1) save the blown up atom positions (setA).
2) reload the model, and save the atoms positions (setB).
3) set the atom positions to setA. (bonds will be there)
4) morph the model back to setB.
Bob
On Wed, Apr 13, 2011 at 2:24 PM, Otis Rothenberger <[email protected]>wrote:
> 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
>>
>>
>>
>> ------------------------------------------------------------------------------
>> 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
>> _______________________________________________
>> Jmol-users mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> --
> 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
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
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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