- chemweb - imperial.ac.uk

Molecule of the Month - April
by Paul May 01 Apr '03

01 Apr '03

Hi, April's Molecule of the Month is the notorious drug Ketamine. The page has been written by an undergraduate student from Bristol: HTML and Chime versions are available: http://www.bristol.ac.uk/Depts/Chemistry/MOTM/motm.htm#apr2003 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> Bumper sticker: "Where are we going? And why are we in this hand-basket?" ------------------------------------------------------------------------------ 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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PS to Report from the ACS in New Orleans
by Rzepa, Henry 29 Mar '03

29 Mar '03

Re 3D viewing, I have found the page http://www.ddd.com/marketsfor3d/mar_main_frm.htm is a useful summary of terms etc. -- Henry Rzepa. Imperial College, Chemistry Dept. +44 0778 626 8220 +44 020 7594 5804 (Fax) 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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Report from the ACS in New Orleans. Part 2
by Rzepa, Henry 28 Mar '03

28 Mar '03

On more directly Web related matters, two sessions at the ACS had relevance, one on XML in Chemistry, and another on "The Scientific Article in the digital World". As it happens these CINF sessions also had counterparts in the COMP sections (indicating again the absurdity of trying to separation of modelling from informatics). The XML session included presentations from Peter Murray-Rust and myself (mine at http://www.ch.ic.ac.uk/rzepa/talks/acs03/ ) on the family of CML languages and the "road plan" for them. Apart from (passionate!) pleas for opendata, opensource, openservices I noted "beyond the article" developments and "beyond the browser" alerting services based on RDF-based metadata. Elsewhere, ThermoML was presented as a physicochemical markup XML language and in the COMP division Jesus Castagnetto talked about the metalloprotein database (MDB) and how XML is being used there. The talk should appear at http://metallo.scripps.edu/talks/ in due course. I was very impressed not only with what these guys are doing but the incredible momentum being generated in bioinformatics compared to chemistry. This latter talk was attended by perhaps 20 people; at a bioinformatics conference I feel 200+ would easily have been there. Its a mystery why chemistry continues to be dominated by a small number of (mostly commercial) providers who "move at the speed the market will bear", which in the case of chemistry continues to be defined as "slowly". The Biogrid/Bio-ontology movements continue to pave the way and put the chemistry community in this area to shame! Regarding the future of the "article", Steve Bachrach made an interesting point that finally an ACS journal has appeared with "supplemental information" comprising Web-activated 3D coordinates (eg. chime) some 9 years after the technology was demonstrated. The RSC by the way did this 8 years ago, in 1995! What is apparent is that "guided data capture" at the authoring point is coming, and that writing an article, or at very least the supplemental information for such, will benefit from an increasing variety of publisher and opensource tools. for example, with M$ Word V 11 coming out soon and being fully XML compliant, and with tools such as OpenOffice also so, along with opensource editors supporting XML and CML, I feel there are grounds for optimism that the "article" and what lies beyond it (see above) is now reinventing itself apace. Can I indulge in just one piece of "real chemistry". Paul Schleyer appears to have resolved one interesting and controversial aspect of aromaticity, ie that aromatic compounds show no bond localisation for annulenes up to around [22]. The X-ray structure of eg [18] annulene indeed shows the bonds to be the same length, to some a fundamental of aromaticity. well, Paul presented very convincing evidence that the structure of [18] annulene is wrong, it being effectively twinned with two superimposed alternating forms. Paul estimates the bond localisation starts at [14] annulene. -- Henry Rzepa. +44 (0870) 132 3747 (eFax) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, 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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Report from the ACS in New Orleans
by Rzepa, Henry 28 Mar '03

28 Mar '03

Its been a few years since I did one of these reports from an ACS meeting, but one item in particular caught my (and a lot of other ) eyes. CAChe were displaying LCD panel monitors which display true 3D images WITHOUT any need for glasses. The technology apparently comes in four flavours, each vying for market, which is a good omen for costs, which are expected to come spiraling down over the next 12 months. The largest display is a 40" (@$17,000), a 20" (@ around $8000) and most interestingly, a laptop to be released later this year. The effects were remarkable, although the depth of stereo vision is probably not (yet) as impressive as dedicated Crystaleyes systems Currently, it does need software drivers (openGL) and so specific software must be enabled. The CAChe software is so, and I gather a Powerpoint enabled 3D display is on the cards; I argued for enabling the Weh browser, perhaps Mozilla/Netscape will do it? >From what we saw, and with the predictions, it does seem that any serious molecular modeller or anyone interested in the 3D properties of molecules will be buying themselves these 3D LCD panels routinely in a years time or so! Apparently, a demonstration might be on the cards at Heathrow Airport on April 24. Anyone who is seriously interested in attending should contact Magda Karabon for free registration at + 48 12 429 43 45 or <mailto:ccs@fqspl.com.pl>ccs(a)fqspl.com.pl -- Henry Rzepa. +44 (0870) 132 3747 (eFax) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, 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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chemical structure ocx control
by Keith Wilkinson 25 Mar '03

25 Mar '03

Dear All, I am developing a freeware database of chemical structures for use in schools teaching International Baccalaureate. The program ties together some information relating to the medicines and drugs IB Chemistry option. I'm using the Accelrys 3D viewer VB .ocx control, which is acts as an enhanced Rasmol, but I cannot find a freely available 2D chemical structure .ocx control. Can anyone advise? Best wishes, Keith --------------------------------------------------------------------------- Keith Wilkinson, Science Department, International School of Lusaka, Zambia tel: +260 (0)1 239546 fax: +44 (0)709 220-5181 E-mail: <mailto:k.wilkinson@dunelm.org.uk> Home URL: <http://www.ecis.org/lusaka> Chemists Net: <http://www.chemclub.com/teachers> --------------------------------------------------------------------------- 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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Exemplarchem Workshop - 19th March
by Rzepa, Henry 07 Mar '03

07 Mar '03

As part of the Exemplarchem exhibition of student work, a workshop/meeting is being organised at Oxford University by the Royal Society of Chemistry on March 19th; http://www.chemsoc.org/exemplarchem/workshop.htm This is both an opportunity to discuss the general issues and actual practice of training students to create chemically-oriented Web-authored materials as part of coursework and to discuss with others the general principles of other aspects of modern authoring (eg for journals etc) including the use of chemical information resources. The meeting will have access to computers, and will include hands on sessions, as well as short talks by the originators of the Exemplarchem exhibitions. If you would like to attend this meeting, please contact the RSC via http://www.chemsoc.org/exemplarchem/workshop.htm or via exemplarchem(a)rsc.org -- Henry Rzepa. +44 (0870) 132 3747 (eFax) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, 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 '03

28 Feb '03

Hi, March's MOTM is Ethyl Acetate (and other esters), and is concerned with the chemistry of smells & odours. It has been written by Simon Cotton from Uppingham School, Rutland, UK, and there are 4 versions available, HTML-only, Chime, VRML and Chemsymphony. http://www.bristol.ac.uk/Depts/Chemistry/MOTM/motm.htm#mar2003 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> Bumper sticker: "Where are we going? And why are we in this hand-basket?" ------------------------------------------------------------------------------ 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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Marvin 3.0 released (s-groups, 3D, charge, pKa, logD, etc.)
by Ferenc Csizmadia 14 Feb '03

14 Feb '03

Marvin Applets and Marvin Beans 3.0 have been released. The packages contain software development tools and applications for chemistry. Marvin Applets and JavaBeans support drawing/displaying chemical structures and handling molecule objects. FREE: - Marvin Applets are free for free web sites. - MarvinSketch and MarvinView applications accessed from ChemAxon's web site http://www.chemaxon.com/marvin/jnlp/index.html - Locally installed MarvinSketch, MarvinView, and MolConverter applications. Important changes: - Abbreviated groups, S-groups. - 3D cleaning, 3D conversion from 2D or SMILES - Elemental Analysis calculations - Tools menu and plugins: Charge distribution, pKa, logP, logD. (Without license key only 1 calculation at a time is allowed) - Creating user defined templates by dragging-and-dropping over template buttons. - Nicer looking molecules; atom properties are displayed separately from element symbols. - Radicals are supported. - Faster import of large XYZ and PDB files. - Molecule-related classes are 20-30% faster, R-group and reaction related classes are easier to use. - Signed applet is the default (allowing clipboard operations and the accessing of the local file system) The software can be tried/downloaded at http://www.chemaxon.com/products.html Online access Applets: http://www.chemaxon.com/marvin/demos.html Applications: http://www.chemaxon.com/marvin/jnlp/index.html Regards, Ferenc -- Dr. Ferenc Csizmadia CEO ChemAxon http://www.chemaxon.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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Molecule of the Month - February
by Paul May 31 Jan '03

31 Jan '03

Hi, February's MOTM is spidroin, the chemical behind spider's webs. It also deals with sider venoms as well. It has been written by Vivienne Li, a second year undergraduate here at Bristol. (It works best in internet Explorer, although other browsers work too). HTML and Chime versions are available: http://www.bristol.ac.uk/Depts/Chemistry/MOTM/motm.htm#feb2003 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> Bumper sticker: "Where are we going? And why are we in this hand-basket?" ------------------------------------------------------------------------------ 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: Public library of Science
by ian.newington＠kodak.com 26 Jan '03

26 Jan '03

Following on from this discussion I've just had an experience where a subscription lapsed (cost savings) and now I am unable to get access to any full text even from the back numbers when we were subscribed. It seems to me that if electronic only journal holdings are to work, the publishers need more sophisticated access control. Why should a library pay the same rate (or often more) for years and then not have access to those years of holdings at a later date? Perhaps there's something to be said for paper after all! Ian Newington R&D Kodak Ltd Tel: +44-(0)20-8424-4451 FAX: +44-(0)20-8424-5788 email: ian.newington(a)kodak.com The views expressed in this email are my personal views and do not necessarily represent those of the company I work for. 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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