Congratulations, and a big thank you, to all involved this is great work.
The potential of the new triad for teaching and learning is clear, and
exciting! The underlying additions to the SMILES capabilities of Jmol sound
very interesting and will offer new opportunities for development of
interactive web pages.
Mike
From: Robert Hanson [mailto:hans...@stolaf.edu]
Sent: 01 February 2014 19:54
To: jmol-users@lists.sourceforge.net; Robert Lancashire
Subject: [Jmol-users] jmol-14.1.8_2014.02.01 -- Get your predicted NMR
spectra here!
Robert Lancashire and I are happy to announce the first online open-source
fully JavaScript fully customizable 1D HNMR prediction tool. Perfect for the
classroom or for research laboratories, a demonstration showing how easy it
is to set up a web page is available
(http://chemapps.stolaf.edu/jmol/jsmol/jsv_predict2.htm). All that is
required a few script tags and a bit of initialization code. Full JavaScript
code is at
http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.8_2014.02.01.zip
This update of Jmol fully integrates JSME, Jmol, and JSpecView into a
JavaScript-only HTML5 triad that can be used on any page and in any
combination on any platform to display and analyze predicted 1D 1HNMR
spectra, allowing for comparison to actual spectra and to each other.
Spectra can be displayed independently, overlaid, or set above one another
in a synchronized set.
Either real or imagined compounds can be drawn quickly using JSME or loaded
from NCI using a chemical name, InChI, InChI-Key, SMILES, or CAS#.
Peaks in the spectrum and atoms in either the 2D drawing or the the 3D
structure can be selected, with corresponding atoms and peaks in the other
applets automatically highlighting.
Spectra can be zoomed, panned, integrated, and saved as PDF files. Peaks and
coupling constants can be measured.
The JSME/Jmol duo by itself allows for simple correlation between 2D
drawings and 3D structures without reference to NMR spectra. In addition,
the JSpecView JavaScript applet can independently display 1D and 2D NMR
spectra originating as JCAMP-DX files locally or from a server as well as
IR, Raman, UV/VIS, GC, GC/MS data in that same format or in AnIML XML
format. (Note that JSpecView is currently being used as the front end for
St. Olaf's fully robotic 400-MHz NMR (http://chemapps.stolaf.edu/nmr/)
JSpecView can also integrate with Jmol to display JCAMP-MOL
(http://chemapps.stolaf.edu/jmol/docs/misc/Jmol-JSpecView-specs.pdf) files,
which are used here for communication with EPFL.
Many thanks to Luc Patiny (EPFL), Peter Ertl (Novartis), and Bruno Bienfait
(Molecular Networks) for their assistance with this very challenging
project. Supreme thanks to Markus Sitzmann for the NCI CACTVS chemical
identifier resolver, which was key to this entire operation. Thanks also to
João Aires de Sousa for the neural-network NMR prediction algorithms and
online service used to generate the NMR spectra.
New capabilities of Jmol originating from this project include the
capability to generate SMILES codes indicating all H atoms explicitly, to
easily compare models of the same compound from two different sources, such
as PubChem and NCI, and to easily map atom numbers between different 2D
and/or 3D mol files originating from different sources using different
algorithms for their construction.
Bob Hanson
Robert Lancashire
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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