January 1999 - 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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February's MOTM - Ptaquiloside
by Paul May 31 Jan '99

31 Jan '99

Hi, The Molecule of the Month for February is Ptaquiloside, which is a poison found in bracken. It's been written by David Bradley, the science writer and editor, and the 3 versions (HTML-only, Chime enhanced, and Chemsymphony Java) can be found from the usual place: 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> <http://www.bris.ac.uk/Depts/Chemistry/staff/pwm.htm> "Who would have thought learning to read & write would come in handy someday" Homer Simpson ------------------------------------------------------------------------- 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 site
by Alistair Lennie 28 Jan '99

28 Jan '99

Dear ChemWeb Please find below the URL of my website which displays crystal structures of minerals using CHIME. http://www.man.ac.uk/Geology/MineralWeb/Admit.html or, if CHIME is already loaded, go straight to http://www.man.ac.uk/Geology/MineralWeb/Mineral_Web.html Alistair Lennie ----------------------------------------------------------------------------------------------------------- Dr. Alistair Lennie Department of Earth Sciences University of Manchester Oxford Road Manchester M13 9PL ENGLAND ph 0161 275 3681 ------------------------------------------------------------------------------------------------------------- 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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OrbVis
by Frank Oellien 25 Jan '99

25 Jan '99

Hello, we have released our new Web-Service 'OrbVis'. OrbVis is an online service for the calculation and visualization of molecular orbitals. The service will visualize all MOs of any reseonable structure you create. It employs a combination of a VRML2.0 plugin and a JAVA1.1 applet with many display options to control the visual appearance. System Requirements: SGI: Netscape Communicator 4.04 with JDK1.1 patch; VRML 2.0 plugin WIN 9x/NT: Netscape Communicator 4.5 or higher; VRML 2.0 plugin http://www2.ccc.uni-erlangen.de/services/orbital/ Yours Frank Oellien -- Frank Oellien Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-26579 Fax (+49)-(0)9131-85-26566 email: franko(a)ccc.chemie.uni-erlangen.de WWW : http://www2.ccc.uni-erlangen.de/people/Frank_Oellien/ http://www2.ccc.uni-erlangen.de/projects/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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'ChemVis' research project
by Frank Oellien 23 Jan '99

23 Jan '99

Hallo ChemWeb community, I would like to present the new pages of the 'ChemVis' research project. The 'ChemVis' project is one of 23 research projects in the strategic research initiative "V3D2" ("Distributed Processing and Exchange of Digital Documents") of the German Research Foundation (Deutsche Forschungsgemeinschaft DFG). Research project: Chemical visualization on the Internet: Embedded dynamic and interactive high-end graphics in digital documents for the visualization of complex factual relationships. Please feel free to visit our sites: http://www2.ccc.uni-erlangen.de/projects/ChemVis/ Yours sincerely, Frank Oellien -- Frank Oellien Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-26579 Fax (+49)-(0)9131-85-26566 email franko(a)ccc.chemie.uni-erlangen.de WWW www2.ccc.uni-erlangen.de/people/Frank_Oellien 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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Provocative article on (chemistry) e-journals
by Rzepa, Henry 22 Jan '99

22 Jan '99

This is a good read; http://www.nature.com/server-java/Propub/nature/397195A0.frameset?context=to One of many points is "will the individual journal" continue to have any identity in the "aggregated journaldatabase of the future". How will the community deal with "impact factors". I found out that some universities, when recruiting staff, often multiply the applicants X most recent publications by the impact factor of each journal, and then compare the results totals amongst the applicants, in all probability appointing the one with the highest total! A better method of course would be the individual citations of each article, but here the oldest article is often the highest ranking, and the lead in for any citations is sometimes 2-3 years. I wonder if anyone has yet managed to work out the "impact factor" of any e-journal (or aggregated collection) yet? 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/ If my digital email signature is invalid, download a new root at http://www.belsign.be/en/services/receive/install-ca.html 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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VRML File Creator - Examples
by Frank Oellien 18 Jan '99

18 Jan '99

Hallo everyone, I have analysed the log file of our 'VRML File Creator' service and noticed that the most people use the default structure and the default settings of the most options. The more interesting features can only be viewed when some option switches are selected. So I have prepared an 'Example' page for a better understanding. You can choose some examples to see some of the most interessting features of our service. VRML File Creator - Main page: http://www2.ccc.uni-erlangen.de/services/vrmlcreator/index.html Example page: http://www2.ccc.uni-erlangen.de/services/vrmlcreator/vrml_example.html Regards Frank Oellien -- Frank Oellien Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-26579 Fax (+49)-(0)9131-85-26566 email franko(a)ccc.chemie.uni-erlangen.de WWW www2.ccc.uni-erlangen.de/people/Frank_Oellien 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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Silicon Graphics
by Dr. Wendy A. Warr 13 Jan '99

13 Jan '99

On Tuesday, I went to the London launch of Silicon Graphics' new family of visual workstations. The first two products are the Silicon Graphics 320 and the Silicon Graphics 540, both based on Intel processors and the Windows NT operating system. The UK entry level price is only 2340 pounds sterling (which is less than I just paid for my IBM ThinkPad!) and the graphics are stunning. The 540 (from 4130 pounds) has integrated media, including uncompressed, professional digital video. The buzzword of the meeting was "breakthrough" - breakthrough in innovation, price-performance, market placing, changing the competitive landscape etc. etc. SGI moves into the NT marketplace with completely compatible technology but with a difference, the Integrated Visual Computing Architecture (IVC). The graphics are incorporated into the Cobalt chipset and the raw performance is six times greater than AGP and more than 3 times greater than the upcoming AGP2. And if don't need fancy graphics, bear in mind that even the disc performance is impressive for that price range. It even looks pretty (for you iMAC fans!). And in case you're into UNIX, it was pointed out that there is interoperability with UNIX. Was there a downside to the meeting? Well, unfortunately it was squarely aimed at the manufacturing and media marketplaces and my only soul-mate there was Rob Scoffin from CambridgeSoft, doing his ChemOffice demos. Perhaps you guys (and gals) with your high end molecular modelling hardware may not feel the impact of this hardware yet but I suggest you take a look. Wendy -- Dr Wendy A Warr Wendy Warr & Associates, 6 Berwick Court Holmes Chapel, Cheshire CW4 7HZ, England Tel/fax +44 (0)1477 533837 wendy(a)warr.com http://www.warr.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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Warr Zone
by Dr. Wendy A. Warr 08 Jan '99

08 Jan '99

For reasons beyond my control, Warr Zone has gone missing from the "new look" Alchemist on ChemWeb. I am particularly sorry that some of the organisations mentioned in this week's column have not had their news drawn to your attention so I am taking the liberty of reproducing this week's column below. The links to the Warr Zone and Filternet archives have also gone missing from ChemWeb but the links from my own site http://www.warr.com to the archives http://chemweb.com/alchem/alchem98/warrzone/wz_current_set.html and http://chemweb.com/alchem/alchem98/archives/ar_current_set.html and http://chemweb.com/alchem/alchem98/filter/fi_current_set.html work OK. ________________________________________________________________________ WARR ZONE January 8, 1999 RSC Wins Award The Royal Society of Chemistry [http://www.rsc.org] has won Best Stand Award at Online Information 98, the worlds largest electronic information exhibition. Presenting the award, Sissel Hafstad (President of EIRENE, the European Information Researchers Network) praised the open and inviting design of the stand and its use of symbolism to achieve maximum impact on a modest budget. The stand had a giant "smoking" flask with a slogan "Solutions for the future". News from ID Business Solutions ID Business Solutions [http://www.idbs.co.uk] has released ActivityBase 3.2, the latest version of its discovery data management system, and an enhanced Object Manager (version 1.1). The company has also announced that it is going to provide chemical storage capabilities as part of the ActivityBase environment. There is a common interface for biological and chemical data with this new technology and it will be possible to store and search molecules, reactions and libraries (product based or reaction based), within a single database schema and combine this data with biological data generated through screening activities. Through the common biology and chemistry interface, researchers will be able to interrogate assay results, mine a database for molecules containing a particular substructure, or design a combinatorial library using generic reactions. Integration of biological and chemical data will enable complex cross discipline queries to be run. IDBS plans to support organic, polymer and organometallic chemistry (and salts of organic compounds), and claims that it will extend chemical representation beyond that currently supported by other software vendors. In particular, the number of chemistry descriptors will be increased to support enhanced stereochemical handling and bond types such as hydrogen and co-ordinate bonds. IDBS currently has a molecule registration capability available as an add-in to ActivityBase. This registration module can "hook in" to third party databases such as MDLs ISIS for storing and retrieving structures. IDBS is proposing a series of phased releases for the new software. The first phase of chemistry component technology is to be incorporated into ActivityBase 4.0, scheduled for release in the second quarter of 1999. Current Drugs Unveils 1999 Plans Current Drugs [http://www.current-drugs.com] will publish six new titles in the Current Opinion series in 1999: Current Opinion in Molecular Therapeutics, Current Opinion in Central and Peripheral Nervous System Investigational Drugs, Current Opinion in Anti-inflammatory and Immunomodulatory Investigational Drugs, Current Opinion in Cardiovascular, Pulmonary and Renal Investigational Drugs, Current Opinion in Anti-infective Investigational Drugs, and Current Opinion in Oncologic, Endocrine & Metabolic Investigational Drugs. The company has unveiled plans for version 3.0 of IDdb. It will have new Alerts, Competitor Analysis, Library and Personalise sections, new facilities for searching and annotation, links to other Internet or intranet resources and a knowledge management environment for linking IDdb intelligence to a companys internal resources. Current Drugs has announced an alliance with the EMC Corporation of Massachusetts to provide its customers with an extranet service for the Investigational Drugs database. Both leaseline and virtual private network options will be on offer. Current Drugs has also announced the forthcoming availability of DrugNet.com, a major new Internet-based service for the international pharmaceutical and biotechnology industries. DrugNet.com will integrate specialist databases, decision support software and competitor intelligence services from a range of publishers and software vendors servicing the biomedical and pharmaceutical sector. It is thought that the product may be launched in the second quarter of 1999. Handbook of Chemistry and Physics CRCnetBASE 1999 All the text and figures of the 79th edition of the Handbook of Chemistry and Physics [http://www.crcpress.com/catalog/478.htm] are now available on CD-ROM as the Handbook of Chemistry and Physics CRCnetBASE 1999, ISBN 0-8493-9720-0, from CRC Press [http://www.crcpress.com] and Springer-Verlag. The Advanced Internet Searchers Handbook This book, by Internet consultant Phil Bradley [philb(a)twilight.demon.co.uk] is written for those who already use the Internet but want to gain access to further information through improved search techniques. It develops understanding of search engines and how they work, and introduces more complex online searching techniques. It also looks at gateways, virtual libraries, USENET groups and commercial databases on the Internet. It costs £29.95 and is published by the Library Association [juliet.prowse(a)la-hq.org.uk] Apologies for duplicate messages and a happy new year to all my readers. Wendy -- Dr Wendy A Warr Wendy Warr & Associates, 6 Berwick Court Holmes Chapel, Cheshire CW4 7HZ, England Tel/fax +44 (0)1477 533837 wendy(a)warr.com http://www.warr.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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Chime XYZ animations, mol editor
by Hens Borkent 08 Jan '99

08 Jan '99

Chimers of the world, There have been several questions lately about Chime animations, based on multiple XYZ files. We have been using these animations for quite a while now, in our educational (organic chemistry) web pages Molecules in four dimensions (http://www.caos.kun.nl/wetche/organic/) Mol4D. Besides ready-made animations, Mol4D features a perl script based Chime molecule editor, to edit mopac input files and produce Chime'd xyz animations on the fly. (Netscape/Windows/MacPPC preferred) We have decided to make all the scripts available to the chime-using community. At the bottom of the page mentioned above there is a link to the 'technical background', that explains which script is used for what. The scripts are to some extent site-specific, of course, but could be adapted for local use. We would like to encourage the use of these scripts, in both ways: improvements on their tasks, and developing more applications in the field of organic chemistry. We intend to maintain a repository of the results, so please inform us if you have a contribution that is useful for others. -- ***** J.H. (Hens) Borkent, CAOS/CAMM Center, *CAOS * P.O. Box 9010, 6500 GL Nijmegen, The Netherlands * / * Tel 0031 24 36 52137 Fax 0031 24 36 52977 * CAMM* e-mail: borkent(a)caos.kun.nl ***** http://www.caos.kun.nl/staff/borkent.html 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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