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
[...@28amen ~/www/mueangchiangrai.net/chemistry]$ ls jmol/JmolAppletSigned0.jar jmol/JmolAppletSigned0.jar http://www.mueangchiangrai.net/chemistry/loadSMILES.html <html> <head> <script src="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> </html> Java Plug-in 1.6.0_20 Using JRE version 1.6.0_20-b02 Java HotSpot(TM) 64-Bit Server VM User home directory = /home/jfl ---------------------------------------------------- c: clear console window f: finalize objects on finalization queue g: garbage collect h: display this help message l: dump classloader list m: print memory usage o: trigger logging q: hide console r: reload policy configuration s: dump system and deployment properties t: dump thread list v: dump thread stack x: clear classloader cache 0-5: set trace level to <n> ---------------------------------------------------- load: class JmolApplet not found. java.lang.ClassNotFoundException: JmolApplet at sun.plugin2.applet.Applet2ClassLoader.findClass(Applet2ClassLoader.java:219) at java.lang.ClassLoader.loadClass(ClassLoader.java:307) at java.lang.ClassLoader.loadClass(ClassLoader.java:248) at sun.plugin2.applet.Plugin2ClassLoader.loadCode(Plugin2ClassLoader.java:532) at sun.plugin2.applet.Plugin2Manager.createApplet(Plugin2Manager.java:2940) at sun.plugin2.applet.Plugin2Manager$AppletExecutionRunnable.run(Plugin2Manager.java:1444) at java.lang.Thread.run(Thread.java:619) Caused by: java.io.IOException: open HTTP connection failed:http://www.mueangchiangrai.net/chemistry/JmolApplet.class at sun.plugin2.applet.Applet2ClassLoader.getBytes(Applet2ClassLoader.java:537) at sun.plugin2.applet.Applet2ClassLoader.access$000(Applet2ClassLoader.java:51) at sun.plugin2.applet.Applet2ClassLoader$1.run(Applet2ClassLoader.java:192) at java.security.AccessController.doPrivileged(Native Method) at sun.plugin2.applet.Applet2ClassLoader.findClass(Applet2ClassLoader.java:189) ... 6 more Exception: java.lang.ClassNotFoundException: JmolApplet
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