December 2001 - chemweb - imperial.ac.uk

Trivial it ain't! More on Quicktime and IE6
by Rzepa, Henry 26 Jun '02

26 Jun '02

This is the official solution for allow plugins (in this case Quicktime) to again be played on MS IE 5.5 SP2 and IE6 XP. One presumes a similar solution will be required for Chime and other Chemical plugins. The example below suggests that an ActiveX control is downloaded from the Internet. I presume a stand alone solution suitable for eg CDROMs will also materialise. Note how the onus is on the content developer to CHANGE their HTML page to make it work. I wonder how many will. (Thanks to Jonathan Brecher for the information!) >Date: Tue, 21 Aug 2001 15:11:58 -0700 (PDT) >Subject: Important News For Quicktime Developers >From: Apple Developer Connection <noreply(a)wwdr.apple.com> >Reply-To: Apple Developer Connection <noreply(a)wwdr.apple.com> >To: undisclosed-recipients:; > > >Windows Internet Explorer 5.5 SP2 and 6.0 with QuickTime >IMPORTANT INFORMATION FOR WEB DEVELOPERS & WEBMASTERS > >Microsoft Internet Explorer for Windows, versions 5.5 SP2 and 6.0 >(soon to be released) no longer support Netscape-style plug-ins, >such as the plug-in installed as part of QuickTime 5.0.2 and earlier >versions. Consequently, Windows customers using these versions of >Explorer who visit your site may be unable to view QuickTime content >in the browser. To mitigate this problem and to ensure a positive >experience for your Web site visitors, you should add to your site >the HTML code that makes available the new ActiveX control for >QuickTime, as described below. > >NOTE: THIS ISSUE AFFECTS ONLY USERS OF INTERNET EXPLORER ON WINDOWS. > >BACKGROUND >QuickTime uses a plug-in mechanism to display movies from your Web >page in the user's browser. Before, you would use an EMBED element >alone to display QuickTime content within the browser, much like in >the example below: > ><EMBED src="sample.mov" width="160" height="144" autoplay="true" >CONTROLLER="false" >PLUGINSPAGE="http://www.apple.com/quicktime/download/"> </EMBED> > >For this mechanism to work, the user must have the QuickTime plug-in >installed on his or her system. If the appropriate QuickTime plug-in >is not installed, when your HTML page with QuickTime content is >loaded into the user's browser, the movie is not visible. Instead, >the browser replaces it with a "broken plug-in icon" and attempts to >assist the user in obtaining the required software. An unfortunate >side effect of this approach is that the user is directed away from >your site and is distracted by the installation process. > >THE ISSUE >Until recently, the plug-in installed as part of QuickTime worked >for both Netscape browsers and Microsoft Internet Explorer on both >Windows and Mac OS. Now Windows users who try to play a QuickTime >movie in Internet Explorer version 5.5 SP2 or later will encounter >the "broken plug-in icon" until they install the new QuickTime >ActiveX control from Apple in addition to the QuickTime plug-in. >Users of other browsers on either Windows or Mac OS are >unaffected--they can continue to use the plug-in installed with >QuickTime and do not need to get the new QuickTime ActiveX control. > >Once users have the new ActiveX control installed, they are also >unaffected; they can also view existing pages. > >THE SOLUTION >When authoring web pages, you can easily prevent this problem by >authoring your HTML to check that the required ActiveX control is >installed wherever you have QuickTime content embedded. This HTML >change will result in web pages compatible with Netscape and >Internet Explorer browsers on both Mac and Windows systems (see >below for more information). > >The required code consists of an HTML OBJECT element with an >enclosed EMBED element as in the following example: > ><OBJECT CLASSID="clsid:02BF25D5-8C17-4B23-BC80-D3488ABDDC6B" >width="160" height="144" >CODEBASE="http://www.apple.com/qtactivex/qtplugin.cab"> ><param name="src" value="sample.mov"> ><param name="autoplay" value="true"> ><param name="controller" value="false"> ><embed src="sample.mov" width="160" height="144" autoplay="true" >CONTROLLER="false" >PLUGINSPAGE="http://www.apple.com/quicktime/download/"></EMBED> ></OBJECT> > >CLASSID must always equal: >clsid:02BF25D5-8C17-4B23-BC80-D3488ABDDC6B >CODEBASE must always equal: >http://www.apple.com/qtactivex/qtplugin.cab >PLUGINSPAGE must always equal: >http://www.apple.com/quicktime/download/ > >The other attributes should be customized to your web page. You need >to substitute "sample.mov" (in both SRC attribute elements) with the >URL of the actual movie to be played. You should also change the >HEIGHT and WIDTH parameters to match the height and width of the >movie (in pixels). > >If you already have EMBED elements for the QuickTime plug-in on the >relevant pages, you need to enclose each of them in an OBJECT >element with CLASSID and CODEBASE parameter values as shown above >and with SRC and other parameter values to match those in your >existing EMBED element. The OBJECT element can use any EMBED >attributes QuickTime understands. Visit >http://www.apple.com/quicktime/authoring/embed.html for more >information. > >For existing web pages, it may be sufficient to add such an OBJECT >element to the "front door" page of your site. Once the OBJECT >element on the "front door" page has caused the user to install the >ActiveX control, all subsequent pages with the original EMBED >elements will work properly. In cases where you cannot be certain >that the "front door" page is always visited, then all your pages >should be revised to use these OBJECT elements. > >HOW IT WORKS >The OBJECT element is used by Internet Explorer on Windows >9x/NT/2000/XP platforms and by other browsers that support the >QuickTime ActiveX control. The enclosed EMBED element is used by >Netscape browsers, Internet Explorer for the Mac, and other browsers >that support the "Netscape style" QuickTime plug-in. Browsers that >understand the OBJECT element ignore the EMBED element; those that >don't understand the OBJECT element use the EMBED element. > >Within the OBJECT element, the CLASSID parameter uniquely identifies >which ActiveX control to use. A CLASSID parameter with the value >"clsid:02BF25D5-8C17-4B23-BC80-D3488ABDDC6B" tells Internet Explorer >to use the QuickTime ActiveX control. (You must use exactly this >value; it is the only value that identifies the QuickTime ActiveX >control). If the user does not already have the ActiveX control >installed on his or her system, the CODEBASE parameter tells the >browser where to find it for downloading. Internet Explorer will >automatically offer to download and install the ActiveX control for >the user, after which the movie can be played without restarting the >browser, or, if QuickTime is not already installed, will prompt the >user to download and install QuickTime. You must always use >"http://www.apple.com/qtactivex/qtplugin.cab" for the CODEBASE URL. >This URL will always have the latest version of the QuickTime >ActiveX control. >Because a browser will use either the OBJECT element or the EMBED >element, but not both, most of the element attributes must be >included in each. Note that in the example above the EMBED element >has autoplay="true" and the OBJECT element has <param >name="autoplay" value="true">, so the movie will begin to play >automatically whether it is loaded with the QuickTime ActiveX >control or the QuickTime plug-in. The only attributes that should >not be duplicated are CLASSID, CODEBASE, and PLUGINSPAGE. CLASSID >and CODEBASE are specific to the OBJECT element. PLUGINSPAGE is >specific to the EMBED element. > >Although Windows Internet Explorer 5.5 SP2 and 6.0 will no longer >use the QuickTime plug-in, once the QuickTime ActiveX control has >been installed on a user's system, these versions of Internet >Explorer will use the installed ActiveX control to satisfy a >properly coded EMBED element. > >ADDITIONAL READING > >For more information on the OBJECT element, see: > * The W3C Web site at > http://www.w3.org/TR/REC-html40/struct/objects.html#edef-OBJECT > >For more information on HTML in general, see: > * HTML & XHTML: The Definitive Guide 4th Edition, > by Chuck Musciano & Bill Kennedy, published by O'Reilly. > * Dynamic HTML: The Definitive Reference, by Danny Goodman, > published by O'Reilly. > >For more information about QuickTime on Web sites, see: >QuickTime for the Web, published by Morgan Kaufmann Publishers. ><http://developer.apple.com/techpubs/quicktime/qtdevdocs/QT4WebPage/QT4WebBo…. >htm> > >For more information on Internet development, see: >http://developer.apple.com/internet/ > >Disclaimer: >IMPORTANT: This Apple software is supplied to you by Apple >Computer, Inc. ("Apple") in consideration of your agreement to the >following terms, and your use, installation, modification or >redistribution of this Apple software constitutes acceptance of >these terms. If you do not agree with these terms, please do not >use, install, modify or redistribute this Apple software. >In consideration of your agreement to abide by the following terms, >and subject to these terms, Apple grants you a personal, >non-exclusive license, under Apple's copyrights in this original >Apple software (the "Apple Software"), to use, reproduce, modify and >redistribute the Apple Software, with or without modifications, in >source and/or binary forms; provided that if you redistribute the >Apple Software in its entirety and without modifications, you must >retain this notice and the following text and disclaimers in all >such redistributions of the Apple Software. Neither the name, >trademarks, service marks or logos of Apple Computer, Inc. may be >used to endorse or promote products derived from the Apple Software >without specific prior written permission from Apple. Except as >expressly stated in this notice, no other rights or licenses, >express or implied, are granted by Apple herein, including but not >limited to any patent rights that may be infringed by your >derivative works or by other works in which the Apple Software may >be incorporated. >The Apple Software is provided by Apple on an "AS IS" basis. >APPLE MAKES NO WARRANTIES, EXPRESS OR IMPLIED, INCLUDING WITHOUT >LIMITATION THE IMPLIED WARRANTIES OF NON-INFRINGEMENT, >MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, REGARDING THE >APPLE SOFTWARE OR ITS USE AND OPERATION ALONE OR IN COMBINATION WITH >YOUR PRODUCTS. >IN NO EVENT SHALL APPLE BE LIABLE FOR ANY SPECIAL, INDIRECT, >INCIDENTAL OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, >PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR >PROFITS; OR BUSINESS INTERRUPTION) ARISING IN ANY WAY OUT OF THE >USE, REPRODUCTION, MODIFICATION AND/OR DISTRIBUTION OF THE APPLE >SOFTWARE, HOWEVER CAUSED AND WHETHER UNDER THEORY OF CONTRACT, TORT >(INCLUDING NEGLIGENCE), STRICT LIABILITY OR OTHERWISE, EVEN IF APPLE >HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. > >---------------------------------------- >--------- ABOUT THIS EMAIL -------- >---------------------------------------- >You are receiving this email because you have agreed to receive >Technical or Marketing information in your Apple Developer >Connection (ADC) Profile. > >If you would prefer not to receive special notices, or the weekly >Apple Developer Connection News in the future, please log on to >http://connect.apple.com, click the "Update Profile" link, and >uncheck the appropriate ADC News box. > >Questions about your ADC Membership: >http://developer.apple.com/contact/programs.html >---------------------------------------- -- Henry Rzepa. +44 (0)20 7594 5774 (Office) +44 (0870) 132-3747 (eFax) Dept. Chemistry, Imperial College, London, SW7 2AY, UK. 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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20 years of history through Usenet
by Ioannis Kerkines 18 Dec '01

18 Dec '01

Not exactly chemistry-related, but still very very interesting, Google has put down a very nice page with memorable Usenet postings since 1981, e.g. the postings of Tim Berners-Lee for WWW, Marc Andreesen for Mosaic and Netscape, Linus Torvalds for Linux, etc. http://www.google.com/googlegroups/archive_announce_20.html Merry Christmas Ioannis 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: Help: FDAT file format
by Michael Engel 16 Dec '01

16 Dec '01

I got the answer already. Thank you very much. No more search is necessary. ----- Original Message ----- > Sorry for crossposting. > If somebody is just now online (ca. 4:00 U.T - 11:00 U.T.) and could find me > the FDAT file documentation of the Cambridge Structure Database > (http://www.ccdc.cam.ac.uk/) . > I am cut off the WWW today and would need the documentation today > Please reply off the list. > Thank you in advance. > Michael K. Engel > mkengel(a)web.de 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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Post doctoral position
by Giulio Vistoli 14 Dec '01

14 Dec '01

Dear CCLers, We have an opening for a post-doctoral position (12 months) in the field of computational and experimental drug design. The position is at the Université de Lausanne, Institut de Chimie Thérapeutique (Prof. Bernard Testa and Dr. Pierre-Alain Carrupt) and will involve collaborative projects with the computational group of Dr. Giulio Vistoli (Dip. di Chimica Farmaceutica, Università di Milano). Keywords include: molecular fields, 3D-QSAR descriptors, physicochemical profiling by experimental and computational methods. The following skills are required: - PhD in pharmaceutical sciences or chemistry; - Very good background in drug design, particular molecular modelling and/or experimental physicochemical techniques; - Knowledge of the most popular molecular modelling packages. Interested persons should send a detailed CV (no attachement) to <Bernard.Testa(a)ict.unil.ch>, with copy to <giulio.vistoli(a)unimi.it> Best regards 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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mol2 and pdb files
by Michael Engel 08 Dec '01

08 Dec '01

Hello, perhaps someone knows the answer or can direct me to a group where I could ask. Thank you in advance. Problem: How can I fix the direction of view of a molecule in a *.mol2 file or in a *.pdb file. Main Problem: I have a lot of structures for the Macintosh crystallographic software MolView. Unfortunately, the printout is not good. Now, I would like to transfer them to the Cambridge Database software Mercury from which a much better printout is possible. However, after transfer, they are shown in a different view than originally saved. Re-reading the file with MolView didn't change the viewing direction. Thanks for any hint. Michael 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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organic spectroscopic unknowns simulation
by Adrian Blackman 04 Dec '01

04 Dec '01

I wish to announce the release of v3 of WinTorg, a Windows PC simulation of spectroscopic organic analysis. Features include: * 100 unknowns (4 spectra each) with a site licence for US$200 * suitable for early university/college organic chemistry students * the unknowns can be identified by spectroscopy alone (or in combination with chemical tests etc. if required) * easy to use (e.g. can be used just with a mouse) * extensive help is available including a worked example and the main spectroscopic assignments are available for each unknown once it has been identified * student progress is reported * can be customised by the instructor (13 controllable features) For more information and free demo version (3 unknowns only) visit http://www.chem.utas.edu.au/staff/blackman/shareware/torganal.htm Dr Adrian Blackman School of Chemistry University of Tasmania Australia -- ____________________________________________________________________ Dr Adrian Blackman Phone: (03) 6226 2183 Int'l 61 3 6226 2183 School of Chemistry Fax: (03) 6226 2858 Int'l 61 3 6226 2858 University of Tasmania PO Box 252-75 Hobart Tasmania 7001 Australia Email: Adrian.Blackman(a)utas.edu.au WWW: http://www.chem.utas.edu.au/staff/blackman/ajb.htm ____________________________________________________________________ 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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Chemical Informtics faculty position at Indiana University
by Wiggins, Gary D. 04 Dec '01

04 Dec '01

Position Title: Tenure-Track Position in Informatics and Chemistry Position Description: Indiana University-Bloomington invites applications for a tenure-track position in chemical informatics at the rank of Assistant Professor beginning August 15, 2002. This will be a joint position between the Department of Chemistry and the School of Informatics. The candidate should be an expert in the area of chemical informatics, with a demonstrated interest in the related areas of bioinformatics and proteomics. The candidate will teach a variety of undergraduate and graduate chemical informatics courses in Chemistry and in Informatics. The candidate will also develop a focus in chemical informatics within an existing discipline in chemistry with a view toward joint research projects. Knowledge and skill in various areas applicable to chemical informatics, such as molecular modeling, chemical structure search and representation systems, design of chemical information systems, chemical database mining, etc., are expected. There is also the possibility in the School of Informatics of teaching in such areas as the logical and mathematical foundations of information, distributed information and knowledge systems, and human-computer interaction. Successful candidates will be expected to develop or to have developed a vigorous, independent research program. Preference will be given to candidates who have shown or show promise of innovative teaching and curriculum development. A Ph.D. or equivalent is required and post-doctoral experience is preferred. The Department of Chemistry (<http://www.chem.indiana.edu/>), a part of the College of Arts and Sciences, has consistently been ranked among the top twenty research universities for chemistry. The School of Informatics (<http://www.informatics.indiana.edu/>), Indiana University's first new school in 28 years, is one of the very first schools in the country dedicated exclusively to informatics, understood as the application of technology to problems in various disciplines. On the Bloomington campus it offers a B.S. degree in Informatics and M.S. degrees in bioinformatics, chemical informatics, and human computer interaction. Applicants should send a letter of application outlining their qualifications, a curriculum vitae, and a list of three references. A sample of written work and evidence of quality teaching are welcome additions. Review of applications will begin January 15, 2002. Direct questions and application materials to Associate Dean Christine Ogan, School of Informatics, 339 Sycamore Hall, 1033 E. Third Street, Indiana University, Bloomington, IN 47405. Indiana University is an Equal Opportunity/Affirmative Action Employer. We strongly encourage applications from women and minority candidates as well as from two-career couples. 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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ArgusLab version 3 (beta) is available
by Mark Thompson 02 Dec '01

02 Dec '01

************************************************************* ArgusLab Molecular Modeling Program version 3.0 beta release is now available (version 2.0 is still freely distributed from our website) ************************************************************* Featuring extensive support for rendering surfaces. Featuring an incredible 3D interactive molecule builder Build and optimize structures for the entire periodic table. Featuring computational methods for spectroscopy, geometry optimizations, energies, and properties Please visit http://www.planaria-software.com to download a copy. See some screenshots at http://www.planaria-software.com/gallery.htm (If you like the program, please tell a friend) New Features in 3.0 -------------------- Support for surfaces: simple, difference, mapped, and mapped difference Easy-to-use Surface construction and editing tool Render surfaces in opaque, translucent, mesh, and dot Generate grid files for surfaces: orbitals, electron density,electrostatic potential, and spin density. Import Gaussian cube files for surfaces. Read molecule structure from Gaussian .log files Clipping plane for surfaces. Automatic assignment of atomic hybridization. Automatic assignment of force field atom type. Automatic ring finder and aromatic ring display. Improved interface to the SCRF solvent model. Printing. Charge equilibration charges for the UFF force field. Extensive support of Undo/Redo for all user-input to the graphics window. Space filling rendermode added. Apply rendermode options to subsets of atoms and bonds. Apply automatic hybrid, ffatom type, and ring finding to subsets of atoms Apply geometry optimization updates to subsets of atoms. Set background color Lots of bug fixes from ArgusLab 2.0 Greatly enhance HTML help system with tutorials. 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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