August 1996 - chemweb - imperial.ac.uk

Unknown features of GIF files
by Rzepa, Henry 16 Aug '96

16 Aug '96

It is a common myth (I certainly believed it) that GIF images are limited to 256 colours. Thus chemical diagrams with lots of depth cueuing, etc etc often loose something in the translation to 256 colour GIF and JPG format has to be used instead. A program is available on http://www.cafe.net/peda/iag/ which demonstrates that more than 256 colours are possible. What this does for network bandwidth however is another matter. Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa(a)ic.ac.uk; Tel (44) 171 594 5774; Fax: (44) 171 594 5804. URL: http://www.ch.ic.ac.uk/rzepa/ (Eudora Pro 3.0) ----- 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)

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Another ChemWeb?
by Paul Deards 15 Aug '96

15 Aug '96

MDL Information Systems and Current Science Group issued a press release yesterday, announcing a new $6M "on-line club" for chemists, to be called ChemWeb. To quote the release: "ChemWeb will provide secure access to a large number of scientific journals, databases, and references as well as discussion groups, electronic meeting rooms, news services, a job exchange and a shopping mall. ChemWeb will build on the success of Current Science Group's BioMedNet, a popular web club for biological and medical scientists, and MDL's database and Web technologies which provide swift, flexible access to molecular and chemical data. Users will be able to search the entire site through text or chemical substructure. ..... ChemWeb will benefit from the design of BioMedNet's proprietary framework as well as MDL's ISIS and database products....ChemWeb will also incorporate MDL's recently announced Chemscape products. ...MDL will offer its chemical databases and Current Science Group will post its journals via ChemWeb. All academic and commercial information publishers will be able to provide services through ChemWeb." The companies will be previewing the site at ACS Orlando, 25-28 August. The press release is a bit sketchy on details, but $6M seems a major investment and it looks like the companies are aiming to make ChemWeb *the* major subscription chemistry service (with a $6M investment, you can bet that this won't be a free-access site!) So, (1) How does this affect this mailing list...can we expect horders of lawyers banging down Henry's door, demanding a name change? (2) Is this the wave of the future? Useful chemical content as a subscription-only service? (3) Most of the comments from this list so far have concerned the free end of the internet. However, there's a lot of people out there (particularly in industry), using these subscription services. Personally, I've never been in an institution that could afford the access fees. But those of you who do have access, what are your opinions? Do these services offer more than you could get for free? How do you rate the individual services? Are they good value-for-money? It would be great to hear some comments, as the subscription side of the internet is often ignored in the press and mailing list/newsgroups. ---------------- Paul Deards Internet Publisher Chemistry and Industry 0171-2353681 x233 pauld(a)chemind.demon.co.uk http://ci.mond.org/ ----- 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)

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Re: Searching e.g. pdb files on Web
by jsb2＠camsoft.com 11 Aug '96

11 Aug '96

>The search engine www.hotbot.com has in the >last day introduced >the facility to search for all documents which reference >e.g. a .pdb file. This returns the result of 4882 for .pdb, >966 for .xyz, 840 for mol, 463 for csml etc. >This can be combined with keyword searches. > >It is simple to imagine how a database could >be constructed quite quickly from a web robot >sent out to retrieve these files. > >Now, the only problem is to assure ourselves >that no other discipline has also used this >namespace, not to mention whether everyone >assumes the same structure for eg xyz or mol This has been done already. See http://schiele.organik.uni-erlangen.de/services/webmol.html for a discussion of these sorts of problems. The short answer is that other disciplines *have* used these namespaces, but that it is save to assume that any file that does not generate an error in a good PDB reader is a valid PDB file. It is important to keep in mind, however, exactly what this sort of search reveals. It will give a list of files that are *individually referenced* on other WWW pages. It will not give any indication of files that are themselves accessible only through another search engine. For example, I think the PDB itself has ore than 4500 entries. These files are not included in the numbers above. The ~11,000 structures we have at http://chemfinder.camsoft.com is probably in the top handful of sites that have chemical structures, but it's not the largest (quality is a different matter; I'm just talking size). I don't think any of these are indexed at hotbot or anywhere else. It is possible to create an index of chemical information on the WWW -- that is what we are doing at chemfinder.camsoft.com. It is not possible, however, to automate the process fully. A discussion of some of the roadblocks to complete automation is on the web at http://www.camsoft.com/chemfinder/errorsfound.html Jonathan Brecher CambridgeSoft Corporation jsb(a)camsoft.com ----- 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)

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Searching e.g. pdb files on Web
by Rzepa, Henry 11 Aug '96

11 Aug '96

The search engine www.hotbot.com has in the last day introduced the facility to search for all documents which reference e.g. a .pdb file. This returns the result of 4882 for .pdb, 966 for .xyz, 840 for mol, 463 for csml etc. This can be combined with keyword searches. It is simple to imagine how a database could be constructed quite quickly from a web robot sent out to retrieve these files. Now, the only problem is to assure ourselves that no other discipline has also used this namespace, not to mention whether everyone assumes the same structure for eg xyz or mol files. See the chemical MIME project for more details of this: http://www.ch.ic.ac.uk/chemime/ Henry Rzepa. +44 171 594 5774 (Office) +44 594 5804 (Fax) ----- 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)

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Elemental Discoveries: Issue 2
by David Bradley Science Writer 09 Aug '96

09 Aug '96

The latest issue of Elemental Discoveries compleat with requisite spelling errors should now be available via the following URL. http://homepages.enterprise.net/bradley/elem1.html The hard copy appears, in New Elements as before, later in the year. Thanks db -------------------------------------------------------- | David Bradley, Science Writer | | Bradley(a)enterprise.net | | Tel/Fax +44 1223 440834 (Intl) | | Tel/Fax 01223 440834 (UK) | | | | http://homepages.enterprise.net/bradley/bradhome.html | | http://ccn.cs.dal.ca/~af693/bradhome.html | -------------------------------------------------------- ----- 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)

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None
by Paul Deards 08 Aug '96

08 Aug '96

Chemistry and Industry, the fortnightly international science and business magazine, has a vacancy for a full-time member of its Web Team, based at its London offices. The successful candidate will help primarily in the production of the magazine's range of innovative and popular web sites, including the on-line version of Chemistry and Industry (http://ci.mond.org/) This will include writing daily news, articles and features for the sites, and participating in the development of new internet services. A science background is required, and experience in the chemical or pharmaceutical industries would be an advantage. The ability to author in HTML would be helpful, but not essential. Rather, we are looking for someone with an enthusiasm for the web and an ability to write quickly, clearly and accurately. Please send a covering letter, detailing the strengths and weaknesses of the current C&I site, and a CV to: The Editor Chemistry and Industry 14/15 Belgrave Square London SW1X 8PS UK applicants only. ----------------- Paul Deards Internet Publisher Chemistry and Industry 0171-2353681 x233 pauld(a)chemind.demon.co.uk http://ci.mond.org/ ----- 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)

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Molecular Diversity(references)
by James J Lieu 07 Aug '96

07 Aug '96

hello, netters: Could someone help me to locate the following references? Since I don't have access to the journal--" molecular diversity". Thanks a million! 1)Molecular Diversity 1, (1996) 183-186, Alasdair A. MacDonald, Sheila H. Dewitt, etc...................... 2)Molecular Diversity 1, (1995) 125-134 Barbara O. Scott, Aaron C. Siegmund, etc.................... PS. My fax is 502-852-8149(James Lieu). I will pay you the cost. ----- 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)

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Re(2): ACS Committee on Nomenclature
by Rzepa,Henry 06 Aug '96

06 Aug '96

I have been invited to a meeting of the ACS nomenclature committee. One item is "Internet Nomenclature". Does anyone have any points they wish me to raise? >Date: Tue, 6 Aug 1996 10:09:56 -0400 >From: pgiles(a)cas.org (Pat Giles - ext 3718 - Room 4144A) >Subject: Re(2): ACS Committee on Nomenclature >To: "Rzepa,Henry" <h.rzepa(a)ic.ac.uk> > >Dear Dr. Rzepa, > >I am pleased that you will be able to join us at our meeting in Orlando. The >meeting will be in Salon 18 of the Omni Rosen Hotel. We expect you to join us >in the afternoon, perhaps around 2pm. > >We would welcome any discussion paper on Internet Nomenclature which you might >have to offer. Henry Rzepa. +44 171 594 5774 (Office) ----- 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)

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Re: drawing lines with Chime?
by Mitchell Miller 05 Aug '96

05 Aug '96

Hello Alan, I don't think it's possible to draw arbitrary figures. However, your idea about using atomss to construct your figure, then use some RasMol script commands to give the carbons a different appearance from the rest of the structure. As for the scripting documentation, I'd suggest downloading the RasMol manual from http://klaatu.oit.umass.edu/microbio/rasmol/getras.htm#rasmanual and then having a look at our Chime Scripting tutorial page (http://www.mdli.com/chemscape/chime/example/spttutor/tutorial.html) Hope this helps! Mitch At 11:43 PM 8/5/96 +0100, Alan Arnold wrote: >Greetings from a far-flung ex-colony, > >To all Chime gurus: Is it possible to draw a series of lines on top of a >displayed molecule using the Rasmol scripting capabilities of Chime? > >For example, I'd like a hexagon to be drawn over a six-membered Si/Al ring >in a zeolite that is diplayed as a live molecule, or display the sides of a >tetrahedron encompassing a SiO4 unit, when a user presses one of those >little crossed form butons. > >I guess that an alternative is to manually construct a fake >hexagon/tetrahedron residue in the chime data file and have the script >highlight these dummy atoms. > >Any examples out there before I reinvent the wheel? > >BTW, where is the chime scripting documentation hidden? > >---- >Alan Arnold, School of Chemistry, University College (UNSW) >Australian Defence Force Academy, CANBERRA ACT 2600 Australia >voice:+61 6 268 8080 fax:+61 6 268 8002 e-mail: apa(a)adfa.oz.au >WWW: http://apamac.ch.adfa.oz.au/apa/apa.html > > > >----- >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) > > Mitchell Miller MDL Information Systems, Inc. (801) 569-1390 VoiceMail (800)955-0051 ext. 2163 mitch(a)mdli.com ----- 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)

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drawing lines with Chime?
by apa＠adfa.oz.au 05 Aug '96

05 Aug '96

Greetings from a far-flung ex-colony, To all Chime gurus: Is it possible to draw a series of lines on top of a displayed molecule using the Rasmol scripting capabilities of Chime? For example, I'd like a hexagon to be drawn over a six-membered Si/Al ring in a zeolite that is diplayed as a live molecule, or display the sides of a tetrahedron encompassing a SiO4 unit, when a user presses one of those little crossed form butons. I guess that an alternative is to manually construct a fake hexagon/tetrahedron residue in the chime data file and have the script highlight these dummy atoms. Any examples out there before I reinvent the wheel? BTW, where is the chime scripting documentation hidden? ---- Alan Arnold, School of Chemistry, University College (UNSW) Australian Defence Force Academy, CANBERRA ACT 2600 Australia voice:+61 6 268 8080 fax:+61 6 268 8002 e-mail: apa(a)adfa.oz.au WWW: http://apamac.ch.adfa.oz.au/apa/apa.html ----- 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)

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