August 2001 - chemweb - imperial.ac.uk

The visualisation of chemical processes for electronic publishing
by Paul May 16 Aug '01

16 Aug '01

Hi, I'm not normally one to blow my own trumpet, but I thought publicising this might be of use to some of you trying to write interactive web-based chemistry reports. It's a paper in PhysChemComm (the RSC on-line Journal) that I've written to tell you the basics of how to jazz up chemical reports or presentations using Chime, VRML, animated gifs, etc, etc. To get the link, your organisation needs to have access to the RSC online Journals. http://hotdog.rsc.org/ej/qu/2001/B103982M/index.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> ICQ: 107669629 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> ------------------------------------------------------------------------------ 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: Chemical formulas as gifs
by Jerzy Krol-Bogomilski 13 Aug '01

13 Aug '01

Hi, I thank to all who responded. You have helped me very much! Now I am able to save organic chemical formulas as GIFs. Regards, Jerzy. Jerzy Kr�l-Bogomilski Ph.D. http://www.geocities.com/jerzor jerzor(a)yahoo.com __________________________________________________ Do You Yahoo!? Send instant messages & get email alerts with Yahoo! Messenger. http://im.yahoo.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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RE: IE and "plugins": correction
by Bachrach, Steven 13 Aug '01

13 Aug '01

I apologize for jumping in here late but I was on vacation this past week WITHOUT my laptop (I recommend this to all!) In any event, I want to clarify one item that Henry mentioned and that is concerning the Microsoft Antitrust lawsuit. Microsoft has not WON this suit, in fact they LOST - the appeals court has simply thrown out the penalty (which was to break up microsoft into two pieces). In fact, Microsoft just lost an appeal to have the original verdict thrown out. So the status is now what will be the penalty - likely not to be busting up Microsoft! But this whole plug-in issue is VERY disconcerning. It would be nice to hear something useful from MDL on the matter! Open source chemistry is of course a very real option, but without the browser framework this becomes a serious development problem. However, the GCC compiler is a major development project so perhaps we can encourage a project to develop an open source browser that supports XML, plugins, java, javascript? Steve -- Steven Bachrach ph: (210)999-7379 Department of Chemistry fax: (210)999-7569 Trinity University 715 Stadium Drive San Antonio, TX 78212 steven.bachrach(a)trinity.edu > -----Original Message----- > From: Rzepa, Henry [mailto:h.rzepa@ic.ac.uk] > Sent: Monday, August 06, 2001 10:57 AM > To: chemweb(a)ic.ac.uk > Subject: IE and "plugins": correction > > > Correction to my earlier posting. I had noted that Adobe "plugins' > do work with IE 5.5 SP2 and IE 6, XP. This is because they are not > plugins but pure ActiveX controls (this from a developer who > should know!) > > So I suppose the next question is whether the "chemically important" > plugins will be upgraded by their developers to ActiveX controls. > MDL presumably will do so, but how many others are out there, > and will they get upgraded? > > Netscape of course will continue to work, but then again the cost > of producing one "plugin" and one "activeX" control for Windows > might mean some developers will chose one or the other but perhaps not > both. With less than 30% of the use and still decreasing, > this might mean the final nail in the coffin > for Netscape. A similar issue confronts "non" Windows platforms. > > It really is difficult to avoid the conclusion that having won its > anti-trust case in the courts in the USA, Microsoft is going to get > even more monopolistic. > -- > > 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) > 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: IE and "plugins": correction
by Miller, Mitch 06 Aug '01

06 Aug '01

Hello, Any idea about where the Java plug-in stands in this? This plug-in was to be the only way to run Java applets in I.E. as there won't native support for Java long-term in I.E. Mitch -----Original Message----- From: Rzepa, Henry [mailto:h.rzepa@ic.ac.uk] Sent: Monday, August 06, 2001 9:57 AM To: chemweb(a)ic.ac.uk Subject: IE and "plugins": correction Correction to my earlier posting. I had noted that Adobe "plugins' do work with IE 5.5 SP2 and IE 6, XP. This is because they are not plugins but pure ActiveX controls (this from a developer who should know!) So I suppose the next question is whether the "chemically important" plugins will be upgraded by their developers to ActiveX controls. MDL presumably will do so, but how many others are out there, and will they get upgraded? Netscape of course will continue to work, but then again the cost of producing one "plugin" and one "activeX" control for Windows might mean some developers will chose one or the other but perhaps not both. With less than 30% of the use and still decreasing, this might mean the final nail in the coffin for Netscape. A similar issue confronts "non" Windows platforms. It really is difficult to avoid the conclusion that having won its anti-trust case in the courts in the USA, Microsoft is going to get even more monopolistic. -- 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) 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: IE and "plugins"
by Anthony Lewis 06 Aug '01

06 Aug '01

This discussion is interesting and it's good to learn that Chime will continue to work with IE. However, one of the best features of Chime is the ability to add interactivity via scripts and I am lead to believe that this is not fully supported by IE and, therefore, that Netscape is the "better" choice. I have to admit to not really understanding why the Chime/IE combination does not work effectively and I'm wondering if this will continue to be so. Can anyone comment on this and are there any examples of where Chime works with one browser and not another? Many thanks, C. Anthony Lewis Petroleum & Environmental Geochemistry Group, Department of Environmental Sciences, University of Plymouth, Plymouth, Devon PL4 8AA, U.K. tel: +44 (0)1752 233000 ext. 2988 FAX: +44 (0)1752 233035 e-mail: calewis(a)plymouth.ac.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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IE and "plugins": correction
by Rzepa, Henry 06 Aug '01

06 Aug '01

Correction to my earlier posting. I had noted that Adobe "plugins' do work with IE 5.5 SP2 and IE 6, XP. This is because they are not plugins but pure ActiveX controls (this from a developer who should know!) So I suppose the next question is whether the "chemically important" plugins will be upgraded by their developers to ActiveX controls. MDL presumably will do so, but how many others are out there, and will they get upgraded? Netscape of course will continue to work, but then again the cost of producing one "plugin" and one "activeX" control for Windows might mean some developers will chose one or the other but perhaps not both. With less than 30% of the use and still decreasing, this might mean the final nail in the coffin for Netscape. A similar issue confronts "non" Windows platforms. It really is difficult to avoid the conclusion that having won its anti-trust case in the courts in the USA, Microsoft is going to get even more monopolistic. -- 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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MS Internet explorer and plugins
by Rzepa, Henry 06 Aug '01

06 Aug '01

More on the issue of plugins not working with the latest releases of IE. We tested the following plugins using IE6 SP1 (released about 2 months ago) and IE6 XP version (released about 2 weeks ago. This was all tested on a Windows 2000 system with all the latest service packs installed, and the latest versions of all the plugins. . IE 6 SP1 IE6 XP 1. Adobe Acrobat 5 works works 2. Adobe SVG 2 works works 3. Chime 2 SP2 works no 4. Apple Quicktime 5 works no 5. NPQuick (3DMF viewer) works no So it seems that only some plugins stop working, ie the full API for plugins is mostly still there. I suspect that some vital new component requiring eg ActiveX has to be built into the plugin to work. Adobe have clearly managed it (we only have V 5 of the reader. I would be interested if someone could report whether V 4 works or does not work with IE6 XP) The final release of IE6 is scheduled for August 15, and we presume it will eventually replace IE 5.0 and 5.5. Because most people will not go to V 6 immediately, one might expect a slate of "my plugins dont work" panics over the next year or so. Its not obvious what the best long term strategy is. Microsoft may well be bent on fully migrating to ActiveX, and its not obvious whether all one's favourite plugins will follow them. Java is more standard, but again its performance is not up to the levels of dedicated plugin code, and again what are Microsoft's plans with their rival "java lookalike". Netscape 6.1 has an interesting strategy of usng XBL, but XBL is merely a proposal to the W3C, and hardly yet standard. Microsoft show no signs of adopting it. -- 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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Chime and Internet Explorer
by Michael Engel 04 Aug '01

04 Aug '01

Hello, probably most of you got this message too. Best regards Michael -----Original Message----- From: ChimeBroadcaster(a)mdli.com [mailto:ChimeBroadcaster@mdli.com] Sent: Saturday, August 04, 2001 4:42 AM Subject: August 3, 2001 Dear Chime and Chime Pro users: MDL has learned that a new service pack of the Microsoft Internet Explorer browser (5.5 SP2) has been released today without support for the Netscape plug-in interface used by Chime and Chime Pro. Our understanding is that future versions of Microsoft Internet Explorer will also lack this interface. This would mean that the Chime and Chime Pro plug-ins would not be supported on these new versions of Microsoft Internet Explorer (including 6.0) until further notice. This issue does not affect the Netscape Communicator 4.7 browser. MDL is working closely with Microsoft to evaluate alternatives for supporting Chime and Chime Pro with new versions of Internet Explorer. Until further notice, Chime and Chime Pro users should continue to use older versions of Internet Explorer (5.5 SP1 and lower) or Netscape Communicator 4.7, which are supported with Chime and Chime Pro 2.6 SP2. MDL will post updates to this information and the Hardware and Software requirements on its MDL Chime site at the following URL: http://www.mdlchime.com/chime/ Thank you for your patience and understanding while we address these issues. Regards, MDL Chime Product Management 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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Postdoctoral and PhD positions at the Computer-Chemie-Centrum
by Frank Oellien 01 Aug '01

01 Aug '01

Hello, the following positions are available in the workinggroup of Prof. Gasteiger at the Computer-Chemie-Centrum. I. SFB A position for graduate studies (PhD track) is available from September 1, 2001, at the Computer-Chemie-Centrum of the University Erlangen-Nürnberg, Germany. We have developed methods for the automatic generation of three-dimensional molecular models for organic and many organometallic compounds. Furthermore, we have developed procedures for the treatment of the conformational flexibility of molecules based on an analysis of X-ray crystallographic data. These methods should now systematically be extended to organometallic structures. The relationships between the 3D structure of organometallic compounds and their catalytic activity should be established by neural networks. The project will be pursued in collaboration with several groups of our university within the consortium (SFB) "Redox-active Metal Complexes". The project has initially be granted for 3 years. Required working field knowledges: well-founded knowledge in Chemisty, acquaintance with electronic data processing. A knowledge of a programming language (such as C, C++ or Java) would be helpful. Please send your applications to: Prof. Dr. Johann Gasteiger Computer-Chemie-Centrum und Institut für Organische Chemie Universität Erlangen-Nürnberg Nägelsbachstrasse 25 D-91052 Erlangen Email: gasteiger(a)chemie.uni-erlangen.de www: http://www2.chemie.uni-erlangen.de ---------------------------------------------------------------------------------- II. BioPath Both, a postdoctoral position and a PhD track position are available from September 1, 2001 at the Computer-Chemie-Centrum of the University Erlangen-Nürnberg, Germany. The regulation of biochemical pathways and the metabolism of compounds presently are of central interest in drug design. We use methods of chemo- and bioinformatics to understand the physicochemical and biochemical influences on the individual reaction steps. We have built a database of biochemical pathways which we can now analyze through a broad range of search criteria. We have developed methods for defining the similarity of reactions and will explore how this corresponds with enzyme classification. Investigations of reaction networks should give us insight how gene expression results in the regulation of biochemical pathways. We hope to also find rules that will allow us the prediction of the metabolism of drugs. The project is funded for 5 years by the German Federal Government and is pursued in collaboration with several bioinformatics groups. We expect interest in the modeling of biochemical reactions and experiences in the use of computers. A knowledge of programming (e.g. C, C++, Tcl Tk, Java) would be helpful. Please send your applications to: Prof. Dr. Johann Gasteiger Computer-Chemie-Centrum und Institut für Organische Chemie Universität Erlangen-Nürnberg Nägelsbachstrasse 25 D-91052 Erlangen Email: gasteiger(a)chemie.uni-erlangen.de www: http://www2.chemie.uni-erlangen.de -- Computer-Chemistry-Center and Institute of Organic Chemistry University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-26579 Fax (+49)-(0)9131-85-26566 email: Frank.Oellien(a)chemie.uni-erlangen.de WWW : http://www2.ccc.uni-erlangen.de/oellien/ http://www2.ccc.uni-erlangen.de/ChemVis/ 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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