Comments on: Embedding Jmol applet in WordPress posts http://www.openscience.org/blog/?p=208 Open source scientific software Fri, 30 Jul 2010 03:41:35 +0000 hourly 1 http://wordpress.org/?v=3.0 By: Myer Nore http://www.openscience.org/blog/?p=208&cpage=1#comment-20303 Myer Nore Tue, 24 Nov 2009 03:26:49 +0000 http://www.openscience.org/blog/?p=208#comment-20303 If only there were a way to embed an applet in wordpress and have it show up in the rss feed. I subscribed to the feed just to see if it showed up - sadly, it didn't. If only there were a way to embed an applet in wordpress and have it show up in the rss feed. I subscribed to the feed just to see if it showed up – sadly, it didn’t.

]]> By: Amay http://www.openscience.org/blog/?p=208&cpage=1#comment-15637 Amay Thu, 11 Sep 2008 07:02:38 +0000 http://www.openscience.org/blog/?p=208#comment-15637 Hi All, I have used the javascript and the code given above in my server.The molecule is loading fine and I am also getting the message "Jmol Script terminated"...But I am getting following error messages from Java Console............. --------------------------------------- Java Plug-in 1.6.0_07 Using JRE version 1.6.0_07 Java HotSpot(TM) Client VM User home directory = C:\Documents and Settings\Pinak ---------------------------------------------------- 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 p: reload proxy configuration 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 ---------------------------------------------------- Jmol applet [null] destroyed Jmol applet null[null] initializing language=en_US AppletRegistry.checkIn(null[null]) (C) 2007 Jmol Development Jmol Version 11.4.6 2007-12-20 06:37 java.vendor:Sun Microsystems Inc. java.version:1.6.0_07 os.name:Windows XP memory:36.3/59.1 appletId:null appletDocumentBase=http://192.168.50.215/resources/bioinfo/geometry1/geometry.php?num=8502&res1=ASP&res2=PHE appletCodeBase=http://192.168.50.215/resources/bioinfo/geometry1/ Jmol applet [null] initializing language=en_US AppletRegistry.checkIn([null]) (C) 2007 Jmol Development Jmol Version 11.4.6 2007-12-20 06:37 java.vendor:Sun Microsystems Inc. java.version:1.6.0_07 os.name:Windows XP memory:35.9/61.4 appletId: appletDocumentBase=http://192.168.50.215/resources/bioinfo/geometry1/geometry.php?num=8502&res1=ASP&res2=PHE appletCodeBase=http://192.168.50.215/resources/bioinfo/geometry1/ FileManager.openFile(8502\8502.pdb) //8502\8502.pdb FileManager opening http://192.168.50.215/resources/bioinfo/geometry1/8502\8502.pdb The Resolver thinks Pdb openFile(8502\8502.pdb)16 ms ModelSet: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false 1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. ModelSet: autobonding; use autobond=false to not generate bonds automatically FileManager.openFile(8502\8502.pdb) //8502\8502.pdb FileManager opening http://192.168.50.215/resources/bioinfo/geometry1/8502\8502.pdb The Resolver thinks Pdb Exception in thread "Thread-692" java.lang.NullPointerException at java.applet.Applet.showStatus(Unknown Source) at org.jmol.applet.Jmol.showStatusAndConsole(Unknown Source) at org.jmol.applet.Jmol$MyStatusListener.notifyScriptTermination(Unknown Source) at org.jmol.viewer.StatusManager.setStatusScriptTermination(Unknown Source) at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source) at org.jmol.viewer.ScriptManager.runScript(Unknown Source) at org.jmol.viewer.ScriptManager.runNextScript(Unknown Source) at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(Unknown Source) at java.lang.Thread.run(Unknown Source) openFile(8502\8502.pdb)15 ms ModelSet: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false 1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. ModelSet: autobonding; use autobond=false to not generate bonds automatically --------------------------------------- I also want to set the parameters such as,spin on,style->scheme->trace,color->atoms->By Scheme->Chain, bla bla.. automatically at the time of loading of the molecule. Please help........Thanks in advance..... Hi All,
I have used the javascript and the code given above in my server.The molecule is loading fine and I am also getting the message “Jmol Script terminated”…But I am getting following error messages from Java Console………….
—————————————
Java Plug-in 1.6.0_07
Using JRE version 1.6.0_07 Java HotSpot(TM) Client VM
User home directory = C:\Documents and Settings\Pinak
—————————————————-
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
p: reload proxy configuration
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
—————————————————-
Jmol applet [null] destroyed
Jmol applet null[null] initializing
language=en_US
AppletRegistry.checkIn(null[null])
(C) 2007 Jmol Development
Jmol Version 11.4.6 2007-12-20 06:37
java.vendor:Sun Microsystems Inc.
java.version:1.6.0_07
os.name:Windows XP
memory:36.3/59.1
appletId:null
appletDocumentBase=http://192.168.50.215/resources/bioinfo/geometry1/geometry.php?num=8502&res1=ASP&res2=PHE
appletCodeBase=http://192.168.50.215/resources/bioinfo/geometry1/
Jmol applet [null] initializing
language=en_US
AppletRegistry.checkIn([null])
(C) 2007 Jmol Development
Jmol Version 11.4.6 2007-12-20 06:37
java.vendor:Sun Microsystems Inc.
java.version:1.6.0_07
os.name:Windows XP
memory:35.9/61.4
appletId:
appletDocumentBase=http://192.168.50.215/resources/bioinfo/geometry1/geometry.php?num=8502&res1=ASP&res2=PHE
appletCodeBase=http://192.168.50.215/resources/bioinfo/geometry1/

FileManager.openFile(8502\8502.pdb) //8502\8502.pdb
FileManager opening http://192.168.50.215/resources/bioinfo/geometry1/8502\8502.pdb
The Resolver thinks Pdb
openFile(8502\8502.pdb)16 ms
ModelSet: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false
1 model in this collection. Use getProperty “modelInfo” or getProperty “auxiliaryInfo” to inspect them.
ModelSet: autobonding; use autobond=false to not generate bonds automatically

FileManager.openFile(8502\8502.pdb) //8502\8502.pdb
FileManager opening http://192.168.50.215/resources/bioinfo/geometry1/8502\8502.pdb
The Resolver thinks Pdb
Exception in thread “Thread-692″ java.lang.NullPointerException
at java.applet.Applet.showStatus(Unknown Source)
at org.jmol.applet.Jmol.showStatusAndConsole(Unknown Source)
at org.jmol.applet.Jmol$MyStatusListener.notifyScriptTermination(Unknown Source)
at org.jmol.viewer.StatusManager.setStatusScriptTermination(Unknown Source)
at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source)
at org.jmol.viewer.ScriptManager.runScript(Unknown Source)
at org.jmol.viewer.ScriptManager.runNextScript(Unknown Source)
at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
openFile(8502\8502.pdb)15 ms
ModelSet: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false
1 model in this collection. Use getProperty “modelInfo” or getProperty “auxiliaryInfo” to inspect them.
ModelSet: autobonding; use autobond=false to not generate bonds automatically

—————————————

I also want to set the parameters such as,spin on,style->scheme->trace,color->atoms->By Scheme->Chain, bla bla.. automatically at the time of loading of the molecule.
Please help……..Thanks in advance…..

]]> By: BH http://www.openscience.org/blog/?p=208&cpage=1#comment-11788 BH Fri, 30 Nov 2007 08:31:33 +0000 http://www.openscience.org/blog/?p=208#comment-11788 it works ... and well. I tried it here http://theobromine.uchini.be/?p=78 More explanations (in english) here http://www.milomuses.com/chemicalmusings/?page_id=343 . No need to add code in the theme's header. it works … and well. I tried it here http://theobromine.uchini.be/?p=78

More explanations (in english) here http://www.milomuses.com/chemicalmusings/?page_id=343 . No need to add code in the theme’s header.

]]> By: Chemdev http://www.openscience.org/blog/?p=208&cpage=1#comment-9839 Chemdev Thu, 06 Sep 2007 13:03:09 +0000 http://www.openscience.org/blog/?p=208#comment-9839 Hi there, I just don't get it running. "...add simple javascript function to your theme’s header:..." Does this mean adding the Code snippet to the -section of my header.php? Thx Hi there,
I just don’t get it running.

“…add simple javascript function to your theme’s header:…”

Does this mean adding the Code snippet to the -section of my header.php?

Thx

]]> By: ChemDev » Blog Archiv » Einbetten von Jmol in WordPress-Blogs http://www.openscience.org/blog/?p=208&cpage=1#comment-9778 ChemDev » Blog Archiv » Einbetten von Jmol in WordPress-Blogs Tue, 04 Sep 2007 11:27:28 +0000 http://www.openscience.org/blog/?p=208#comment-9778 [...] existiert ein weiteres Tutorial auf The OpenScience Project. Dieses beschreibt zwar einen Weg, der es ermöglichen soll, ein Jmol-Applet direkt in ein [...] [...] existiert ein weiteres Tutorial auf The OpenScience Project. Dieses beschreibt zwar einen Weg, der es ermöglichen soll, ein Jmol-Applet direkt in ein [...]

]]> By: plonewars.com - » Embedding Jmol applet in Wordpress posts http://www.openscience.org/blog/?p=208&cpage=1#comment-8785 plonewars.com - » Embedding Jmol applet in Wordpress posts Mon, 25 Jun 2007 20:00:32 +0000 http://www.openscience.org/blog/?p=208#comment-8785 [...] Embedding Jmol applet in Wordpress posts [...] [...] Embedding Jmol applet in WordPress posts [...]

]]> By: mela http://www.openscience.org/blog/?p=208&cpage=1#comment-5766 mela Wed, 21 Mar 2007 15:48:12 +0000 http://www.openscience.org/blog/?p=208#comment-5766 How would you set it up so that it starts to spin on the x axis as soon as you load the .mol file? How would you set it up so that it starts to spin on the x axis as soon as you load the .mol file?

]]> By: Weblog Tools Collection » Blog Archive » WordPress Plugin Releases for 1/18 http://www.openscience.org/blog/?p=208&cpage=1#comment-2640 Weblog Tools Collection » Blog Archive » WordPress Plugin Releases for 1/18 Thu, 18 Jan 2007 16:20:51 +0000 http://www.openscience.org/blog/?p=208#comment-2640 [...] Embed Jmol Applet into Wordpress using this hack from OpenScience, embed Jmol Applets into your Wordpress blog posts. I love the caffeine molecule in the example. (No Ratings Yet)  Loading ... [...] [...] Embed Jmol Applet into WordPress using this hack from OpenScience, embed Jmol Applets into your WordPress blog posts. I love the caffeine molecule in the example. (No Ratings Yet)  Loading … [...]

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