- chemweb - imperial.ac.uk

New version of Babel (openbabel)
by Rzepa, Henry 15 Aug '03

15 Aug '03

A useful chemistry programs is Babel, which serves to interconvert (in probably a lossy manner) many of the chemical file formats that are in common or less common use. After several generations, Babel re-emerged as OpenBabel, and has a Web site at http://openbabel.sourceforge.net/. The current release (labelled Open Babel 1.100.1 ) has recently been recompiled to include a CML module which accepts both CML1 and CML2 as both inputs and outputs. Because the OpenBabel site itself (somewhat in the tradition of true Unix-oriented sites) does not offer precompiled binaries, we have compiled these for four platforms and offer such downloads from http://cml.sourceforge.net/new/ for MacOS X, SGI (Irix 6.5), Linux (Redhat 8) and Windows. The executables themselves only run from a command line (so dont expect a graphical interface). Thus Unix/MacOS X users will be familiar with eg babel -H (to get help on operation) and Windows/DOS users c:\path\babel.exe -H Typically the program is used as babel -i<input format> filename -o<output format> filename. For CML conversions the conventional use would be babel -i<input format> filename -ocml output.xml -x2apn (the last flag means use CML2, in array mode, with indented output and namespace prefix) Old time users should not entirely abandon the original version of babel, since this appears to support some formats (eg the Cambridge FDAT mode) which the new one does not. -- 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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Molecule of the Month - August
by Paul May 31 Jul '03

31 Jul '03

Hi, August's MOTM is Fluoxetine, which is the active ingredient in Prozac, the World's most widely used antidepressant drug. The pages have been written by Gemma Veitch, who is a student at Imperial College London, and was one of the entries for last year's ExemplarChem competition. The first two pages require Chime to see the structures (otherwise you just see a missing image marker), but the other pages with the chemical info on are Chime free. http://www.bristol.ac.uk/Depts/Chemistry/MOTM/motm.htm#aug2003 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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Document management
by Michael Engel 29 Jul '03

29 Jul '03

Hello, it is more a general question than a chemical one. I have huge amounts of pdf files. I often would like to add a note like a "post-it" and be able to retrieve this later including this note. Can you recommend a software which is able to do such things ? OS: either Linux (preferred) or Windows And another question: is there a fileformat preferable to pdf ? Thank you 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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Jmol v7 release
by E.L. Willighagen (Egon) 12 Jul '03

12 Jul '03

Dear all, with some delay (due to a rather interesting drug design course last week), I am proud to announce the release v7 of Jmol. Changes since v6 A much faster implementation of the rebonding algorithm is now used. VASP and Gaussian 03 readers were added. Reading of Jaguar 4.2.77, ABINIT, and AcesII files was fixed. Many thanx to the users and the developers for noticing and fixing these issues. About Jmol Jmol is a Java molecular viewer for three-dimensional chemical structures, both molecular and condensed. Features include reading a variety of file types and output from quantum chemistry programs. Multi-frame files can be animated and normal modes displayed as calculated with quantum programs. Jmol supports Chime and Rasmol scripts, and the applet can be addressed with JavaScript. The application runs on J2SE 1.4 systems, but the applet runs even on old Java 1.1 systems, such as the Netscape 4.5/4.7 browsers. More information about the project can be found at the website, which features examples of the applet and a few screenshots of the application: http://jmol.sf.net/ Jmol is OpenSource and licensed with the GNU LGPL license. The Future Work is undergoing to hava Jmol support more file types, including output of programs which is divided over several files. In addition, a true from-scratch 3D engine is being written that will allow for even more astoundishing graphics including molecular surfaces. kind regards, Egon Willighagen 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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Chime => Jmol: http://jmol.sourceforge.net/scripting.html
by Rzepa, Henry 01 Jul '03

01 Jul '03

Over the years, a large body of molecular data has been rendered within Web pages using the popular Chime browser plugin. Unfortunately, the "plugin" concept has become rather frayed; some browsers have difficulty with Chime, others simply do not support it (particularly those on eg Linux and other new generation operating systems such as MacOS X). If you visit http://jmol.sourceforge.net/scripting.html however, you will note that another 3D molecule display program called JMol has come on by leaps and bounds, due particularly to the efforts of a number of recent enthusiastic contributors. Unlike Chime, JMol is <<opensource>> and hence not limited to the generosity of a single commercial company. In particular, the molecular scripting/style language which has become known as "Rasmol script" is increasingly well implemented in JMol, and many of the effects hitherto limited purely to Chime can now be replicated. It WILL require the Web page to be edited (the original design of the plugin syntax was not robust, and hence was very much plugin specific). One particularly exciting feature is that JMol is fully CML compliant, which means that all molecules can be carried in this format rather than older formats such as the Molfile (an illustration of the problems with the latter is that each atom line is defined by a line break character, which can vary or even break depending on the operating system). It should be possible therefore for any web page designed to use JMol to be FULLY XML compliant in all its data; e.g. XHTML for description and prose CML for molecular information SVG for 2D diagrams RSS for metadata. (only eg Rasmol script remains to be XML-ified!) -- 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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Molecule of the Month - July
by Paul May 29 Jun '03

29 Jun '03

Hi, July's MOTM is Caeruloplasmin, which is a novel copper metalloprotein, and may well be the biggest molecule we've ever featured in the MOTM series. It was written by John Maher from Bristol, and although most of the site can be viewed in normal HTML it requires Chime to see the structure properly. http://www.bristol.ac.uk/Depts/Chemistry/MOTM/motm.htm#july2003 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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More RSS applications
by Rzepa, Henry 27 Jun '03

27 Jun '03

This is the third posting on this series on the application of XML and RSS-metadata to the Web. 1. http://www.courseforum.com/projectforum/ is an interesting concept: "ProjectForum 2.3 is web-based collaboration software for workgroup/project coordination. The new version makes an RSS feed available in every forum for tracking changes with RSS newsreaders, simplifies page appearance and layout for easier navigation, makes it easier to refer to pages in other groups or projects, and more" 2. http://www.usercreations.com/spring/ "Spring 1.3.1 is an alternative desktop option that includes folder-less groups, desktop web personalization ... RSS-based news headlines, desktop ... charts ... and other features. The new version adds RSS transform for application/xml and application/rdf+xml MIME types, improves Friend of A Friend (FOAF) support, saves originals of transformed files and opens them when doing View Source, and more" The latter opens up the prospect of finding an "object" on your desktop (latterly called a document) and right mouse clicking to produce a context-sensitive set of actions that can be carried out on it (as for example if its a CML chemical object, calculate eg its molecular weight, or indeed its Hartree-Fock energy!) Both the above use XML (but neither CML directly) to achieve their design. One might imagine that the 19 year old design of the "windowing desktop" may be about to enter a new metaphor; it will be interesting to see which community adopts this first (chemistry ? ) -- 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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VEGA1.5.0...... VEGA is back
by Giulio Vistoli 24 Jun '03

24 Jun '03

Dear Collegues, we are glad to announce the new release of VEGA1.5.0 (http://www.ddl.unimi.it/) our well known program to convert, manage and visualize of 3D structures for several platforms (Win32, Linux, Irix, AmigaOs). We consider this release a significant breakthrough in the development of this program. Among the several features added in VEGA1.5.0, the most important are: 1. merging function, that allows format conversion transferring only selected information types from one file to another; 2. a powerful tool to build solvent box and solvate any molecule adding the ions. 3. a 3D molecular editor with add, remove, change atom capability and bond manipulation (add, remove, change, connectivity rebuilder and bond type finder). 4. PSF X-Plor topology saver The full list of the significant new features of this version are: - PDB 2.2 loader and saver. - Experimental PSF X-Plor topology saver. - Improved GAMESS support. - Added the capability to read the connectivity and the bond types of Alchemy, CSSR, MDL Mol, Mol2, PDB (including all subformats), QMC and IFF file formats. - Ultra fast connectivity routine. - Read & write substructure record in Mol2 file format. - New trajectory file formats: Quanta conformational search (CSR), ESCHER Next Generation solutions. - Added the lipole measure (Broto & Moreau, Ghoose & Crippen) in the trajectory analysis. - Support of multiple chains in IFF file format. - Bond, CFF91, CHARMM 22 for nucleic acids, CHARMM 22 for proteins, H-bond, MM2, MM3, force field templates. - The atom type length is expanded from 4 to 8 characters. - Added acetone, ammonia, chloroform, dicloromethane, formaldehyde, methane, methanol octanol-water solvent clusters. - Basic 3D molecular editor with add, remove, change atom capability and bond manipulation (add, remove, change, connectivity rebuilder and bond type finder). - Molecular similarity toolbox (molecular superimposition). - Change torsion dialog box. - Solvent cluster builder. - Add ions function. - Merge file function. You can merge two files specifying the parts to keep or discard (e.g. coordinates, atom types, atomic charges, etc). - ClustalX plugin. - Atom constraints dialog box for dynamics simulations (e.g. NAMD). - 3D interactive monitors for distance, angle, torsion, angle between two planes. - World relative translation and rotation of each molecule. - Open/save in selection tool (trajectory analysis). - Select molecules and select segments dialogs. - Remove molecules and remove segments dialogs. Giulio Vistoli & Alessandro Pedretti --------------- Giulio Vistoli Istituto di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano Italia Tel. +39-02-50317545 Fax +39-02-50317565 giulio.vistoli(a)unimi.it http://www.ddl.unimi.it 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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Creating RSS feeds
by Rzepa, Henry 13 Jun '03

13 Jun '03

I am getting regular queries from people interested in setting up chemical RSS feeds. Some general advice I have found is useful (a) Use standard RSS 1.0 (rather than the older 0.91 etc) (b) Add <?xml-stylesheet href="http://www.w3.org/2000/08/w3c-synd/style.css" type="text/css"?> to the top, being a CSS stylesheet which renders the contents sensible on Web browsers. Another way of doing this is http://rssxpress.ukoln.ac.uk/view.cgi?rss_url=http://www.ch.ic.ac.uk/index.… which applies an XSLT stylesheet (rather than CSS) to achieve a rather more flexible rendering. I expect that this approach could also be used to eg preselect items of interest from the RSS (c) Its also useful to deploy DC metadata (particularly date, but also author) so that items can be sorted by these categories (not all RSS clients display these fields, but the better ones do!) Do it like follows <dc:creator>Henry Rzepa</dc:creator> <dc:date>2003-05-21T16:15:00-05:00</dc:date> <dc:subject>Biological and biophysical chemistry</dc:subject> Interestingly, I attended a "semantic Web road show" yesterday where one example of a challenging search was presented as "where do I find an article written by X in the year Y on the topic Z" (If anyone can get Google to respond sensibly to such a query let me know!) Of course, you will realise that including the creator, the date and the subject in an RSS field merely requires the RSS client to perform booleans on these fields (A= and B= and C= ). Sadly, no RSS client appears yet quite capable of such actions (but we hope it will come with V 2 of such clients!) Also on the horizon are "peer2peer" RSS clients, whereby if a local search of RSS channels and items therein draws a blank, it can go off and search other peers in the "community", much in the mannere that eg Gnutella does for eg Music. As an aside, we investigated Gnutella and its cousins a few years back, but the almost total lack of meta data included in this formalism meant that the only meaningful searches could be conducted on filename, which turned out not to be productive. I have not revisited this recently, but if anyone who has up to date information on peer2peer file sharing systems knows more please let this list know! -- 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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The "deep net" and Turbo10
by Rzepa, Henry 04 Jun '03

04 Jun '03

http://turbo10.com/ claims that (a) most search engines access only the surface net, comprising only 10% of the whole, whereas (b) they access the "deep net" including the other 90%. A moments inspection reveals they do this by in fact creating channels (aggregated collections of search engines) which themselves can index and retrieve documents others cannot. All of this of course is actually a fairly apt description of much of chemistry, which could fairly be said to be "deep" (along with the likes of SciFinder, Crossfire, etc) http://turbo10.com/ currently claim to include some 1100 such "deep net" search engines, amongst them for example I spotted the chemsoc.org engine (although I did not find many other overtly chemical search engines). The media appear to have recently discovered turbo10 and its currently being much hyped up (to the extent the site is actually disabled at the moment due to high load). The site also claims you can design your own "deep net" search; hence I wonder if anyone reading this list has perhaps tried to create a "deep chemistry" collection? If I throw modesty to the winds, I might point out our own "deep chemistry" concept, published in 2000; http://www.ch.ic.ac.uk/rzepa/ijc/search_channels/ It is also interesting to speculate whether RSS (upon which I posted some weeks ago) might form the basis of another form of "deep net" search, but one constructed more on a peer2peer community basis. If anyone wants to see the article we ended up writing on that subject, its at http://www.ch.ic.ac.uk/rzepa/rss/ (and published in the Internet J. Chemistry). If you want to find out more about how RSS might develop in this direction, go to http://www.newsmonster.org/semantic.html By the way, the known collection of RSS chemistry sites now includes eg Webelements: http://www.webelements.com/board/backend.php IJC: http://www.ijc.com/abstracts/rss.xml etc etc (dont try to open these in Web browsers, but register them in RSS clients). -- 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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