October 1998 - 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)

2 1

Molecule of the Month - November
by Paul May 30 Oct '98

30 Oct '98

Hi, November's MOTM is Polythiophene, a conducting polymer with a nice spiral shape. It's written by Peter Tebbutt of Cherwell and is available in Chemsymphony format. The direct link is: http://www.chemsymphony.com/gallery/html/plythiophe.html and the MOTM page as usual is: http://www.bristol.ac.uk/Depts/Chemistry/MOTM/motm.htm --- Another plea: I have a MOTM planned for December, but after that I have nothing confirmed. Does anyone fancy immortalising themselves as the author of a MOTM page? The 'prestigious' January 1st slot (the 4th Birthday of the MOTM page) is still available... 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> "Ha! Your superior intelligence is no match for our puny weapons" Simpsons ------------------------------------------------------------------------- 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)

1 0

Release of ChemSymphony Beans 1.1
by Adam Hodgkin 30 Oct '98

30 Oct '98

Dear InternetChemist Cherwell Scientific is pleased to announce today the release of ChemSymphony Beans 1.1. For full details see: http://www.chemsymphony.com/ The new release has many important features which broaden the range of the toolkit. In particular we now have a 3D sketching tool, we have a simplified Marquee component, we now offer comprehensive JavaDocs on the public classes and the www site is deeper, broader and better indexed. Perhaps of greatest interest to the ChemWeb list, we are simultaneously releasing 5 ChemSymphony JavaBeans under a Lite licence. We invite you to download these FREE beans if you are curious to find out what these software components can do for Chemistry. Adam --- --- Adam Hodgkin | e-mail: adam(a)cherwell.com Chairman | Phone: +44 (0)1865 784810 Cherwell Scientific Publishing | Fax: +44 (0)1865 784801 Oxford OX4 4GA, UK | URL: http://www.cherwell.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)

1 0

The "What's related" Feature of Netscape: An analysis
by Rzepa, Henry 28 Oct '98

28 Oct '98

A few weeks ago, I posted something about how relevant the What's related" feature in Netscape was when pointed as a chemistry page. Someone has done a thorough analysis of the security and privacy implications of this feature. Although not specifically chemical in nature, it does raise some interesting issues of privacy relating to firewalls etc. Not for the faint hearted. And anyone in industry behnd a firewall, do NOT READ this if you want peace of mind. http://www.interhack.net/pubs/whatsrelated/ 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)

1 0

None
by armel＠fluo.univ-lemans.fr 27 Oct '98

27 Oct '98

Identité Message:<4.0.1.19981027151451.00e9d8c0(a)fluo.univ-lemans.fr> X-Sender: armel(a)fluo.univ-lemans.fr X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0.1 Date: Tue, 27 Oct 1998 16:39:28 +0100 To: chminf-l@listserv.indiana.edu,chemweb@ic.ac.uk From: Armel Le Bail <armel(a)fluo.univ-lemans.fr> Subject: Updating the ISI's most cited authors lists Cc: alb(a)cristal.org Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Colleagues, Now almost one year that the ISI's most cited chemists (10858 cited at least 500 times) and physicists (1120 first) lists are freely available at http://www.cristal.org/cit.html (US) or at http://fluo.univ-lemans.fr:8001/cit.html (France). The search engines were asked for ~13000 names/month and various partial or full lists were downloaded ~2000/month since December 1997, as a mean. Peoples may be interested by the knowledge of their own rank or by the rank of colleagues. Institutions may use those lists for evaluation. Students may decide to make a post-doc according to informations from those lists. Etc. For inverse reasons, there could be individuals or groups working against those lists publication. However, the lists gather citations in the range 1981-June 1997. They are now outdated. May I remember the story of the lists availability. Following the publication of the 50 most cited chemists by D. Pendleburry from ISI, it was clear that a full list of 10858 names had been built. After discussions, I bought this full chemists list US$ 1000, sharing the cost with a group of 36 colleagues. Then, ISI sent me also the 10 first pages of the physicists list, for free. The Web access was then tolerated. There is unfortunately no evidence that ISI will distribute updated lists (in spite of asking me for my search engine PERL script and of being interested in the number of Web access, month after month). Maybe it is to the Scientific Community to insist for obtaining them. They are at the ISI disposal, at the easy click of a button. I did not obtained any answer to my recent queries about updating. Some of you could have more influence... Armel Le bail PS - A huge correspondence was initiated by these lists availability. Some typical comments are below : > > It is a pity that ISI is a for-profit organisation! You did a fine service= =20 > to the community by making the list available. There should > be a way that scientists have access to this information WITHOUT=20 > paying money for it! > > I really appreciate what you did. This has been a wonderful service to= the=20 > community. > I wonder if you have analyzed the data in anyway. More specifically is=20 > there even a rough relationship between total citations and rank? For=20 > example is a log-log plot of rank vs total citations linear? If so=20 > what is the slope? This would allow one to see eg if there is any real=20 > difference between being ranked 200 vs 400 or 1000 vs 3000 etc etc. > Just a thought. > > Do you have available on line on the web a ranked=20 > list of the 10,000 or so most cited physicists?=20 > (like your list for chemists). > For instance, all physicists with more than 500 citations.=20 > Many researchers and faculty members would be very, very=20 > interested in that list. Please let me know how to access it. > > Do you plan tu update the list? > > Great!!! Thanks a lot!! Your stuff is extremely interesting and=20 > we welcome your activities really gratefully.=20 > Would you mind to comment about my querries? > a) Is the list of citations free of selfcitations? > b) Do you involve journals dealing with electrochemistry? > I miss some people on your list who are active in this field=20 > and who enjoy rather frequent quoting. Etc All the 1998 Nobel in Chemistry and Physics, but Kohn, were inside these lists. Kohn being probably ranked >1120 in the physicists list (with a chemistry Nobel, and this suggests some discrepancies between ISI and the Nobels about what are exactly chemistry and physics :-) Author(s) Name Average citation Total articles Total citations Rank by total citations TSUI DC 36.08 184 6638 71 STORMER HL 54.50 98 5341 133 LAUGHLIN RB 81.00 46 3726 374 POPLE JA 79.80 176 14044 2 Armel Le Bail - Universit=E9 du Maine, Laboratoire des Fluorures, CNRS ESA 6010, Av. O. Messiaen, 72085 Le Mans Cedex 9, France 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)

1 0

ACS acquires HDS
by Dr. Wendy A. Warr 27 Oct '98

27 Oct '98

Apologies for multiple postings. (Have sympathy for me too - I'll have 20 error messages by the end of today.) ACS announced October 20 that it had completed the acquisition of Hampden Data Services. I'll leave it to Eric (Shively) to post the full press release. Perhaps I'll write about it in this week's Warr Zone (at http://ChemWeb.com) 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)

1 0

Re: SMILES strings and on-line tutorials
by peter.ertl＠cp.Novartis.com 22 Oct '98

22 Oct '98

Dear Anthony and other smiling colleagues, The next version of our Novartis molecular editor applet (planned to be released sometimes in November) will have built-in SMILES canonizer, so it will create unique SMILES for (nearly) any molecule independent on the way how the molecule was drawn. (The applet is freely available for non-commercial use, if interested contact me directly.) One nice interactive chemical nomenclature tutorial is already available on the web. Prof. Reusch solved the problem with non-unique SMILES by checking all (2 or 3) possibilities. See http://www.cem.msu.edu/~reusch/OrgPage/Questions/MOLEDITOR/strctur1.htm Greetings peter ertl ======================================================== Dr. Peter Ertl Novartis Crop Protection AG Lead Discovery WRO-1060.7.20 CH-4002 Basel, Switzerland tel. (+41)61-6972468 fax. (+41)61-6975541 peter.ertl(a)cp.novartis.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)

1 0

SMILES strings and on-line tutorials
by C Anthony Lewis 22 Oct '98

22 Oct '98

Dear Colleagues, Recently, I have been playing with the CS ChemDraw Net plug-in, with the aim of constructing tutorial pages to help 1st year chemistry students convert systematic names into stick diagrams. I had the idea that I could use the SMILES string available from the Java applet suplied by CambridgeSoft along with a little bit of JavaScript to test if the structure drawn by the student corresponds to the name supplied. However, after a few tests I realised the major flaw in my idea... any particular structure does not have a unique SMILES string (I would like to add in my defence that I knew this but had forgotten about it in my excitement about the possibility of creating the tutorials). I am aware that methods of creating "unique" strings have been discussed but I have not investigated this yet. However, with the CS plug-in (or the Office Pro suite) it is possible to create different SMILES strings depending on how the structure is draw so the availability of these methods is somewhat academic. So, I am wondering if anyone on the List has attempted to do anything similar and/or if they have been successful... and would like to share theire experiences with the List. Of course, for simple structures it is relatively straightforward (if a little dull) to work-out all the SMILES strings (and then test all the possibilities with the JavaScript) but for more complex "simple" branched structures it would be considerable more time consuming. This also makes me wonder if it is possible to calculate the total number of SMILES strings for a structure? Thanks for any comments... Anthony Lewis C. Anthony Lewis Petroleum & Environmental Geochemistry Group, Department of Environmental Sciences, University of Plymouth, Plymouth, Devon PL4 8AA, U.K. tel: +44 (0)1752 233000 ext. 2988 FAX: +44 (0)1752 233035 e-mail: calewis(a)plymouth.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)

2 1

MGMS Meeting
by Dr. Wendy A. Warr 13 Oct '98

13 Oct '98

The Molecular Graphics and Modelling Society is organising a Young Molecular Modeller's Forum (i.e., for current students doing PhDs) at Glaxo Wellcome, Medicines Research Centre, Gunnels Wood Road Stevenage, Herts, on Wednesday, November 18th 1998 If interested please register at http://www.mgms.org/register_young.htm Programme: Alex Ninaber, The biological implications of damage to DNA incorporating an 8-oxodeoxyguanine Nick Luscombe, Protein-DNA interactions: a three-dimensional analysis Lesley Adams, Molecular modelling of pyrrolo[2,1-c][1,4]benzodiazepines Sarah Harris, Applications of Principal Component Analysis to Molecular Modelling Graham Tyrrell, Modelling the Myosin Molecular Motor Derek Smith, Modelling of Antifreeze Protein Interactions with Ice Lewis Whitehead, Computer Simulation of Membrane Proteins and the Development of Reduced Representation Models for Membrane Lipids Adam Moore, Dynamics of ligand interactions : Experiment and Simulation Richard Henchman, The Generation of OPLS-like Charges from the Molecular Electrostatic Potential using Restraints Justin Wansbury, The Use Of Molecular Modelling In The Study of Non-Oxide Structures Containing Transition Metals Thuy Tran, QSAR as a tool for modelling Vitamin E and Related Polyphenols' Antioxidant Activity Nick Jewell, FBSS - Using Molecular Fields as a Novel Alignment Method for 3D QSAR Malcolm Morrison, Pharmacophore Generation Using Field-Based Methods Presentation of award 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)

1 0

Report on Dallas ACS meeting
by Dr. Wendy A. Warr 12 Oct '98

12 Oct '98

...with apologies for duplicate postings. Somewhat belatedly, we have mounted the contents list for our six-monthly report at http://www.warr.com/dallas.html Most people who are interested will have received these details and an order form by snail mail about a month ago. The Dallas report has the usual section on news and new products (about 36 pages this time - some of it news from companies which did not exhibit), while the technical papers section this time covers COMP rather than CINF. (CINF had a stronger program in Boston, so the next report will be biased towards CINF.) Do send enquiries by e-mail - I don't want to turn this message into a sales pitch. 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)

1 0