- chemweb - imperial.ac.uk

marvin 1.2 applets drawing and displaying structures
by Ferenc Csizmadia 04 Dec '98

04 Dec '98

The 1.2 version of the Marvin applets for drawing and displaying chemical structures and substructures can now be downloaded at http://www.chemaxon.com/marvin. New features: - (Unique) SMILES/SMARTS output - Improvements in the user interface - More documentation Some other features: - Molfile input and output - Molfile compression/decompression for fast data transfer - Automatic charges and H atoms - checking valence errors - query atoms and bonds - stereo chemistry - advanced user interface - zooming - templates - merging of fragments Ferenc ~~~~~~ Ferenc Csizmadia, Ph.D. ChemAxon Ltd. Valyog u. 7, H-1032 Budapest, Hungary http://www.chemaxon.com T:+3620 9570988 Email: fcsiz(a)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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"enhanced" Electronic Journals
by Rzepa, Henry 03 Dec '98

03 Dec '98

Following Paul May's http://www.rsc.org/ej/qu/1998/F9808830/index.htm I further note that "chiming" articles is "bandwaggoning" (I might add following the ground breaking examples from the CLIC project in 1996 and 1997, ie http://chemcomm.clic.ac.uk/navi.pl?clicenhanced/ccc/communications/c02788#s… ) For "imitations", see for example the J. Phys. Org. Chem http://www.rsc.org/ej/qu/1998/F9808830/index.htm who call the technique "dynamic electronic enhancement". The RSC also has such enhanced articles in its own Phys org journal, ie Perkin 2. See for example http://www.rsc.org/suppdata/perkin2/1998/2695/index.html (although in this case the enhancement is part of the supplemental data, is NOT part of the intrinsic journal article itself, and depends entirely on what the authors submit to the journal. Most of the supplemental data is in fact available as Word documents) Pity that the current Chime has many features disabled for non Windows NT computers (ie Macs), and will not be available at all for Unix. For example, the use of Linux is rapidly growing, but such users cannot take advantage of these enhanced articles. Personally, to address these issues, I think Java is the way! See for example http://origin.ch.ic.ac.uk/molda/ for a certificate-authenticated modelling tool which could e.g. become a component of an e-journal, or http://origin.ch.ic.ac.uk/vchemlab/cos/signed_applet.html for authenticated interfaces to databases etc. 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)

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Re: Virtual Journals, Chime & Jcamp (fwd)
by Dr. Wendy A. Warr 02 Dec '98

02 Dec '98

Gary Wiggins wrote: > > ---------- Forwarded message ---------- > Date: Tue, 1 Dec 1998 19:09:59 +0000 (GMT) > From: Paul May <paulmay(a)tlchm.bris.ac.uk> > To: Chemistry Wem-Users list <chemweb(a)ic.ac.uk> > Subject: Virtual Journals, Chime & Jcamp > > Hi, > > I thought you might be interested to know that a paper I submitted to the > new RSC e-Journal PhysChemComm has been published only 20 days after > submission! This is certainly a record for me, and probably goes to > highlight another advantage that e-Journals have over paper-only Journals > - if the paper is written in a web-friendly format and all the > correspondance is done via email, then the refereeing > time, handling time and admin time can be significantly reduced, and > *extremely rapid* publication times can result. > I am glad for Dr. May's sake that his paper was published so quickly. I have nothing against e-publishing (indeed many of my own business interests are in that area) but I would sound a note of caution. In my experience (as an editor of an ACS journal) it is unusual even for a reviewer to reply within 3 weeks. I am not writing this message as a criticism of our reviewers. Ninety-nine percent of them go to a lot of trouble reading papers with great care and writing really incisive reviews, despite the fact that they have a heavy burden of teaching and research (and increasing amounts of admin duties). Moreover, some of our reviewers are in industry and score no points at all for reviewing papers. It is no mean task to review fairly the sort of papers we receive, many of them packed with math and full of abstruse concepts. We also have many authors whose mother tongue is not English, whose work needs extensive editing, and not a few authors who do not have easy access to the sort of facilities US authors enjoy. 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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[Fwd: Fifth International Conference on Chemical Structures - Call for Papers]
by Dr. Wendy A. Warr 01 Dec '98

01 Dec '98

-- 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

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Virtual Journals, Chime & Jcamp
by Paul May 01 Dec '98

01 Dec '98

Hi, I thought you might be interested to know that a paper I submitted to the new RSC e-Journal PhysChemComm has been published only 20 days after submission! This is certainly a record for me, and probably goes to highlight another advantage that e-Journals have over paper-only Journals - if the paper is written in a web-friendly format and all the correspondance is done via email, then the refereeing time, handling time and admin time can be significantly reduced, and *extremely rapid* publication times can result. If you're interested, the paper is about the Raman spectra of adamantane and diamond, and contains some neat (well, we think so!) links between interactive Jcamp spectra and Chime structures. You can click on the individual peaks in the Raman spectra and the Chime window shows you an animation of the vibrational mode which we think caused that peak. Great for demonstrating to students the relationship between symmetry, structure and spectroscopy... <http://www.rsc.org/ej/qu/1998/F9808830/index.htm> or via the PhysChemComm listings at: <http://www.rsc.org/is/journals/current/PhysChemComm/pcccon.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> <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)

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VRML Creator
by Frank Oellien 01 Dec '98

01 Dec '98

Hallo everyone, you are welcome to test our new VRML generator for chemical structures. It implements some new features like I) switching between different display styles within one VRML scene, II) measuring of bond distances and bond angles by clicking on the atoms, III) labeling of atoms with atomic property data etc. Our service allows you to import the most common chemical structure exchange formats. I have tested it on a SGI O2 with Netscape 4.05/Cosmoplayer 1.0 and on a PC/Win NT4 with Netscape 4.05/Cosmoplayer 2.1 and IE 3.0/WorldView 2.1 without any problems. http://www2.ccc.uni-erlangen.de/services/vrmlcreator/index.html Best regards Frank Oellien -- Frank Oellien Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-26579 Fax (+49)-(0)9131-85-26566 email franko(a)ccc.chemie.uni-erlangen.de WWW www2.ccc.uni-erlangen.de/people/Frank_Oellien 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 01 Dec '98

01 Dec '98

Hi, December's MOTM is LSD, and has been written by myself. Versions using HTML only, Chime and Chemsymphony are all available from: <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> <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)

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Chemistry teaching and Internet
by Dr. Wendy A. Warr 30 Nov '98

30 Nov '98

In preparing my chemweb (the list) filter for ChemWeb.com (The Alchemist at http://ChemWeb.com) I noticed the message about the use of the Internet for teaching science and it reminded me that I had intended to reply. At least two of the ChemWeb/VEI events have concerned education - check out the Library at http://chemweb.vei.co.uk/ Also, I have written a (free) report at http://www.warr.com/chemint.html about the Chemistry and the Internet conference held in Irvine in September. Some of the presenations in Irvine were related to education. 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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MDPI's Molecules and Springer's "Molecules Online"
by Shu-Kun Lin 30 Nov '98

30 Nov '98

Dear colleagues: Thanks for the concern regarding my trouble from Springer. In answering many requests, I would like to put the open letter to Springer's "Molecules Online" editor here, where I have presented some simple facts. I already contacted with Springer's "Molecules Online" editor before. But he never gave me a reply. I am very busy and do not really have time to bother anyone or to prepare such long letter to anybody. Thanks again. Shu-Kun Lin --------- Open letter to the editor of Springer's "Molecules Online" http://www.mdpi.org/molecules/protest/indexp.htm Dear Dr. Stephen Hanessian: In order to protect the basic freedom of press and information exchange of so many of our fellow scientists who are the authors, the subscribers, and the supporters of our journal Molecules (vol.3, 1998, http://www.mdpi.org/molecules/) from further damage by Springer Verlag, on a very basic ethical ground and in light of the following reason, please consider whether you resign from the editor-in-chief position of Springer's "Molecules Online". MDPI's Molecules and Springer's "Molecules Online" could have been published separately as two independent journals. However, Springer created the problem by insisting that "Molecules Online" is not a separate journal, and started this year to launch it as a "continuation" of our journal Molecules. Springer claimed in a hegemonic manner that MDPI's Molecules is not allowed to publish and only its journal can publish. The fact is that Molecules is not Springer's trademark of publication. (History will witness that Springer will finally loss this case generated by itself because it violated the basic human rights of free press.) Please also be reminded another simple fact that the founding editor (Dr. Shu-Kun Lin) of Molecules is still alive, active and has been continuously and successfully editing this journal and has never invited anybody to replace him. It has been demonstrated that I have credit to run Molecules, even though I never pretended to have any great achievement in organic synthesis (I only imagined a little bit to have chance to win a Nobel prize, I mean Nobel Peace Prize, due to my novel theoretical work on diversity assessment, my practical work on diversity preservation of both substance sample and information, and my strong advocacy on press freedom). Molecules is started as the first journal to support the preservation of molecular diversity by samples deposit. It has been treated as MDPI's official journal since 1995 as you may find from MDPI paid advertisement published in scientific journals in 1995, including several issues of "Synthesis" in 1995. We also used MDPI fund to pay all the editorial work, including paying a guest editor. Springer never paid me a penny during the whole year of 1996. Springer only provided publication service for the journal edited by me and for vol.1 publication only, before Springer unilaterally and suddenly terminated the contract of publication service at the end of 1996. Because of the ruthless harassment from Springer, we cannot make our papers published by MDPI in 1997 and 1998 available to the public for months and cannot publish any of the recently accepted manuscripts. During recent six months, Springer even insisted on deleting all of our papers published already in Molecules vol.2, 1997 and vol.3, 1998. Published papers are very much like born babies. Can you put them back into their mother's body? From this case, as you might have also realized, Springer's present executive in this division of publication has no respect on our scientists' basic rights. Like many of your colleagues in Basel, Switzerland, I have attended your lectures and I like them very much. You are a good scientist. You should have no difficulty to launch your own new journal successfully. To our scientists in organic chemistry, Springer might be a great company because it was the publisher of Beilstein database (This database is definitely no longer published by Springer now). However, it is not so great as to risk one's reputation and to let Springer continue to use your name and to put you on a position only to try to destroy your fellow scientists' established journal Molecules. The case of Molecules already caused public anger against Springer. My colleagues and I will greatly appreciate it if you support our Molecules instead of collaborating with Springer to destroy it. We want to go on with our unique publication policy of Molecules and continue our great efforts to preserve and exchange chemical samples and experimental data. With best regards, Sincerely, Dr. Shu-Kun Lin Editor-in-Chief, Molecules (ISSN 1420 3049) http://www.mdpi.org/lin/ Basel, 30 November 1998, via e-mail 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: ORGLIST: Challenge: To find Reaction with most bond forms/cleaves (fwd)
by G.P.Moss 30 Nov '98

30 Nov '98

If you include enzymic reactions then an 11-bond example is the cyclisation of squalene epoxide to a number of triterpenoids such as hopanol. In the laboratory this type of acid catalysed cyclisation does occur but I doubt if an 11-bond example is known. Gerry Moss _________________________________________________________________________ Dr GP Moss Telephone: +44 171 775 3262 Department of Chemistry Queen Mary & Westfield College Facsimile: +44 181 981 8745 Mile End Road London E1 4NS, United Kingdom E-mail: g.p.moss(a)qmw.ac.uk World Wide Web server: http://www.chem.qmw.ac.uk/ IUPAC chemical nomenclature data base: http://www.chem.qmw.ac.uk/iupac/ IUBMB biochemical nomenclature data base: http://www.chem.qmw.ac.uk/iubmb/ 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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