- chemweb - imperial.ac.uk

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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Molecule of the Month - december
by Paul May 30 Nov '01

30 Nov '01

Hi, December's Molecule of the Month is the famous explosive, nitrogen triiodide. It's been written by Simon Cotton of Uppingham School in Rutland, and all versions (HTML, Chime, VRML and Chemsymphony) are available. 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> ICQ: (available on request) 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> "I think you'll find our findings find favour" Dr Terrible's House of Horrible ------------------------------------------------------------------------------ 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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Digital archive seminar
by Wendy Warr 27 Nov '01

27 Nov '01

Seminar on Digital Preservation of the record of Science state of the art Paris, France, February 14-15 2002 ICSTI, the International Council for Scientific and Technical Information, has been encouraging discussion, debate and actions on ensuring that the record of Science continues to preserved. With the progressive movement towards digital production and distribution of scientific information there is a risk that the record represented by this material will be lost. Although many of the parties concerned with digital production and distribution have taken measures to preserve the material the effort is diffused and overall co-ordination may be necessary. .... Many other bodies in the Science community, such as CODATA, IUPAP, ICSU, interests from the international standards arena, those concerned with the creation of open archives as well as the scientific publishing community both the traditional and the newer actors, are all involved in one sense or another with preservation. In addition the library community and the representatives of the history of science community are intimately concerned. While, as noted, many activities and initiatives are under way and research programmes are in progress, the cost of digital preservation can be significant and the need to avoid duplication of effort is paramount. The need for a federal approach to both the preservation process and access to the archives has been suggested; this requires co-ordination. ... ... The topics to be discussed will be of interest to: · authors and publishers of scientific information, in particular developers of newer digital methods; · those concerned with the short and long term storage and distribution of this material, librarians and archivists; · developers of computer systems for digital archiving; · those involved in the creation of national and international standards, as well as subject or data-type oriented codes of practise; · national and international representatives from the Science community, specifically the professional and other bodies with interests in science subjects; · representatives of the scientific data community. The meeting will be held at the premises of UNESCO, with the kind permission of the Assistant Director General for Science. There is no fee for attendance but neither UNESCO nor ICSTI is in a position to offer support for travel or accommodation. Further details from ICSTI icsti(a)icsti.org or fax (in Paris) +33 1 42 15 12 62 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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Fw: 6ICCS
by Wendy Warr 16 Nov '01

16 Nov '01

Posted to chemweb, lisukolug, Daresbury list. Apologies for duplication. 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 ----- Original Message ----- From: "Guenter Grethe" <guenter(a)mdli.com> To: "Don Parkin" <d.parkin(a)dl.ac.uk>; "Geoff Downs" <geoff(a)bci2.demon.co.uk>; "Gerald Maggiora" <gerald.m.maggiora(a)am.pnu.com>; "Guenter Grethe" <Guenter(a)mdli.com>; "Jacques Weber" <weber(a)sc2a.unige.ch>; "Johnny Gasteiger" <gasteiger(a)torvs.ccc.uni-erlangen.de>; "Kimito Funatsu" <funatsu(a)tutkie.tut.ac.jp>; "Peter Willett" <p.willett(a)sheffield.ac.uk>; "Rainer Moll" <dr.rainer.moll(a)t-online.de>; "Vincent van Geerestein" <vincent.vangeerestein(a)organon.com> Cc: "'Wendy Warr'" <wendy(a)warr.com> Sent: Friday, November 16, 2001 6:29 AM Subject: 6ICCS > Dear colleagues, > > below is the URL for the Sixth International Conference on Chemical > Structures to be held June 2 - 6, 2002, in Noordwijkerhout. The URL will be > listed on several listservers (CHMINF, COMP, Diversity, ISIS-FORUM, and > MEDI). Please feel free to list it on any other appropriate server you have > access to or publish it in your organization's newsletter. The present > version of the website is mainly intended as a 'Call for Papers'. We are > still working on the registration details. > > http://chemweb.com/docs/6iccs/6iccs.html > > With best regards, > Guenter > > Dr. Guenter Grethe > Director, Scientific Applications > Product Development, Research Group > 14600 Catalina Street > San Leandro, CA 94577 > Tel.: (510) 357-2222, ext.1430 > Fax: (510) 614-3616 > e-mail: guenter(a)mdli.com > http://www.mdli.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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Summary: Monitors command in rasmol/chime
by Bachrach, Steven 13 Nov '01

13 Nov '01

Hens Borkent sent me a note informing me that the Monitors command is actually a rasmol script and he pointed me to the rasmol manual page. Here is the information on this command: ************************ Monitor Syntax: monitor <number> <number> monitor {<boolean>} The RasMol 'monitor' command allows the display of distance monitors. A distance monitor is a dashed (dotted) line between an arbitrary pair of atoms, optionally labelled by the distance between them. The RasMol command 'monitor <number> <number>' adds such a distance monitor between the two atoms specified by the atom serial numbers given as parameters Distance monitors are turned off with the command 'monitors off'. By default, monitors display the distance between its two end points as a label at the centre of the monitor. These distance labels may be turned off with the command 'set monitors off', and re-enabled with the command 'set monitors on'. Like most other representations, the colour of a monitor is taken from the colour of its end points unless specified by the 'colour monitors' command. Distance monitors may also be added to a molecule interactively with the mouse, using the 'set picking monitor' command. Clicking on an atom results in its being identified on the rasmol command line. In addition every atom picked increments a modulo counter such that, in monitor mode, every second atom displays the distance between this atom and the previous one. The shift key may be used to form distance monitors between a fixed atom and several consecutive positions. A distance monitor may also be removed (toggled) by selecting the appropriate pair of atom end points a second time. ******************** It would be a nice feature if rasmol/chime could also display angles and dihedral/torsional angles. Thanks to Hens for the definitive answer. 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 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: Model for Sharpless Expoxidation
by Bachrach, Steven 12 Nov '01

12 Nov '01

This is a nicely done page. I noticed an interesting trick (near the bottom of the page) of displaying a bond distance within chime. The key seems to be the "monitor" keywork within the embed command. There is no mention of this command in the MDL chime pages. Can anyone shed some light onto its use - it looks pretty straightforward but I would like more complete info. Thanks 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, November 12, 2001 4:00 AM > To: chemweb(a)ic.ac.uk > Subject: Molecule-of-the-month: Model for Sharpless Expoxidation > > > Hens Borkent has produced an interactive guided tour through > the complexity > of the Sharpless epoxidation reaction , one of the > discoveries for which the Nobel > prizes were awarded this year. > > It is a new "Molecule of the Month" at Imperial College; > http://www.ch.ic.ac.uk/motm/borkent/sharpless.html > > The original page can be seen at > http://www.cmbi.kun.nl/~borkent/projects/sharpless.html > > If anyone knows of other collections of guided tours through molecules > (or in this case transition states) which are insufficiently > exposed, do please > let this list know. > > -- > > 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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Molecule-of-the-month: Model for Sharpless Expoxidation
by Rzepa, Henry 12 Nov '01

12 Nov '01

Hens Borkent has produced an interactive guided tour through the complexity of the Sharpless epoxidation reaction , one of the discoveries for which the Nobel prizes were awarded this year. It is a new "Molecule of the Month" at Imperial College; http://www.ch.ic.ac.uk/motm/borkent/sharpless.html The original page can be seen at http://www.cmbi.kun.nl/~borkent/projects/sharpless.html If anyone knows of other collections of guided tours through molecules (or in this case transition states) which are insufficiently exposed, do please let this list know. -- 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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Scientific Websites being hijacked by pornographic websites?
by Lachlan Cranswick 09 Nov '01

09 Nov '01

Hi, As pointed out a while back - the scientifically very useful Webmolecules website was hijacked to become a porn site due to non payment of domain registration) http://www.webmolecules.com/ (does anyone know if they have a new address?) Another addition to the pornography domain that was recently pointed out to me was: Scientific American and Nature Science and Technology Jobs http://www.scitechjobs.com ---------- My main query - does anyone know of the software that these porn people are using to find possible scientific sites to hijack - when domain registration is about to expire - then make a payment for it. The implication is they are able to analyse the significance of a scientific website (a colleague has suggested they use how many other sites link to it) - find out when the domain expires - then place a order (automatically via credit card?) to obtain it a few seconds(?) after domain registration has officially expired? Am mainly interested in seeing if this domain expirey software can be used to warn domain owners prior to their domains expiring. Thanks in advance, Lachlan. PS: Are there any "academic" resources showing how effective/profit making these hijackings might be to their new owners? E.g., what percentage of people who click through expecting a scientific site keep within the site. ----------------------- Lachlan M. D. Cranswick Collaborative Computational Project No 14 (CCP14) for Single Crystal and Powder Diffraction Birkbeck University of London and Daresbury Laboratory Postal Address: CCP14 - School of Crystallography, Birkbeck College, Malet Street, Bloomsbury, WC1E 7HX, London, UK Tel: (+44) 020 7631 6849 Fax: (+44) 020 7631 6803 E-mail: l.m.d.cranswick(a)dl.ac.uk WWW: 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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