- chemweb - imperial.ac.uk

Molecule of the Month - June
by Paul May 02 Jun '03

02 Jun '03

Hi, June's MOTM is actually a group of molecules called Pnictogens, which are compounds of phosphorus, arsenic, antimony, and bismuth, and which form all sorts of useful semiconductor materials. The page has been written by David Bradley. http://www.bristol.ac.uk/Depts/Chemistry/MOTM/motm.htm#june2003 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> Bumper sticker: "Where are we going? And why are we in this hand-basket?" ------------------------------------------------------------------------------ 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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Autmated vs Manual use of e-Journals?
by Rzepa, Henry 02 Jun '03

02 Jun '03

An interesting incident occurred here last week which I thought I might share here, because of the interesting implications it has. Access to one publisher's ejournals here at Imperial was discovered to be barred one morning; urgent enquiries established that one possible cause was an apparent detection by the publisher of "systematic downloading" of articles from one journal by "suspected automated means". I think in fact that most publishers have clauses somewhere in their conditions of use which prohibit this. It is ironic of course that whilst computers and software have automated and systematised much else in the scientific publishing process, the actual act of downloading a file must still apparently be done by manual means. Juxtapose this onto the vision some have of a "Semantic Web" where machine software is enabled to do many (routine) actions currently done in a slow (and error prone manner) by humans. The "chemical semantic web" is young still, but some small aspects could be achieved. One could easily imagine bibliographic software which could be primed with user keywords (metadata) to automatically retrieve articles from journals of interest to its (human!) controller, perhaps initiated by the RSS mechanism I posted to this forum a few weeks ago. I suspect however that such use would probably contravene many a publishers conditions of use. It will be interesting to see how publishers respond to such trends, or conversely whether the limitations imposed by publishers inhibit the development of such automation. -- Henry Rzepa. Imperial College, Chemistry Dept. +44 0778 626 8220 +44 020 7594 5804 (Fax) 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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JChem 2.0.1 released
by Ferenc Csizmadia 27 May '03

27 May '03

Apologies for multiple postings. JChem 2.0.1 has been released. The package contains Java applications and software development tools for chemistry. The software is portable (runs under Windows, Mac OS X, Unix, etc.) JChem Base provides chemical database searching capabilities by integration into relational database engines supporting SQL. Modules: - Standardizer (new): Structure canonization tool converting molecules from different formats into standard representation. - Screen (new): Screening based on pharmacophore or chemical fingerprints or other descriptors. - Reactor (new): Generating reaction products from reaction equations and reactants. - Fragmenter (new): Generating building blocks based on Recap rules from molecule libraries. - Metabolizer (new): Metabolism simulation using user-defined transformation rules. - JKlustor: clustering and diversity calculations based on molecular fingerprints or other properties. The software can be tried/downloaded at http://www.chemaxon.com/products.html Online demos: http://www.jchem.com/examples.html Regards, Ferenc -- Dr. Ferenc Csizmadia Managing Director ChemAxon http://www.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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Marvin 3.1.3 released
by Ferenc Csizmadia 27 May '03

27 May '03

Apologies for multiple postings. Marvin Applets and Marvin Beans 3.1.3 have been released. The packages contain software development tools and applications for chemistry. Marvin Applets and JavaBeans support drawing/displaying chemical structures and handling molecule objects. FREE: - Marvin Applets are free for free web sites. - MarvinSketch and MarvinView applications accessed from ChemAxon's web site http://www.chemaxon.com/marvin/jnlp/index.html - Locally installed MarvinSketch, MarvinView, and MolConverter applications. Recent changes: - New installer of Marvin Beans for Windows and Mac OS X (Shortcuts for the MarvinSketch and MarvinView applications) - MarvinSketch can open 3D viewer windows. - Extended Molfile (V3) export. - Improved partial charge, pKa, logD predictions - Chart display for logD prediction - Atom polarizability plugin - Improved PDB support - Faster loading of applets The software can be tried/downloaded at http://www.chemaxon.com/products.html Online access: Applications (If you have Java installed): http://www.chemaxon.com/marvin/jnlp/index.html Applet demos: http://www.chemaxon.com/marvin/demos.html Examples for developers: http://www.chemaxon.com/marvin/doc/dev#examples Regards, Ferenc -- Dr. Ferenc Csizmadia CEO ChemAxon http://www.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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RE: Accelrys ViewerLite
by Parkin, D (Don) 22 May '03

22 May '03

On Tuesday 21 May, David Roberts wrote:- >> It has just come to my attention that Accelrys has withdrawn its excellent free >> molecular viewing package ViewerLite and now only offers ViewerPro which retails >> at $299. I would be interested (a) to know the reaction of other users of this software >> to the news and (b) if there are any alternative freeware applications that offer the >> same or similar functionality particularly for viewing crystal lattices. Have you looked at Mercury from the Cambridge Crystallographic Data Centre. It is a free product (subject to conditions of use) and can be used to view crystal lattices. Packing can be done and Angles and Distances measured. (see http://www.ccdc.cam.ac.uk/prods/mercury/index.html) Regards Dr. Don Parkin --------------------------------------- Chemical Database Service, Daresbury Laboratory, Warrington, Cheshire WA4 4AD Phone: +44 1925 603162 e-mail: d.parkin(a)dl.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)

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Viewer Lite
by Keith Wilkinson 21 May '03

21 May '03

Dear Colleagues, Is there any legal implication in an institution supplying students (or continuing to supply students) with the Viewer Lite (once free and now obsolete) burned onto a CD-rom, whether as a library item for borrowing (and installation) or as the Open Uni do in their excellent courseware, supply the student with the installation program on a CD along with other software? In that way, perhaps the program could continue in circulation? I cannot otherwise think of an immediate replacement, although there are a host of molecular viewers available. This is indeed a bad day for the chemical educational community. regards, Keith /*--------------------------------------------------------------------- Keith Wilkinson, Science Department, International School of Lusaka, Zambia tel: +260 (0)1 239546 fax: +44 (0)709 220-5181 E-mail: <mailto:k.wilkinson@dunelm.org.uk> Home URL: <http://www.ecis.org/lusaka> Chemistry : <http://www.chemclub.com/teachers> teachers e-mail discussion forum ----------------------------------------------------------------------*/ 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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Accelrys ViewerLite
by D.R.Roberts 21 May '03

21 May '03

It has just come to my attention that Accelrys has withdrawn its excellent free molecular viewing package ViewerLite and now only offers ViewerPro which retails at $299. I would be interested (a) to know the reaction of other users of this software to the news and (b) if there are any alternative freeware applications that offer the same or similar functionality particularly for viewing crystal lattices. David Roberts > _______________________________________ > > Dr David R. Roberts > Senior Lecturer in Chemistry > Chemistry Department > The Open University > Walton Hall > Milton Keynes > MK7 6AA > United Kingdom > > Tel +44 (0)1908 653219 > Fax +44 (0) 1908 858327 > e-mail d.r.roberts(a)open.ac.uk > www http://www2.open.ac.uk/Chemistry/DRR.html > <http://www2.open.ac.uk/Chemistry/DRR.html> >

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Molecule of the Month - May
by Paul May 30 Apr '03

30 Apr '03

Hi, May's Molecule of the Month is really a colection of molecules all based around so-called 'N3 amide dyes', which are currently being investigated for use in the next generation of solar cells. The page has been written by Jean-Jacques Lagref from Novartis in Switzerland. http://www.bristol.ac.uk/Depts/Chemistry/MOTM/motm.htm#may2003 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> Bumper sticker: "Where are we going? And why are we in this hand-basket?" ------------------------------------------------------------------------------ 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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On Blogging, RSS and Metadata
by Rzepa, Henry 29 Apr '03

29 Apr '03

Its interesting how cultures and communities are regarded. This email is about metadata (worthy, but boring), RSS (yet another acronym, and hence nerdish) and Blogging (a turn off for purists, a revolution for others). >From what I can gather, the chemistry community has not (at least overtly) adopted any of these with any enthusiasm. The purpose of this email is to convince you that I think enthusiasm deserved. So, if I have caught your attention, let us proceed. Once upon a time, Web sites were controlled by Webmasters, and some over a period of time become "must visit" sites, others less so. Content was king, as the saying goes. Then static content started being replaced by dynamic content, generated from databases etc; a popular combination nowadays is PHP/MySQL. The poor user had to visit almost on a daily basis to get the most out of the site, and of course it did not scale (no-one has to the time to visit even a few sites on a regular basis). The problem was "metadata", ie how did you find out if the site (in its daily reincarnation) might be of interest? Then, about 1999, Netscape, followed by others, introduced "Web Logging", pronounced "Blogging". This is essentially a regularly updated (probably daily) diary of items and events, probably written by an individual, and disseminated via a personal web server. Suddenly faced with perhaps having to visit 1000s or more web sites, the blogging community woke up to "metadata". A standard (by then based on XML) for specifying this was invented, called RSS. Being more a cultural phenomenon (and not invented by computer scientists, who looked down on much of this) it almost inevitably bifurcated into RSS 1.0 (the purist camp, who based it on a standard known as RDF) and RSS 2.0 (yes, its confusing, based on an "easy to use" version proposed by Dave Winer). There are many ways of thinking about RSS; the one I find most rewarding is to think of it doing for hyperlinks what HTML did for content, ie it provides a formal link management format which separates most importantly the content from the manner in which it is presented to the user. So, a Blog can now promote its presence by offering what is called an RSS feed (or channel) with carefully crafted metadata indicating what items there are, when/where they were posted, who wrote them, and (perhaps most importantly) what can be done with them and how they relate to each other RSS channels can now be aggregated, or organised into subjects, themes, communities etc, using RSS aggregators (of which there are around 10 now for various OS platforms). You can also search for them using "syndicators" and also perform Google like searches on just them (and not the web in general). So why should the chemistry community generate enthusiasm about RSS? Well, think of a published chemistry journal. Its really just a very high class Blog (which is enhanced with peer review, etc). You as reader can perhaps visit 5 e-journals a day and check to see what is new. But often, you will only do two things a) look at the graphical abstract, or table of contents b) prize open an Acrobat file to see if you are really interested in it. The latter has the undesirable consequence that after several years of doing this, you will have perhaps 1000 un-manageable Acrobat files on your hard disk (yes, I know you can organise them with EndNote, but in truth, its a pretty primitive system). Far better then to create an RSS entry for each new journal article, and have the user subscribe to the journal "channel". So here I issue my first rallying call. Can I urge all chemistry journals to offer an RSS feed or channel for their readers? If you have managed to read this far, you are probably wishing for some examples. so, invoke the following link http://purl.org/net/syndication/subscribe/?rss=http://www.ch.ic.ac.uk/rzepa… This takes you to a syndicator, and it will check (actually XML validate) http://www.ch.ic.ac.uk/rzepa/index.rss, this being the RSS feed for my Blog (well, previously known as Web page). It will offer you information about 9 RSS clients or aggregators, and if you have them installed, it will insert this feed into your local copy. You do this to all RSS feeds you wish to have (say about 100?) including the journals I encouraged above! You leave this program running, and it will periodically check to see what is new and alert you. Some RSS clients will do more (much more is promised!). NewsMonster will index and archive the RSS feeds, so that you (will be able to) search the entire aggregate, and also archive so that entries that scroll off the bottom remain on your hard disk. Arguably, you need no longer download those Acrobat files, but merely ensure you have a pointer to them so that you can access them whenever you need. This is not the place to go into what else can be achieved with RSS (being XML, it can be manipulated in astounding ways), how it is created, how it can be extended etc; a more formal article is on its way exploring this in a chemical sense. So, to find out how/whether RSS is useful to chemists, can I issue my second rallying call Will all chemistry content provider who have new and interesting announcements to make on web sites consider putting up an RSS feed For example, http://xml.mfd-consult.dk/syn-sub/?rss=http://www.ch.ic.ac.uk/motm/index.rss will announce new entries for our local Molecules of the Month pages. -- Henry Rzepa. +44 (0870) 132 3747 (eFax) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, 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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More on RSS Feeds
by Rzepa, Henry 29 Apr '03

29 Apr '03

Following up on my earlier posting, it struck me that one interesting immediate application is to use it as an aggregator for seminars and talks given at various university departments and elsewhere. Such does not really exist in any (maintainable) form, and a little thought suggests that the ways of communicating interesting talks by people are relatively un-impacted by eg the Web etc (most explicit lists of colloquia are normally mounted as eg an Acrobat file, and not updated for years!) So http://rssxpress.ukoln.ac.uk/view.cgi?rss_url=http://www.ch.ic.ac.uk/index.… is another way of viewing an RSS feed on merely a Web browser (as an easier alternative to installing it into an RSS aware client. The above does not really handle the metadata properly; thus the date of each seminar is declared as so called DC data and hence only viewed by a program that can process it. It follows of course that one could sort such RSS feeds by eg data (week, month, year etc) or perhaps by location, and certainly by topic or speaker. Thus you might use it to find out any presentations on asymmetric catalysis in Edinburgh in 2003 (I cannot wait to see the ACS national meeting lists so presented, finding something in the 5000 or so talks and posters is always a challenge!). On the premise that one should only introduce one acronym per message, I will note http://www.opml.org/ which is a sort of meta-metadata description. Thus collections of RSS feeds (or subscriptions) can be outlined using opml, and a set of subscriptions generated in one program can be imported into another using a .opml file (many of the RSS clients support this). And on a historic note, I find it interesting that the first use of such outlining files was by Doug Engelbart in the 1960s (he of the invention of the mouse and much more). OPML files, by the way can be "viewed" by the appropriate stylesheet transform (eg <?xml:stylesheet type="text/xsl" href="opml.xslt" version="1.0"?> a process which illustrates that the family of XML languages can be converted from one to the other, with only as much information loss as you wish to occur. You will no doubt appreciate that "chemistry" can participate in this process quite happily via its own XML sub-family (which includes eg the CML family, now about five strong by the way). Also on the above theme, I hope its only a matter of time before "industrial strength" programs such as e.g. EndNote start to support RSS and the concepts outlined above. -- Henry Rzepa. +44 (0870) 132 3747 (eFax) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, 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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