<head>
<script src="jmol/Jmol.js
<view-source:http://www.mueangchiangrai.net/chemistry/jmol/Jmol.js>"></script>
<script>var s = "load SMILES
'Oc1ccc(cc1)C3(OC(=O)c2ccccc23)c4ccc(O)cc4'"; jmolInitialize('jmol/',
UseSignedApplet);</script>
</head>
<body onload="jmolApplet(400);jmolScript(s);"></body>
Should read:
<head>
<script type="text/javascript" src="jmol/Jmol.js
<view-source:http://www.mueangchiangrai.net/chemistry/jmol/Jmol.js>"></script>
<script>var s = "load SMILES
'Oc1ccc(cc1)C3(OC(=O)c2ccccc23)c4ccc(O)cc4'"; jmolInitialize('jmol/',
UseSignedApplet);</script>
</head>
<body>
<script type="text/javascript">
jmolInitialize("jmol", true) // presuming the applet files are in jmol/
jmolApplet(400, s)
</script>
</body>
The advantage of this is that Jmol will load any file -- imaginary or not.
The disadvantage is that you have to used the signed applet, and the
software on the other end of that load operation has some limitations -- but
it is overall VERY good for small molecules or ones such as these. We're
using http://cheminfov.informatics.indiana.edu/rest/thread/d3.py/SMILES/ for
this service.
On Tue, Aug 17, 2010 at 11:05 PM, John Francis Lee <[email protected]> wrote:
> I'm sorry to be such a nuisance. I attach a file detailing my problem.
>
> Basically, the complaint is the the jmolApple0.jar (sic) cannot be
> found. I can find it :) And it does point to a jmol-12.0.6 directory.
>
> http://www.mueangchiangrai.net/chemistry/loadSMILES.html
>
> Thanks for all your help.
>
> On 08/17/2010 11:24 PM, Oliver Stueker wrote:
> > Hi,
> >
> > with Jmol 12.0 you can use the following Jmol Script command:
> >
> > load SMILES "Oc1ccc(cc1)C3(OC(=O)c2ccccc23)c4ccc(O)cc4"
> >
> > (see: http://chemapps.stolaf.edu/jmol/docs/?&fullmanual=1&ver=12.0#k428)
> >
> > That works for me with the Application. On a webpage you probably need
> > to use the signed Applet.
> > (see: http://jmol.sourceforge.net/jslibrary/#jmolInitialize )
> >
> > Oliver
> >
> > On Tue, Aug 17, 2010 at 01:46, John Francis Lee <[email protected]>
> wrote:
> >> Worked like a charm! Thanks.
> >>
> >> I went to the website, pasted the SMILES string into a box labeled
> >> SMILES and up popped the structure!
> >>
> >> Then I chose XYZ under download and downloaded the file.
> >>
> >> I opened jMol and then opened the file I downloaded and voila... the
> >> molecule magically appeared.
> >>
> >> I wonder if I could do that in that in a browser window?
> >>
> >> If I knew the SMILES string for a given molecule could I send an http
> >> GET to the cdb.ics.uci.edu server and get back a file the jMol applet
> >> could read and display?
> >>
> >> On 08/17/2010 02:25 PM, Maurice Schroff wrote:
> >>> Dear Mr. Lee
> >>>
> >>> As Jmol is a sort of "molecule viewer" it has no possibility to model
> >>> molecules. However you can search various of pre-modeled molecules e.g.
> at
> >>> http://cdb.ics.uci.edu/cgibin/ChemicalSearchWeb.psp . Jmol can read
> >>> different formats including.xyz, .mol , .mol2 and .pdb
> >>> Alternatively you could try to model using ChemDraw or Freeware as
> >>> ACD/ChemSketch
> >>>
> >>> Regards,
> >>> Maurice
> >>>
> >>> -----Ursprüngliche Nachricht-----
> >>> Von: John Francis Lee [mailto:[email protected]]
> >>> Gesendet: Dienstag, 17. August 2010 08:50
> >>> An: [email protected]
> >>> Betreff: [Jmol-users] How to create jmol models
> >>>
> >>> Hi,
> >>>
> >>> Let me just blurt out my question : how can I make jmol models of
> molecules?
> >>>
> >>> Say I go to wikipedia and look up phenolphthalein. There I find
> >>>
> >>> IUPAC name : 3,3-bis(4-hydroxyphenyl)isobenzofuran-1(3H)-one
> >>> CAS number : 77-09-8
> >>> SMILES : Oc1ccc(cc1)C3(OC(=O)c2ccccc23)c4ccc(O)cc4
> >>>
> >>> Is any or all of this sufficient to model phenolphthalein in jmol?
> >>>
> >>> I looked at the wiki, expecting to find a whole section on how to do
> this,
> >>> but I didn't recognize the instructions for doing so, if they're there.
> >>>
> >>> Thanks for any help you might give me.
> >
> >
> ------------------------------------------------------------------------------
> > This SF.net email is sponsored by
> >
> > Make an app they can't live without
> > Enter the BlackBerry Developer Challenge
> > http://p.sf.net/sfu/RIM-dev2dev
> > _______________________________________________
> > Jmol-users mailing list
> > [email protected]
> > https://lists.sourceforge.net/lists/listinfo/jmol-users
> >
>
>
> --
> "This message may have been intercepted and read by U.S. government
> agencies including the FBI, CIA, and NSA and/or the present government
> of Thailand without notice or warrant or knowledge of sender or recipient."
>
> John Francis Lee
> 246/3 Thanon Kaew Wai
> Mueang Chiangrai 57000
> Thailand
>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by
>
> Make an app they can't live without
> Enter the BlackBerry Developer Challenge
> http://p.sf.net/sfu/RIM-dev2dev
> _______________________________________________
> 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
------------------------------------------------------------------------------
This SF.net email is sponsored by
Make an app they can't live without
Enter the BlackBerry Developer Challenge
http://p.sf.net/sfu/RIM-dev2dev
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
