Bob,
I really want to do that in the worst way. I mean animate it back together
rather than just reload it. Do you have any ideas?
Hmm... I wonder if reloading it with connect delete, followed by a delay
loop reconnecting bonds, followed by a proper load to correct multiple
bonds would make it look like a reverse animation?
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal, IL 61790-4160
http://chemagic.org
----------------------------------------
From: "Robert Hanson" <[email protected]>
Sent: Wednesday, April 13, 2011 2:50 PM
To: [email protected], [email protected]
Subject: Re: [Jmol-users] An Old Paper and Jmol/Resolver
Great --
-- I suggest a "put it back together" link.
On Wed, Apr 13, 2011 at 12:28 PM, Otis Rothenberger <[email protected]>
wrote:
Bob,
I put a Google Standard InChI search link on my IL State Fair ACS kiosk toy
suggestion:
http://chemagic.com/web_molecules/acs.aspx
Users can play with it to see what they think about the Google search
approach. I hope the toy instructions are fairly intuitive. Here's my point
of view and some specific notes relate the Google search:
My View:
I'm interested in developing more high school teacher interest in Jmol. To
this end, I'm hoping to do some local section ACS speaking in the near
future. I think any useful student utility that helps break an
understandable mind set that Jmol is simply a "see the pretty molecule
spin" application is a useful addition. I say understandable because "Jmol
2011" is really not that well known outside a small circle of users.
Notes:
1) Google has obviously put some specific thought into chemical searching
via InChI - some specifics below.
2) For some reason, Resolver has some problems with the cyclooctatetraene
InChI. I suspect this is related to flat (aromatic) vs tub (not aromatic)
confusion in the SMILES. Without putting up a "did you mean" warning,
Google appends the search URL InCHI to improve the search.
3) Taxol seems to be big test compound with this toy, so I'll make a
special Taxol note here. Resolver has some issues with % in some SMILES.
I don't think so. Must be your escaping. This works just fine in Jmol:
load $taxol
x = {*}.find("SMILES")
load smiles @x
I have not been able to work this all out, but I suspect it's a query
string issue with the percent sign location in certain SMILES. I've tried
escaping the % sign itself with little success. I dodge this issue by
trapping Jmol SMILES that have a %. I then have JME read the Jmol molfile,
and I use the JME SMILES for this molfile. This, of course, produces the
non-isomeric SMILES. I'd trap only problem SMILES if I could figure out the
specific nature of this % sign problem. Back to Google: The search works.
Google has obviously done a thorough job of indexing InChI's.
I note that "cholesterol" also picks up a related isomer, lathosterol, in a
Google search.
Just to test pushing Jmol Script's ability to make these loading queries, I
added a feature that will select PubChem's 2D sdf file if the 3D sdf is not
available. Taxol is just such a model.
?? the 3D mol file of taxol is available. What's the issue?
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal, IL 61790-4160
http://chemagic.org
----------------------------------------
From: "Robert Hanson" <[email protected]>
Sent: Wednesday, April 13, 2011 6:22 AM
To: [email protected], [email protected]
Subject: Re: [Jmol-users] An Old Paper and Jmol/Resolver
Otis, are you suggesting we add a "Google" menu item in Jmol?
ruary 5, 1900
----------------------------------------------------------------------------
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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
------------------------------------------------------------------------------
Forrester Wave Report - Recovery time is now measured in hours and minutes
not days. Key insights are discussed in the 2010 Forrester Wave Report as
part of an in-depth evaluation of disaster recovery service providers.
Forrester found the best-in-class provider in terms of services and vision.
Read this report now! http://p.sf.net/sfu/ibm-webcastpromo
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