Bob,
Yeah, it's amazing how fast this is done. It's not a database look-up.
It's being done on the fly from SMILES.
But here's the big thing. The Resolver molfile has stereo information. I
checked this out because on the Web site their embedded JME will
translate the word taxol (or any SMILES) into a complete stereo drawing
in JME. When I checked their code, I discovered that they are actually
loading JME files (not molfies) into JME. Some how they are generating
JME files from SMILES.
Before I bother Markus again, I'm going to try to load their molfiles
into JME to see if the stereo drawing renders. JME does not read files
from server. You have to feed it a string. Further the molfile string
needs to be line break tweaked. I'm just now looking into this.
Otis
Otis Rothenberger
chemagic.com
On 9/3/2010 10:50 AM, Robert Hanson wrote:
Ho, ho, HO! No kidding! Wow... 3D to 2D! I suppose you want this as a
built-in Jmol option now...
On Thu, Sep 2, 2010 at 9:24 PM, Otis Rothenberger
<osrot...@chemagic.com <mailto:osrot...@chemagic.com>> wrote:
The NIH Resolver will generate a gif image of the Lewis line
structure
of a submitted SMILES. I ignored this feature because I thought it was
just another pretty little picture. Boy was I wrong!
A JavaScript construct of the following form:
var tempStr = "<img width='" + sz + "' height='" + sz + "'
src='http://cactus.nci.nih.gov/chemical/structure/"; +
escape(jmolSmiles)
+ "/image' />";
sz = desired gif size
jmolSmiles = an evolving model kit mode model.
When rendered the above gif not only has appropriate bond wedges. The
chiral carbons are conveniently labeled R or S
If you want to see a quick demo of this, go to
http://chemagic.com/web_molecules/script_page_large.aspx
The default model will be just fine. Click The Molecular Editor Link;
click the Image link, click the NIH 2D Capture link.
We edit models using our own Edit screen interface rather than the
Jmol
native interface. Play with editing, and you'll see that Resolver gets
it right. You need to click the image capture link each time.
There are some problems with complex aromatics (e.g. taxol), but I'm
working on this problem.
Otis
--
Otis Rothenberger
chemagic.com <http://chemagic.com>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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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