January 2000 - chemweb - imperial.ac.uk

Molecule of the Month -February - Frankinscence
by Paul May 31 Jan '00

31 Jan '00

Hi, I know it's a bt late for Christmas, but February's molecule of the month is Frankinscence, or rather, its main component Boswellic acid. All 4 versions are available (HTML-only, Chime, VRML and Chemsymphony), although the last 3 versions also use fancy tricks like style-sheets and dHTML as well. If you have an older browser, I'd suggest you try the HTML only version first. 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> 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> "Nobody in football should be called a genius. A genius is a guy like Norman Einstein" Football commentator Joe Theismann ------------------------------------------------------------------------------ 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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CSA Trust seeks award applicants
by Dr. Wendy A. Warr 21 Jan '00

21 Jan '00

Please do forgive duplicate postings. The Trust wants the maximum publicity for this good cause. Please hit the delete button now if you do not want to apply for research funding and all your colleagues are equally uninterested. CHEMICAL STRUCTURE ASSOCIATION TRUST - YEAR 2000 AWARD The Chemical Structure Association Trust is an internationally recognised Trust established to promote education, research or development in the area of systems and methods for the storage, processing and retrieval of information about chemical structures, reactions and compounds. Applications are invited for the Year 2000 Chemical Structure Association Trust Award. The Trust is offering an Award of up to two thousand pounds sterling for the best applicant seeking funds for education or research in chemical information. Anyone working in the field of chemical information research can apply and application can be made for funds to attend a relevant conference, for travel (e.g. to collaborate with another research group) or for hardware or software to assist with the research project. The award is unlikely to be given exclusively for hardware and software. The application should include: 1. A statement of academic qualifications 2. Details of relevant work and a statement of research recently completed by the applicant 3. The purpose for which the award is required. The clarity and relevance of this statement will be crucial in the evaluation of the applicants 4. Letters from two academic references to support the application. Award winners are expected to write a short report, within one year of receiving the money, giving details of how the money was spent. The Trust has previously supported the continuation of research studies in biomedical interactions including molecular recognition processes and drug design; a novel combination of reaction indexing and synthesis planning; clustering of chemical structures for property prediction; and investigation of reaction mechanisms. The work of younger scientists in developing countries has also been made possible in conjunction with some of the awards. Recent award winners, and their areas of research, are as follows: - Marina Molchanova, Zelinsky Institute of Organic Chemistry, Moscow (use graph theoretical and combinatorial algorithms in structure generation) - Weifan Zheng, University of North Carolina (QSAR and combinatorial chemistry) - Aniko Simon, University of Leeds (chemical literature data extraction) - Eugene Babaev, Moscow State University (computer-assisted synthesis) - Gareth Jones, University of Sheffield (for presentation of paper on genetic algorithms at an ACS National Meeting) - Vladimir Kvasnicka, Slovak Technical University (neural networks for prediction of physiochemical properties) - Rainer Herges, University of Erlangen-Nuernberg (reaction databases and quantum chemistry) Applications must be submitted by 30 April 2000, preferably by e-mail, to the Chairman of the Awards sub-committee, Professor Michael Lynch, at: Michael F Lynch <M.Lynch(a)sheffield.ac.uk> Any postal applications should be sent to: Dr Clive Weeks Secretary of the Chemical Structure Association Trust 39 Rounton Road Church Crookham Fleet, Hants GU13 0JH UK The Award will be presented at the International Chemical Information Meeting in Annecy in October. -- 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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Browsers and Chemistry
by Rzepa, Henry 20 Jan '00

20 Jan '00

After a period of relatively little change in the browser stakes (ie Netscape about 40%, IE about 60%), I note with interest that at least two "new" versions of browsers are nearing completion. iCab (which is a Mac only: http://www.icab.de/ )) browser now at 1.8, seems to support eg the Chime and Chem3D chemistry plugins fairly well. iCab works some many (most?) chemistry types, but apparently does not like some data sets. It works fine on http://www.ch.ic.ac.uk/ which contains a pdb file embedded. iCab is interesting because it supports HTML version 4, including a nice <object> cascade which can cascade down your list of "installed" chemistry until it finds something you can support. Hence if no e.g. Chime to render the pdb file, then pass on to eg a Java attempt. If that is blocked, then pass to eg a GIF image, and finally eg text. Finally, the thing done "properly"! Also, I note with interest that Mozilla M12 (aka Netscape 5) is finally looking like a product nearing completion. It crashes on my system in trying to render a Chime pdb file. Anyone else have any experiences? Get it from http://www.mozilla.org/ I note that like IE 5 (and very shortly 5.5? ) Mozilla contains an XML parser, and does some very nice things with stylesheets! To conclude, I might mention Amaya 2.4, which is at http://www.w3.org/Amaya/ supports HTML 4, XHTML, stylesheets, and MathML (but not plugins!). It also has a nice built in editor. Actually, this feature of a validating component, is also part of iCab, and probably Mozilla. Henry Rzepa. +44 (0)20 7594 5774 (Office) +44 (0)20 7594 5804 (Fax) 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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Chemistry and the Internet
by Dr. Wendy A. Warr 09 Jan '00

09 Jan '00

There is a (free) report on the meeting Chemistry and the Internet 1999 at http://www.warr.com/chemnt99.html 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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Re: Molecule of the Month - january 2000 (VRML problems)
by Paul May 05 Jan '00

05 Jan '00

Hi, > > Hello Paul, hello ChemWeb useres, > > I have developed the tool (VRML File Creator for Chemical Structures) which Paul > has used to create the VRML scene of the DNA. The VRML scene includes a switch > node to change between the various display styles. However IMHO it is not > necessary to display the structure in all of these display styles. The 'Capped' > styles shows all important things of the DNA. Paul please create another VRML > scene of the DNA but only in the capped display style. This WRL file should be > much smaller than 1.3 MB. You can add this file as an alternative smaller VRML > scene. Ok, I'll make a capped version of it sometime tis week. On the subject of large VRML files, is there a list which shows which of the popular VRML viewers support gzipped VRML files? If most of them do, then there's no danger in using the gzipped files. But if Cosmoplayer is the only one that supports gzipped files, we'll have to make do with the full (large) files in order to allow everyone to see the files. 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> 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> "Nobody in football should be called a genius. A genius is a guy like Norman Einstein" Football commentator Joe Theismann ------------------------------------------------------------------------------ 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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GZipping for VRML2
by Paul May 04 Jan '00

04 Jan '00

Hi, > >On the subject of large VRML files, is there a list which shows which of > >the popular VRML viewers support gzipped VRML files? > > > It's part of the VRML2 specification, so any VRML2 viewer must be able > to read gzipped worlds. For other purposes I've been trying out a > range of viewers and they all worked fine with gzipped files. They > were: > > Microsoft's version of WorldView > WorldView > Blaxuun Contact > Cosmo > Cordona That's useful to know, since this list seems to contain most of the biggees. > > Because VRML2 is plain text, the compression in going to gzipped is > huge, so it should be a matter of habit for anything other than the > smallest of worlds. My 1.3 Mb DNA file gzipped down to 120 kb, i.e. a factor of 10. The 'capped' version of the file, however, was still 500 kb. Either way, I've now put all 3 versions (full file, capped file and gzipped file) onto the MOTM page. 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> 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> "Nobody in football should be called a genius. A genius is a guy like Norman Einstein" Football commentator Joe Theismann ------------------------------------------------------------------------------ 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 - january 2000
by Paul May 03 Jan '00

03 Jan '00

Happy new millennium to all of you! The first Molecule of the Month for the new millennium is, appropriately, DNA, and is available in all four versions (HTML-only, Chime, Java and VRML). It was written by myself, and is available from the usual URL: http://www.bris.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> 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> "Nobody in football should be called a genius. A genius is a guy like Norman Einstein" Football commentator Joe Theismann ------------------------------------------------------------------------------ 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: Molecule of the Month - january 2000 (fwd)
by Armel Le Bail 03 Jan '00

03 Jan '00

At 21:18 02/01/2000 +0000, L. Cranswick wrote: >One I do like (cannot trace the original web homepage) >is VRWeb for Windows from Graz University of Technology, >Austria. Very fast and easy to use. > >Is a version with the GSAS software sites: > ftp://ftp.lanl.gov/public/gsas/ms-dos/ > http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/gsas/public/gsas/ms-dos/ VRWeb can also read gzipped VRML files but that version is too old (1996) and limited to VRML 1.0. It will not read the DNA files in VRML 2.0. Best, Armel Le Bail http://www.cristal.org/ 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: Molecule of the Month - january 2000 (fwd)
by L.M.D.Cranswick＠dl.ac.uk 02 Jan '00

02 Jan '00

I must admit not being that impressed with the commercially oriented VRML viewers: in either being too slow or crashing too often. One I do like (cannot trace the original web homepage) is VRWeb for Windows from Graz University of Technology, Austria. Very fast and easy to use. Is a version with the GSAS software sites: ftp://ftp.lanl.gov/public/gsas/ms-dos/ http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/gsas/public/gsas/ms-dos/ Lachlan. Armel wrote: > Paul May wrote: > > >The first Molecule of the Month for the new millennium is, appropriately, > >DNA, and is available in all four versions (HTML-only, Chime, Java and > >VRML). > > The VRML version contains a quite big file (1.3Mo) > which may discourage users to download. > > One tip about big VRML files : > > The best (?) VRML viewer, Cosmo Player, is able > to read gzipped VRML files. The compression factor > is generally better than 10:1. > > The trick is to apply gzip : > gzip *.wrl > > This produces a series of *.wrl.gz filles which you > may rename as *.wrl (suppressing .gz). Those files > are read directly by Cosmo Player (and may be other > VRML viewers, but I don't know exactly). > > If you want to recover the original files, rename all > those compressed files as *.wrl.gz and un-gzip them by : > gzip -d *.wrl.gz > -- Lachlan M. D. Cranswick Collaborative Computational Project No 14 (CCP14) for Single Crystal and Powder Diffraction 15th December 1999 to 4th March 2000 Queen's University, Dept Geological Sciences, Miller Hall, Union St, Kingston, Ontario Canada, K7L 3N6 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 http://www.ccp14.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: Molecule of the Month - january 2000
by Armel Le Bail 02 Jan '00

02 Jan '00

Paul May wrote: >The first Molecule of the Month for the new millennium is, appropriately, >DNA, and is available in all four versions (HTML-only, Chime, Java and >VRML). The VRML version contains a quite big file (1.3Mo) which may discourage users to download. One tip about big VRML files : The best (?) VRML viewer, Cosmo Player, is able to read gzipped VRML files. The compression factor is generally better than 10:1. The trick is to apply gzip : gzip *.wrl This produces a series of *.wrl.gz filles which you may rename as *.wrl (suppressing .gz). Those files are read directly by Cosmo Player (and may be other VRML viewers, but I don't know exactly). If you want to recover the original files, rename all those compressed files as *.wrl.gz and un-gzip them by : gzip -d *.wrl.gz Happy Y2K, Armel Le bail http://www.cristal.org/ 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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