January 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
by Paul May 31 Jan '98

31 Jan '98

Hi, February's MOTM is Sulfanilamide, which is an antibiotic drug. The page has been written by Peter Tebbutt from Cherwell Scientific Publishing, and is a really good example of how java applets on a page can really enhance scientific presentations. The page also contains information on various other molecules which are structurally related to Sulfanilamide, such as Protonsil, folic acid, and sulfathiazole. The direct URL is: http://www.cherwell.com/chemsymphony/sulfanil.html or via the MOTM page at: http://www.bris.ac.uk/Depts/Chemistry/MOTM/motm.htm Regards, ------------------------------------------------------------------------- Dr Paul May, School of Chemistry, University of Bristol, UK tel: +44 (0)117 928-9000 x4276, fax: +44 (0)117 925-1295 <mailto:paul.may@bris.ac.uk> <http://www.bris.ac.uk/Depts/Chemistry/staff/pwm.htm> "Can you imagine a world in which there are no hypothetical situations?" ------------------------------------------------------------------------- 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

share your results by publishing short notes
by Shu-Kun Lin 27 Jan '98

27 Jan '98

Hi, colleagues: If you have some pieces of experimental results regarding a natural product, I would like to invite you to publish them and share them with other chemists. Molecules publishes in a column of "MolBank" very short notes of experimental data records for individual molecules. Any scattered unassembled experimental data for individual compounds which is conventionally not publishable is particularly welcomed, to be published as one-paper one-page for one structure and given special page numbers (M1, M2, etc.). We continue to publish in vol.3, 1998, see http://mdpi.org/molbank/ website. So far all the short notes in this section were covered by indexing and abstracting services. This publication is completely nonprofit activiy. I need your contributions! Shu-Kun Lin --------------------------------------------------------- Dr. Shu-Kun Lin Molecular Diversity Preservation International (MDPI) Saengergasse 25, CH-4054 Basel, Switzerland MDPI http://www.mdpi.org/ Molecules: http://www.mdpi.org/molecules/ e-mails: Lin(a)ubaclu.unibas.ch Lin(a)mdpi.org Tel. +41 79 322 3379, Fax +41 61 302 8918 -------------------------------------------------------- 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

Pharmaceutical XRD Data plus warning for QARR Participants
by L.M.D.Cranswick＠dl.ac.uk 26 Jan '98

26 Jan '98

Pharmaceutical XRD Data plus warning for International Quant Analysis Round Robin participants Hi All, Announcement relating to the International Union of Crystallography, Commission on Powder Diffraction, Quantitative Analysis Round Robin. If other people in your department or laboratory may be interested in this International Quantitative Analysis Project, please consider posting up a printout of the web-page the local notice-boards - or forwarding this message on. Topics for today's message: - Warning about Siemens/Bruker and XDA formatted data grabbed from CPD Round Robin Web site prior to Jan 26 1998. - Pharmaceutical Powder XRD Data now Available for Analysis. ----- Warning: about converted data on the CPD Quantitative Analysis Round Robin Web Site at: http://www.dl.ac.uk/SRS/XRD/IUCR/QARR/ http://www.dl.ac.uk/SRS/XRD/IUCR/QARR/data-kit.htm Up till Jan 26, Bruker/Siemens RAW files and XDA format files were not converted correctly. If anyone grabbed these files previous - clear the cache of your web-browser, press the reload button and grab these files again. If unsure or you wish to check validity of converted files - compare with the LHPM *.dat files on the web site. Be aware that due to the different ways programs interpret the compress/encrypted Philips RD XRD format for reading and conversion - counts may be not completely identical - but very close within an ESD of the "X-ray count". The Philips RD format is known for using a compression/ encryption method that slightly modifies the raw counts passed from the XRD to the Philips datalogging software RD files. Best place for more elaboration on this is the VLGM list where this has been a known and discussed problem: http://www.geol.uni-erlangen.de/vlgm/index.html (No room here for a big rant on binary raw data formats - "It's not malicious - just incrediably evil!") ----- Pharmaceutical Powder XRD Data now Available for Analysis. Another update that the "Standard" Pharmaceutical data for the International Union of Crystallography (IUCr) - Commission on Powder Diffraction (CPD) - Quantitative Phase Analysis Round Robin is now available over the web at: http://www.dl.ac.uk/SRS/XRD/IUCR/QARR/ http://www.dl.ac.uk/SRS/XRD/IUCR/QARR/data-kit.htm (the Inorganic/Mineral samples of course are still there) Crystal structure information from the literature relevant to the Pharmaceutical data will be added later on the Web-site. This is intended for those who do not have access to their own or a library structure database and are using structure based methods. --- People who ordered pharmaceutical samples - these are now in the post. Please note that people who want to run samples are not limited to Powder Diffraction in their analytical methods. (i.e., XRF, Web Chemical, IR, etc can be used) but we request as their is no chemical ambiguity in the phases/compounds present (as was originally intended) that you use your "usual" single method - whatever that may be. --- Other updates are: Besides the standard data archived in ZIP format, tar.Z and tar.gz have now been added. Other data formats are slowly being added - latest is DBWS format. Nearly every Powder Diffraction program in existence should be able to use one of the formats present - with possible minor changes in the header(?). If not, please email me. It has been reported that when grabbing individual files, Netscape seems to be corrupting the binary Siemens/Bruker RAW and Philips RD files (might be interpreting them as ASCII?). Quickish solution is just to grab one of the archive files. ---- Again, if any queries on this, feel free to email. Lachlan. -- Lachlan M. D. Cranswick CCP14 for Single Crystal and Powder Diffraction Daresbury Laboratory, Warrington, WA4 4AD U.K Tel: +44-1925-603703 Fax: +44-1925-603173 Room C14 E-mail: l.cranswick(a)dl.ac.uk Personal Crystallographic WWW: http://www.unige.ch/crystal/stxnews/stx/volnteer.htm Commission on Powder Diffraction, Quantitative Phase Analysis Round Robin: http://www.dl.ac.uk/SRS/XRD/IUCR/QARR/ Society of Crystallogaphers in Australia (SCA): http://www.sca.asn.au/ Australasian Web Publishers Association: (AWPA): http://www.awpa.asn.au/ Australian X-ray Analytical Association (AXAA): http://www.latrobe.edu.au/www/axaa/ 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

Chime and Internet Explorer 4.0
by Rzepa, Henry 26 Jan '98

26 Jan '98

There is great interest in Microsoft and its policy with Internet Explorer, and some interesting comments from Michael Toy of Netscape about "We are working hard to figure out not only how we make the source available, but to also really get out of the way of a net-community based effort to make great client-side software". This has been interpreted by some as saying that Netscape will release the source code for V 5 of their browser, and then hand over further development to the community. Anticipating that the chemical community might in the medium term have to rely on Internet Explorer only, I decided to see how Version 1 of Chime would work with the latest released version of IE 4.0. Microsoft, whilst they had <10% of the browser "market", took at least some care to be "compatible" with Netscape, and this included supporting the Netscape plug-ins. The Chime plug-in mostly worked with IE 2 and 3 (although it was flaky, as the developers of Chime themselves pointed out). All you had to do was to insert Chime into the IE plug-ins folder, and it (sort of) worked. Now that Microsoft reputedly have >50% of the browser market, they appear to have a rather different attitude. It may be a salutory lesson for the future. Firstly, let me say how Netscape handled plug-ins. By installing a plug-in, the user automatically had configured for them all the appropriaate MIME types supported by that plug-in. This included lets say chemical/x-pdb for a typical chemical MIME type. Microsoft handle MIME in a much more complicated way. On Windows, its via the system wide registry. On a Mac, they attempt to achieve such a system wide configuration by using a separate program called Internet Config. What follows here is specifically for the Mac. I have not yet done this on a PC. When I installed IE 4 on my Mac, I specifically asked that all the preferences be imported from Netscape rather than using Internet-config 1.4 (which does not recognise plug-ins). This should have included configuring IE 4 to use the Chime plug-in. I had carefully first installed a copy of Chime in the IE plug-in folder before starting it. So what in the end happened? IE ignored all the Netscape chemical MIME types, and despite being asked not to, defined the (two only of about 10) chemical types defined by default by Internet Config. These were not associated with the Chime plug-in but instead the option set was to "save to disk". Now, IE DOES offer a reconfiguration option to instead resolve the file to a plug-in. If this is set manually to Chime, and IE 4.0 is offered a pdb file, it again refuses to use Chime, and instead IE cycles in a hung loop. Arguably, all of this might just be an "oversight" or "bug" in IE 4.0, or a newly introduced incompatibility with Chime 1.0 which might be fixed at version 2.0. But it does mean that a chemical use with a Mac trying to migrate to IE might be tempted to give up with Chime, and find it easier to say %$! to plug-ins, they are only ropey old Netscape technology anyway. Presumably, if we REALLY care about chemistry, we will re-invent the web the Microsoft way using ActiveX (at our own time and expense) and all will work again. On a PC. Probably not on Unix or Mac. Or maybe the future is with XML custom solutions, of which CML (chemistry markup language with Peter Murray-Rust's JUMBO CML viewer) is one example. Microsoft, I might add, are ardent adoptees of XML. Perhaps the common denominator that the chemical community was briefly able to achieve during the period 1996-1997 with the "old style" web browser and a plug-in such as Chime was just a temporary phenomenon. Arguably, one might look back to that period as a golden, simple one where many people could be molecularly enfranchised with little effort. We may never see its like again. Henry Rzepa. +44 171 594 5774 (Office) +44 594 5804 (Fax) +44 575 1839 (Home) 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)

2 1

RE: Free Netscape (fwd)
by David Hughes 26 Jan '98

26 Jan '98

Microsoft may have some technical issues to clear up with respect to security with Internet Explorer, too, before they can declare victory in the browser wars. See http://www.techweb.com/infoseek/news/story/TWB19980123S0007 for details. David Hughes MDL Information Systems AG ("But speaking for myself, not for my employer.") > -----Original Message----- > From: Dr. Alan Mills [SMTP:alan@venus.co.uk] > Sent: Monday, January 26, 1998 11:32 AM > To: ChemWeb List > Subject: Free Netscape (fwd) > > > Game's not Over, Henry - see below. > > The US Courts are also trying to inflence events. > > > Rgds., > > Alan Mills at Venus Internet Ltd, 24 Denmark Street, London WC2H 8NJ, > UK > email:alan@venus.co.uk web:http://www.venus.co.uk > Tel: +44 (0)171 240 5858 Fax: +44 (0)171 240 5859 > Providing Web and Internet services and solutions > > > > ---------- Forwarded message ---------- > Date: Mon, 26 Jan 1998 09:38:04 +0000 (GMT) > From: Brian Kelly <lisbk(a)ukoln.ac.uk> > To: web-support(a)mailbase.ac.uk > Subject: Free Netscape > > netscape have announced that the Navigator / Communicator browser will > be > available for free. In addition the source code of the browser will > be > available. > > Interesting? > > See <URL:http://www.netscape.com/news.html> > > Brian > > ------------------------------------------------------ > Brian Kelly, UK Web Focus > UKOLN, University of Bath, BATH, England, BA2 7AY > Email: b.kelly(a)ukoln.ac.uk URL: http://www.ukoln.ac.uk/ > Homepage: http://www.ukoln.ac.uk/ukoln/staff/b.kelly.html > Phone: 01225 323943 FAX: 01225 826838 > > > > 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)

1 0

Free Netscape (fwd)
by Dr. Alan Mills 26 Jan '98

26 Jan '98

Game's not Over, Henry - see below. The US Courts are also trying to inflence events. Rgds., Alan Mills at Venus Internet Ltd, 24 Denmark Street, London WC2H 8NJ, UK email:alan@venus.co.uk web:http://www.venus.co.uk Tel: +44 (0)171 240 5858 Fax: +44 (0)171 240 5859 Providing Web and Internet services and solutions ---------- Forwarded message ---------- Date: Mon, 26 Jan 1998 09:38:04 +0000 (GMT) From: Brian Kelly <lisbk(a)ukoln.ac.uk> To: web-support(a)mailbase.ac.uk Subject: Free Netscape netscape have announced that the Navigator / Communicator browser will be available for free. In addition the source code of the browser will be available. Interesting? See <URL:http://www.netscape.com/news.html> Brian ------------------------------------------------------ Brian Kelly, UK Web Focus UKOLN, University of Bath, BATH, England, BA2 7AY Email: b.kelly(a)ukoln.ac.uk URL: http://www.ukoln.ac.uk/ Homepage: http://www.ukoln.ac.uk/ukoln/staff/b.kelly.html Phone: 01225 323943 FAX: 01225 826838 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

Award winninmg chemists sought
by Dr. Wendy A. Warr 21 Jan '98

21 Jan '98

(With apologies for duplicate postings) BS/MS Chemists Sought for Technical Achievement Awards The Organic Division of the ACS is seeking to increase the involvement of Bachelor's- and Master's-level chemists in Divisional activities. Although these individuals regularly make important contributions in the workplace, all too often they receive little or no recognition for their efforts from the scientific community. As one of the means to address this situation, the Organic Division has instituted an annual symposium at the Fall ACS meeting to recognise the achievements of non-Ph.D. chemists. They are now seeking nominations for the coming year's programme. The seventh annual Symposium on Technical Achievements in Organic Chemistry will be held at the 216th National Meeting of the ACS in Boston, Massachusetts during the week of August 23-27, 1998. The invited speakers will present their recent discoveries in basic or developmental research. The Division is looking for candidates who are both excellent scientists and good communicators. To nominate a chemist for this symposium, please send a letter describing the nominee's contributions to Dr. Anthony W. Czarnik IRORI Quantum Microchemistry, 11149 North Torrey Pines Road, La Jolla, CA 92037-1031, USA, and include a copy of the candidate's curriculum vitae. Deadline for receipt of nominations is February 28, 1998. Enquiries to aczarnik(a)irori.com -- 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

Academic Collaboration sought
by Adam Hodgkin 20 Jan '98

20 Jan '98

Hello Internet Chemist Is there an academic group that would be interested to collaborate with us on this innovative and useful project. ChemSymphony is a platform-independent set of interactive Java applets that allows 3-D molecular structures to be easily incorporated into HTML documents. The structures can be manipulated in real time, rendered in a variety of styles which may be edited by the user. We will shortly release a 2D sketcher. The ChemSketcher has been developed primarily as a tool for generating, editing and manipulating search queries. It is not intended to be a Desktop publishing tool, rather it allows user to quickly enter/edit his own structures so that these can be passed to other applets for searches, calculations, listing, display etc. Our alpha-test version of the sketcher can be seen at: http://www.cherwell.com/cssubmit/ (an unlinked page and no documentation yet). While testing the ChemSketcher applet it has struck us that the ChemSymphony suite can be used to create a valuable Internet resource. From the sample page we have the ChemSketcher pointing to two or three databases which the user can then search. The procedure is as follows: 1.The user draws a chemical fragment a 'substructure' which is a subset of what he seeks. 2.When the substructure is complete the user moves to another SubmitStructure applet where he can generate a SMILES string which he may then submit to a database. 3.The applet knows which database to search because it obtains this information from some parameters in the HTML page in which the applet is itself embedded. Look at the source for the page. 4.An efficient and powerful feature of this arrangement is that the SubmitStructure applet takes the parameters from the HTML page and uses them to create an option on its Action menu for the user. The Action Menu and the combination of Applets can handle a very large list of databases which can be extended by the simple procedure of copying, pasting and editing some simple HTML code. A crucial element of this procedure is that the list of target databases can be indefinitely and automatically extended. This opens the possibility of setting up a procedure which could search the complete www for molecular structures, or allow the enduser to select a set of databases which he wishes to search on a periodic basis, or to select subsets which are known to be efficient for special purposes. This would be a nice project for a collaboration with an academic group which is trying to build internet resources for chemists. Being a dedicated software company we do not have the motivation to search the web for molecular resources and develop the editorial resource base that should support an effort of this kind but we would be very interested to work with a group that does want to do this. Java is clearly the best way of doing this. If you are interested in helping this to happen, please contact me Adam Adam Hodgkin adam(a)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

Copyright for postings to this list.
by Rzepa, Henry 13 Jan '98

13 Jan '98

Part of this is a cross posting from the chminf-l by Patrick van der Walk, so apologies to those who have seen it. It contains some interesting aspects of copyright. As far as this list is concerned, I concur with the conclusions below, ie the copyright for each posting to this particular list resides with the poster. Actually, I confronted this problem about 1 year ago. I wanted to "distill" the list as it then was onto an ECTOC CD, so that the list could be archived "for posterity". I was advised I would have to contact everyone who had posted for their permission to do this. I gave up instantly any idea of such a project. Which is a shame, because few if any discussion lists have ever been properly preserved for "posterity". Some might say thank goodness, but I still think its a bit of our history, and feel its a shame to loose it (apart from the warts. We could certainly do with loosing those. Some of you will know what I mean by that). Does anyone have any strong opinions on whether lists like these deserve to be preserved, or to be lost? > >"ChemConnect runs a 'Chemistry Journals Page Alert'. This is a service >to those who want to be informed when we have additions or changes in >our chemistry journals page at ><http://www.chemconnect.com/library/journals.shtml>. > >Recently we increased our service to our subscribers by sending >out a supplement with information and news about (on-line) >chemistry journals. One of our sources for this information is >the CHMINF-L discussion list. However, we are not familiar with >the copyright regulations concerning such a public list. > >Does the CHMINF-L discussion list have any 'copyright' >regulations on the postings? Do we need to ask the individuals >for permission to use their postings?" > >Miloslav Nic suggested that chminf-l should contain something like >GNU (http://www.gnu.org/) General Public License >http://www.gnu.org/copyleft/gpl.html > >I asked the opinion of Barbara Polansky, the copyright expert at ACS and >she gave me permission to post her comments to appropriate lists/people. > >"Whenever anyone sends a comment to a listserv, it's like they're >writing a letter, and the one who writes a letter is the copyright owner >(unless the message is written within the scope of one's employment >duties, in which case the employer is considered the author). > >Everyone "understands" that listserv messages are posted for the public >to read, and that others might re-post all or portions of the original >message in a comment, and perhaps forward the message for other >discussion, such as you have done for me. This does not put the >messages in the public domain, just because the posting is available to >the public. So, if the messages are used for other purposes, e.g. sent >to people who _subscribe_ to a service, then the postings would be used >in a commercial sense, and I would recommend that the individual >writers' permissions be obtained." > >To Mr van Der Valk, Barbara added > >"Even if the "subscription" is non-paying, I would still recommend that >you get permission from the authors because they are not submitting >their message to your service. It would be as if they are writers for a >magazine, and find that you have snatched up their piece. This is just >my recommendation, and I'm sure you will hear from others who might >think that this is fair use. I always recommend... better to be safe >than sorry." 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