- chemweb - imperial.ac.uk

teaching spectroscopy software - new release
by Adrian Blackman 17 Sep '02

17 Sep '02

Do you teach organic spectroscopy and/or qualitative analysis? If so then you might be interested in the Windows program WinTorg, version 3.2 of which has just been released. WinTorg simulates the process of identifying unknown organic compounds. It is suitable for use by early university or college level students. Spectroscopy is emphasised. There are 100 compounds each having pmr, cmr, ir, ms spectra and uv data together with other information. The unknowns can be identified by spectroscopy alone or in combination with chemical tests. WinTorg is easy to use, has extensive help available and can be customised. Student progress is recorded and reported. A free demonstration/shareware version (having only 3 compounds) is available. For more details see http://www.chem.utas.edu.au/staff/blackman/shareware/torganal.htm Registered users of WinTorg who purchased the program within the last 12 months can obtain a free upgrade on request. Adrian Blackman (author) School of Chemistry, University of Tasmania

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Re: KParts plugin based on KDrawChem
by E.L. Willighagen 13 Sep '02

13 Sep '02

On Friday 13 September 2002 14:28, Francesco Bresciani wrote: > > I am much interested in a KParts plugin voor > > KDrawChem. I am not much of a KDE programmer, > > that is why I relay this wishlist item to you. > > > > Such plugin would be great for embedding chemical structures in KWord > > (etc) documents. > > a Read-Only Part is already available in Kemistry 0.6 (but it doesn't work > due to an undefined symbol in a library, this bug is fixed in CVS). With > this part is possible to see chemical structures in Konqueror (the > supported file types are CML, MDL and the XDrawChem/KDrawChem native > format) > > We are currently working an a true KOffice part but currently I cannot say > when it will be available. That is very great news! Does the Konqueror plugin also work for "viewing" chemical files on the internet? Egon 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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Bulletin boards
by Rzepa, Henry 10 Sep '02

10 Sep '02

Quick follow up to my previous post. http://www.phpbb.com/ is another "off the shelf" opensource system using the combination of PHP and MySQL that provides a flexible bulletin board system which we intend using locally. The combination is widely used in e-commerce as well. If anyone is using an interesting combination of PHP and MySQL do please post it to this list (One that appears coming is the XML-isation of PHP/SQL ). 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 Inventory
by Rzepa, Henry 10 Sep '02

10 Sep '02

As legislation and good practice increasingly requires "wet" chemistry departments to take good care of their stock of chemicals, and the safety and disposal requirements become more stringent, so keeping good inventories becomes crucial. I noted that such inventories have been kept in some sort of e-form since around the mid 1980s, but often on software not well designed for the purpose. There are of course some specifically designed packages, eg ISISBase from MDL, Chemfolder from ACD, ChemFinder and e-labnotebook Cambridgesoft, Chemical Inventory from a company of the same name. There are probably a few others (apologies for not mentioning them). Where a consolidated database exists, its often rear-ended by eg Oracle, or other heavy duty systems, and clearly the market is designed for the large pharmas. Here for example, our financial system runs under Oracle, and of course its highly secure, not intuitive to the average academic or student, requires a Java plugin and a 600+ MHz system to run (that specification is not ours!) and dare I say it, not exactly fast! The increasing popularity of Opensource software led us to speculate how easily it might be to construct such a system using open standards, opensource tools, and W3C protocols. We did this because a) the software noted above, which often has many strengths, b) is also often not free, and c) not easily extensible or adaptable to local needs. We needed something Web based, and (almost) as easy to fine tune as eg HTML. We came up with ChemStock. This uses widely accepted software such as Apache Web server, openSSL for security, LDAP for directory queries, PHP as a scripting front end and MySQL as the database engine. A demo version for anyone interested is at http://www.ch.ic.ac.uk/csdemo/ It took about four weeks to write about 1200 lines of PHP, ( but no hard core "code" was involved) and we anticipate it will be readily maintainable. We hope it will run on pretty much any browser since (the theory is) it emits only standard XHTML. Thus far, its been tested with 45,000 entries with no speed hit (queries take just a few seconds, and a full export of the entire database only a minute or so). We have probably reinvented the wheel, but using PHP was an interesting learning curve. If any chem dept out there finds it useful we hope to distribute a tarball shortly. If anyone has an alternative system which is as easy if not easier to set up and use, do let the list know! -- Henry Rzepa. +44 (0870) 132 3747 (eFax) +44 0778 6268 220 (Mobile) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College, London, SW7 2AY, 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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Announcing VEGA1.4.2
by Giulio Vistoli 04 Sep '02

04 Sep '02

Dear collegues, we are glad to announce the new release of VEGA1.4.2 ( http://users.unimi.it/ddl ) our well known program to convert, manage and visualize of 3D structures for several platforms (Win32, Linux, Irix, AmigaOs). New features of VEGA1.4.2: - PowerNet plugin: TCP/IP protocol, PDB direct connection, script managment interface. - REBOL scripting language. Some scripts are included in the package. - AMD Athlon/Duron and Pentium 4 optimizations. - Edit atom dialog box. - GAMESS output loader. - Updated Gasteiger-Marsili charge attribution. - Bug fixes and new extended commands. REBOL is a messaging language that provides a broad range of practical solutions to the daily challenges of Internet computing. REBOL offers a new approach to the exchange and interpretation of network-based information over a wide variety of computing platforms. REBOL scripts are as easy to write as HTML or shell scripts: a script can be a single line or an entire application. The PowerNet plugin includes a useful interface to manage the REBOL scripts. Trough these scripts it's possible to control the VEGA function in order to automate the most common and repetitive operations. Giulio Vistoli & Alessandro Pedretti --------------- Giulio Vistoli Istituto di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano Italia Tel. +39-02-50317522 Fax +39-02-50317565 giulio.vistoli(a)unimi.it http://users.unimi.it/ddl 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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iMol molecule viewer for MacOS-X
by Mark Winter 03 Sep '02

03 Sep '02

Dear colleagues I see we have an *early* version of a molecule viewer for OSX. See http://www.pirx.com/iMol/ -- Dr Mark J Winter Department of Chemistry, The University, Sheffield S3 7HF, England tel: +44 (0)114 222 9304 fax: +44 (0)114 222 9303 e-m: mark.winter(a)sheffield.ac.uk http://www.shef.ac.uk/chemistry/staff/mjw/mark-winter.html WebElements is the periodic table on the world-wide web: http://www.webelements.com/ The Sheffield Chemdex is a listing of chemistry sites on the world-wide web: http://www.chemdex.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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Molecule of the Month - September
by Paul May 01 Sep '02

01 Sep '02

Hi, September's MOTM is the molecule Ibogaine, which is a controversial potential remedy for addictive drugs. it has been written by David Bradley, and all 4 interactive versions are available. http://www.bristol.ac.uk/Depts/Chemistry/MOTM/motm.htm#sept2002 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> "It's a proven fact. There's no scientific evidence for it, but it's still a fact." Dr Fox, Brass Eye. ------------------------------------------------------------------------------ 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 - August
by Paul May 01 Aug '02

01 Aug '02

Hi, August's MOTM is Uranium Hexafluoride, known for its uses in the nuclear industry. It has been written by Simon Cotton of Uppingham School again. HTML-only, Chime, VRML aned ChemSymphony versions are all available. http://www.bris.ac.uk/Depts/Chemistry/MOTM/motm.htm#aug2002 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> "It's a proven fact. There's no scientific evidence for it, but it's still a fact." Dr Fox, Brass Eye. ------------------------------------------------------------------------------ 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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Instructions for ArgusLab 3.0 -> 3.1 upgrade
by Mark Thompson 18 Jul '02

18 Jul '02

Apologies for the continued bandwidth... We neglected to mention that the ArgusLab 3.1 upgrade is free to ArgusLab 3.0 users. The instructions for what to do are contained in the readme.txt file contained in the download. Basically, you simply uninstall your copy of ArgusLab 3.0 and install ArgusLab 3.1. Your eLicense should recognize 3.1 with no further effort on your part. Please send us email at "bugs(a)arguslab.com" if you have any problems. Cheers, Mark 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 3.1 release available !
by Mark Thompson 17 Jul '02

17 Jul '02

************************************************************* ArgusLab version 3.1 now available Download a full-featured trial version at: http://www.arguslab.com ************************************************************* New features added: 1. Improved interface in the molecule builder 2. Improved for automatically adding bonds 3. Export images to bitmap, JPEG, and TIFF file formats 4. Export POV-Ray image files. (spectacular ray-traced images) 5. Improved Help System with more Tutorials and FAQs 6. Improved "clean geometry" will un-flatten rings 7. Full control over Atom colors 8. Enter explicit coordinates for atoms from right-click menu 9. Modify bond lengths from right-click menu 10. Reads older PDB file formats. 11. Lots of bug fixes. ArgusLab features: Extensive support for rendering surfaces. Powerful 3D interactive molecule builder. Build and optimize structures for the entire periodic table. Support for spectroscopy, geometry optimizations, energies, and many properties. ================================= Mark Thompson, Ph.D. Planaria Software Seattle, WA. http://www.arguslab.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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