, distance, angle, torsion and angle betwee two planes). - Win32: Dhrystone Test plugin (tstdhry.dll) to test the CPU performance. - Win32: joystick control. - Win32: color requester. - Win32: customizable atom selection. - Win32: some new commands can be send trough the standard window port, in order to interpret complex command sequences. - Win32: now the trajectory animation is compatible with the new refresh mode. - Win32: the selection tool for trajectory analysis supports the atom picking. - Win32: the trajectory files can be opened directly with File -> Open menu item. - Win32: dynamic loading for devil.dll, fmod.dll, ilu.dll, ilut.dll, libbz2.dll and zlib32.dll. - Win32: VEGA select the dll with the optimizations for the installed CPU. - Win32: new menu items: Help -> Last error and Display -> Select -> None. - Win32: new demo music by Chris Hülsbeck. Moreover the most important feature of this release is the new plugin architecture to expand the VEGA capabilities so that everyone can collaborate to VEGA project by writing your source code in order to add custom applications to VEGA platform. If you create a plugin, please communicate us in order to point out your products in our website The VEGA team Alessandro Pedretti & Giulio Vistoli 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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Molecule oft he Month - April
by Paul May 01 Apr '02

01 Apr '02

Hi, April's Molecule of the Month is beta-Carotene, the pigment that provides the yellow/orange colour in leaves, carrots and margarine. It has been written by Martha Evens, who is an undergraduate student at Bristol, as part of her web project in preparation for the Exemplarchem competition last year. Versions are available for HTML-only and Chime. http://www.bris.ac.uk/Depts/Chemistry/MOTM/motm.htm#apr2002 Regards, ----------------------------------------------------------------------------- Dr Paul May, School of Chemistry, University of Bristol, UK tel: +44 (0)117 928-9927 fax: +44 (0)117 925-1295 <mailto:paul.may@bris.ac.uk> Mobile: 07811371539 Home URL: <http://www.bris.ac.uk/Depts/Chemistry/staff/pwm.htm> Molecule of the Month: <http://www.bristol.ac.uk/Depts/Chemistry/MOTM/motm.htm> "Cyanide is so poisonous that one drop of it on a dog's tongue will kill the strongest man" ------------------------------------------------------------------------------ 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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Use of SVG in Chemistry and xml2svg Transformations
by Rzepa, Henry 07 Mar '02

07 Mar '02

Some discussion on another list (the SVG developers) has prompted me (and others) to summarise progress in the "XML" solution to handling and in particular displaying of chemical content. Unlike HTML, which is predominantly a display and text-based format where chemical content has to be included via "legacy" formats such as eg Molfiles, or via images, XML is designed for essentially complete semantic markup of content. Because no browser could easily handle such a broad scope, the concept is that XML documents will be displayed by appropriate transformation of the content into a small set of generic display formats which the browser CAN handle. The pre-eminent XML-based graphical format is SVG (scalable vector graphics) and hence the issue now resolves to how to transform any particular XML component to eg SVG, generically referred to here as xml2svg (although this does not preclude transformation to older non-XML formats such as Molfile and hence use of eg Chime). Listed below are some useful sites which cover issues of handling XML, and converting it to SVG 1. http://www.adobe.com/svg/demos/main.html which has an XSLT-based cml2svg converter 2. http://www.xml-cml.org/jumbo3/jumbo3-JS/ being a JavaScript based dynamic cml2svg converter. The http://www.xml-cml.org/ site has much other information about XML and CML. Also there you will find XACE (eXtensible annotating chemical editor), based on JME, but with "XML" wrappers. Work on XACE Mk II is well under way. 3. The cml2xbl2svg concept, originally part of Croczilla (http://www.croczilla.com/svg/) now part of one of the builds of Mozilla 0.9.8, and expected to be a permanent part of the Mozilla 1.0 release. 4. http://www.schemasoft.com/MathML/ which is a mathml2svg converter based on XSLT 5. See http://www.web3d.org/TaskGroups/source/xj3d.html being an XML version of VRML, and for which a viewer is now available. ( http://www.adobe.com/svg/demos/main.html also does 3D rotations) 6. http://www.ch.ic.ac.uk/rzepa/xml/ where the process of converting cml2svg, and in general then on to PDF using FOP, is described A XSLT stylesheet for the conversion is at http://www.ch.ic.ac.uk/rzepa/xml/fop.html The above article was published as G. V. Gkoutos, P. Murray-Rust, H. S. Rzepa, and M. Wright, Internet J. Chemistry, 2001, article 13. 7. Jiri.Jirat has written a custom CML2SVG converter (XSLT), the results can be viewed at: http://zvon.org/xxl/CML1.0/Output/index.html 8. Marvin outputs SVG, and reads, inter alia, CML http://www.chemaxon.com/marvin/ There is no doubt much more out there. This collection also illustrates one very powerful aspect of XML, which is the re-usability of various generic tools in a chemical context, a phenomenon that is largely new (previously the chemical community had to pretty much write its own tools!). If anyone in their travels comes across other interesting examples of xml2xml (in the generic sense) tools, and interesting examples say from the bio-informatics and other physical sciences, do please let this list know. -- Henry Rzepa. +44 (0870) 132 3747 (eFax) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College, London, SW7 2AY, UK. 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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Molecule of the Month - March
by Paul May 28 Feb '02

28 Feb '02

Hi, March's Molecule of the Month is RU-486, also known as Mifepristone, which is better known as the 'morning after pill'. it has been written by Fyaz Ismail, a lecturer in the Dept of Pharmacy and Chemistry, Liverpool John Moores University. Molecule of the Month: http://www.bristol.ac.uk/Depts/Chemistry/MOTM/motm.htm Regards, ----------------------------------------------------------------------------- Dr Paul May, School of Chemistry, University of Bristol, UK tel: +44 (0)117 928-9927 fax: +44 (0)117 925-1295 <mailto:paul.may@bris.ac.uk> Mobile: 07811371539 Home URL: <http://www.bris.ac.uk/Depts/Chemistry/staff/pwm.htm> Molecule of the Month: <http://www.bristol.ac.uk/Depts/Chemistry/MOTM/motm.htm> "Cyanide is so poisonous that one drop of it on a dog's tongue will kill the strongest man" ------------------------------------------------------------------------------ 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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TGA info/data concerning CuSO4.5H2O
by Mike Cole 25 Feb '02

25 Feb '02

Hi there, Does anyone know of a good source of information concerning the structural characteristics of CuSO4.5H2O (especially when linked to Thermal Gravimetric Analysis). Thanks Mike Dr. Michael Cole Department of Chemistry & Materials Manchester Metropolitan University Manchester M1 5GD Tel. 0161 247 1427 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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