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?"
------------------------------------------------------------------------------
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List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)
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.
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List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)
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.
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List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)
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
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List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)
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.
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List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)
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?"
------------------------------------------------------------------------------
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List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)
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.
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