All, My Firefox on Window 7 just updated to 3.6.14. After the update, I started seeing intermittent Jmol applet corruption. This can be initiated with a page reload. I noticed it first on a page I was working on, but I also checked it on this page:
http://chemapps.stolaf.edu/jmol/docs/examples-12/jmol-flot-energy.htm?model= data/cyclohexaneFlip.jmol And this page: http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm Two reloads corrupted the applet on both pages. Once corrupted, you have to quit Firefox and restart to load the applet again. I've attached the Java Console reports for these cases at the end of this email. I am using an older version of Java. This is because recent Java updates have a security problem with local host development. Oracle is aware of the local host problem, but they essentially say too bad! Nevertheless, I do not see the Jmol applet corruption problem with this older version of Java in Chrome or MSIE. Does anyone else see this problem with the new version of Firefox on Windows? It's late in Florida, so I'm not going to update Java now. I'm hoping that I get some feedback on this issue and the latest version of Java before I take that step tomorrow. Otis FIRST CONSOLE REPORT Java Plug-in 1.6.0_21 Using JRE version 1.6.0_21-b06 Java HotSpot(TM) Client VM User home directory = C:\Users\OSR ---------------------------------------------------- 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> ---------------------------------------------------- urlImage=jar:http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSign ed0.jar!/jmol75x29x8.gif Jmol applet jmolApplet0__10146987661545__ initializing AppletRegistry.checkIn(jmolApplet0__10146987661545__) 1738 script command tokens applet context: -applet-signed-threaded appletDocumentBase=http://chemapps.stolaf.edu/jmol/docs/examples-12/jmol-flo t-energy.htm?model=data/cyclohexaneFlip.jmol appletCodeBase=http://chemapps.stolaf.edu/jmol/docs/examples-12/ (C) 2009 Jmol Development Jmol Version: 12.1.38_dev 2011-02-16 08:29 java.vendor: Sun Microsystems Inc. java.version: 1.6.0_21 os.name: Windows 7 memory: 5.2/16.1 processors available: 2 useCommandThread: true appletId:jmolApplet0__10146987661545__ (signed) defaults = "Jmol" backgroundColor = "lightblue" language=en_US antialiasDisplay = true loadstructcallback = "plotEnergies" animframecallback = "doHighlight" FileManager.getAtomSetCollectionFromFile(data/cyclohexaneFlip.jmol) FileManager opening http://chemapps.stolaf.edu/jmol/docs/examples-12/data/cyclohexaneFlip.jmol openFile(data/cyclohexaneFlip.jmol): 453 ms FileManager opening http://chemapps.stolaf.edu/jmol/docs/examples-12/data/cyclohexaneFlip.jmol FileManager.getAtomSetCollectionFromFile(http://chemapps.stolaf.edu/jmol/doc s/examples-12/data/cyclohexaneFlip.jmol|chxinv.xyz) FileManager opening http://chemapps.stolaf.edu/jmol/docs/examples-12/data/cyclohexaneFlip.jmol The Resolver thinks Xyz openFile(http://chemapps.stolaf.edu/jmol/docs/examples-12/data/cyclohexaneFl ip.jmol|chxinv.xyz): 413 ms reading 630 atoms ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false 35 models in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. Default Van der Waals type for model set to Babel 630 atoms created Time to autoBond: 50 ms ModelSet: autobonding; use autobond=false to not generate bonds automatically 35 models ColorManager: color "roygb" range 0.0 0.0 Model = 2, Energy = -160.4 kJ/mol Model = 3, Energy = -157.8 kJ/mol Model = 4, Energy = -154.1 kJ/mol Model = 5, Energy = -149.8 kJ/mol Model = 6, Energy = -145.3 kJ/mol Model = 7, Energy = -141.0 kJ/mol Model = 8, Energy = -137.5 kJ/mol Model = 9, Energy = -135.2 kJ/mol Model = 10, Energy = -134.2 kJ/mol Model = 11, Energy = -134.6 kJ/mol Model = 12, Energy = -136.2 kJ/mol Model = 13, Energy = -138.5 kJ/mol Model = 14, Energy = -141.1 kJ/mol Model = 15, Energy = -143.8 kJ/mol Model = 16, Energy = -146.1 kJ/mol Model = 17, Energy = -147.7 kJ/mol Model = 18, Energy = -148.3 kJ/mol Model = 19, Energy = -147.1 kJ/mol Model = 20, Energy = -145.0 kJ/mol Model = 21, Energy = -142.3 kJ/mol Model = 22, Energy = -139.4 kJ/mol Model = 23, Energy = -136.8 kJ/mol Model = 24, Energy = -135.0 kJ/mol Model = 25, Energy = -134.2 kJ/mol Model = 26, Energy = -134.7 kJ/mol Model = 27, Energy = -136.6 kJ/mol Model = 28, Energy = -139.5 kJ/mol Model = 29, Energy = -143.3 kJ/mol Model = 30, Energy = -147.5 kJ/mol Model = 31, Energy = -151.7 kJ/mol Model = 32, Energy = -155.7 kJ/mol Model = 33, Energy = -158.7 kJ/mol Model = 34, Energy = -161.0 kJ/mol Model = 34, Energy = -161.0 kJ/mol Model = 34, Energy = -161.0 kJ/mol Model = 33, Energy = -158.7 kJ/mol Model = 32, Energy = -155.7 kJ/mol Model = 31, Energy = -151.7 kJ/mol Model = 30, Energy = -147.5 kJ/mol Model = 29, Energy = -143.3 kJ/mol Model = 28, Energy = -139.5 kJ/mol Model = 27, Energy = -136.6 kJ/mol Model = 26, Energy = -134.7 kJ/mol Model = 25, Energy = -134.2 kJ/mol Model = 24, Energy = -135.0 kJ/mol Model = 23, Energy = -136.8 kJ/mol Model = 22, Energy = -139.4 kJ/mol Model = 21, Energy = -142.3 kJ/mol Model = 20, Energy = -145.0 kJ/mol Model = 19, Energy = -147.1 kJ/mol Model = 18, Energy = -148.3 kJ/mol Model = 17, Energy = -147.7 kJ/mol Model = 16, Energy = -146.1 kJ/mol Model = 15, Energy = -143.8 kJ/mol Model = 14, Energy = -141.1 kJ/mol Model = 13, Energy = -138.5 kJ/mol Model = 12, Energy = -136.2 kJ/mol Model = 11, Energy = -134.6 kJ/mol Model = 10, Energy = -134.2 kJ/mol Model = 9, Energy = -135.2 kJ/mol Model = 8, Energy = -137.5 kJ/mol Model = 7, Energy = -141.0 kJ/mol Model = 6, Energy = -145.3 kJ/mol Model = 5, Energy = -149.8 kJ/mol Model = 4, Energy = -154.1 kJ/mol Model = 3, Energy = -157.8 kJ/mol Model = 2, Energy = -160.4 kJ/mol Model = 1, Energy = -161.5 kJ/mol Model = 2, Energy = -160.4 kJ/mol Model = 3, Energy = -157.8 kJ/mol Model = 4, Energy = -154.1 kJ/mol Model = 5, Energy = -149.8 kJ/mol Model = 6, Energy = -145.3 kJ/mol Model = 7, Energy = -141.0 kJ/mol Model = 8, Energy = -137.5 kJ/mol Model = 9, Energy = -135.2 kJ/mol Model = 10, Energy = -134.2 kJ/mol Model = 11, Energy = -134.6 kJ/mol Model = 12, Energy = -136.2 kJ/mol Model = 13, Energy = -138.5 kJ/mol Model = 14, Energy = -141.1 kJ/mol Model = 15, Energy = -143.8 kJ/mol Model = 16, Energy = -146.1 kJ/mol Model = 17, Energy = -147.7 kJ/mol Model = 18, Energy = -148.3 kJ/mol Jmol applet jmolApplet0__10146987661545__ destroyed CommandWatcher InterruptedException! org.jmol.viewer.ScriptManager$CommandWatcher@a084f8 Jmol applet jmolApplet0__921189882275827__ initializing AppletRegistry.checkIn(jmolApplet0__921189882275827__) applet context: -applet-signed-threaded appletDocumentBase=http://chemapps.stolaf.edu/jmol/docs/examples-12/jmol-flo t-energy.htm?model=data/cyclohexaneFlip.jmol appletCodeBase=http://chemapps.stolaf.edu/jmol/docs/examples-12/ (C) 2009 Jmol Development Jmol Version: 12.1.38_dev 2011-02-16 08:29 java.vendor: Sun Microsystems Inc. java.version: 1.6.0_21 os.name: Windows 7 memory: 11.0/20.6 processors available: 2 useCommandThread: true appletId:jmolApplet0__921189882275827__ (signed) urlImage=jar:http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSign ed0.jar!/jmol75x29x8.gif defaults = "Jmol" backgroundColor = "lightblue" language=en_US antialiasDisplay = true loadstructcallback = "plotEnergies" animframecallback = "doHighlight" FileManager.getAtomSetCollectionFromFile(data/cyclohexaneFlip.jmol) FileManager opening http://chemapps.stolaf.edu/jmol/docs/examples-12/data/cyclohexaneFlip.jmol openFile(data/cyclohexaneFlip.jmol): 162 ms FileManager opening http://chemapps.stolaf.edu/jmol/docs/examples-12/data/cyclohexaneFlip.jmol FileManager.getAtomSetCollectionFromFile(http://chemapps.stolaf.edu/jmol/doc s/examples-12/data/cyclohexaneFlip.jmol|chxinv.xyz) FileManager opening http://chemapps.stolaf.edu/jmol/docs/examples-12/data/cyclohexaneFlip.jmol The Resolver thinks Xyz openFile(http://chemapps.stolaf.edu/jmol/docs/examples-12/data/cyclohexaneFl ip.jmol|chxinv.xyz): 185 ms reading 630 atoms ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false 35 models in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. Default Van der Waals type for model set to Babel 630 atoms created Time to autoBond: 22 ms ModelSet: autobonding; use autobond=false to not generate bonds automatically 35 models ColorManager: color "roygb" range 0.0 0.0 Model = 2, Energy = -160.4 kJ/mol Model = 3, Energy = -157.8 kJ/mol Model = 4, Energy = -154.1 kJ/mol Model = 5, Energy = -149.8 kJ/mol Model = 6, Energy = -145.3 kJ/mol Model = 7, Energy = -141.0 kJ/mol Model = 8, Energy = -137.5 kJ/mol Model = 9, Energy = -135.2 kJ/mol Model = 10, Energy = -134.2 kJ/mol Model = 11, Energy = -134.6 kJ/mol Model = 12, Energy = -136.2 kJ/mol Model = 13, Energy = -138.5 kJ/mol Model = 14, Energy = -141.1 kJ/mol Model = 15, Energy = -143.8 kJ/mol Model = 16, Energy = -146.1 kJ/mol Model = 17, Energy = -147.7 kJ/mol Model = 18, Energy = -148.3 kJ/mol Model = 19, Energy = -147.1 kJ/mol Model = 20, Energy = -145.0 kJ/mol Model = 21, Energy = -142.3 kJ/mol Model = 22, Energy = -139.4 kJ/mol Model = 23, Energy = -136.8 kJ/mol Model = 24, Energy = -135.0 kJ/mol Model = 25, Energy = -134.2 kJ/mol Model = 26, Energy = -134.7 kJ/mol Model = 27, Energy = -136.6 kJ/mol Model = 28, Energy = -139.5 kJ/mol Model = 29, Energy = -143.3 kJ/mol Model = 30, Energy = -147.5 kJ/mol Model = 31, Energy = -151.7 kJ/mol Model = 32, Energy = -155.7 kJ/mol Model = 33, Energy = -158.7 kJ/mol Model = 34, Energy = -161.0 kJ/mol Model = 35, Energy = -161.6 kJ/mol Model = 34, Energy = -161.0 kJ/mol Model = 33, Energy = -158.7 kJ/mol Model = 32, Energy = -155.7 kJ/mol Model = 31, Energy = -151.7 kJ/mol Model = 30, Energy = -147.5 kJ/mol Model = 29, Energy = -143.3 kJ/mol Model = 28, Energy = -139.5 kJ/mol Model = 27, Energy = -136.6 kJ/mol Model = 26, Energy = -134.7 kJ/mol Model = 25, Energy = -134.2 kJ/mol Model = 24, Energy = -135.0 kJ/mol Model = 23, Energy = -136.8 kJ/mol Model = 22, Energy = -139.4 kJ/mol Model = 21, Energy = -142.3 kJ/mol Model = 20, Energy = -145.0 kJ/mol Model = 19, Energy = -147.1 kJ/mol Model = 18, Energy = -148.3 kJ/mol Model = 17, Energy = -147.7 kJ/mol Model = 16, Energy = -146.1 kJ/mol Model = 15, Energy = -143.8 kJ/mol Model = 14, Energy = -141.1 kJ/mol Model = 13, Energy = -138.5 kJ/mol Model = 12, Energy = -136.2 kJ/mol Model = 11, Energy = -134.6 kJ/mol Model = 10, Energy = -134.2 kJ/mol Model = 9, Energy = -135.2 kJ/mol Model = 8, Energy = -137.5 kJ/mol Model = 7, Energy = -141.0 kJ/mol Jmol applet jmolApplet0__921189882275827__ destroyed CommandWatcher InterruptedException! org.jmol.viewer.ScriptManager$CommandWatcher@180f96c java.net.MalformedURLException: no protocol: JmolAppletSigned0.jar at java.net.URL.<init>(Unknown Source) at java.net.URL.<init>(Unknown Source) at sun.plugin.util.GrayBoxPainter.setProgressFilter(Unknown Source) at sun.plugin2.applet.Plugin2Manager.setupGrayBoxPainter(Unknown Source) at sun.plugin2.applet.Plugin2Manager.access$600(Unknown Source) at sun.plugin2.applet.Plugin2Manager$AppletExecutionRunnable.run(Unknown Source) at java.lang.Thread.run(Unknown Source) exception: name. java.lang.IllegalArgumentException: name at sun.plugin2.applet.Applet2ClassLoader.addJar(Unknown Source) at sun.plugin2.applet.Applet2Manager.loadJarFiles(Unknown Source) at sun.plugin2.applet.Plugin2Manager$AppletExecutionRunnable.run(Unknown Source) at java.lang.Thread.run(Unknown Source) Exception: java.lang.IllegalArgumentException: name SECOND CONSOLE REPORT Java Plug-in 1.6.0_21 Using JRE version 1.6.0_21-b06 Java HotSpot(TM) Client VM User home directory = C:\Users\OSR ---------------------------------------------------- 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> ---------------------------------------------------- urlImage=jar:http://chemagic.com/code/jmol/JmolApplet0.jar!/jmol75x29x8.gif Jmol applet jmolApplet0__521449542350511__ initializing AppletRegistry.checkIn(jmolApplet0__521449542350511__) 1738 script command tokens applet context: -applet appletDocumentBase=http://chemagic.com/web_molecules/script_page_large.aspx appletCodeBase=http://chemagic.com/code/jmol/ (C) 2009 Jmol Development Jmol Version: 12.1.35 2011-02-04 07:49 java.vendor: Sun Microsystems Inc. java.version: 1.6.0_21 os.name: Windows 7 memory: 4.7/16.1 processors available: 2 useCommandThread: false appletId:jmolApplet0__521449542350511__ defaults = "Jmol" backgroundColor = "black" language=en_US FileManager.getAtomSetCollectionFromFile(../models/2-chlorobutane_(R).txt) FileManager opening http://chemagic.com/models/2-chlorobutane_(R).txt The Resolver thinks Mol2 openFile(../models/2-chlorobutane_(R).txt): 861 ms reading 14 atoms ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false 1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. Default Van der Waals type for model set to Babel 14 atoms created ModelSet: not autobonding; use forceAutobond=true to force automatic bond creation pickcallback = "processPick" messagecallback = "processMessage" debugScript = false bondPicking = true modelkitMode = false bondPicking = true modelkitMode = false bondPicking = true Jmol applet jmolApplet0__521449542350511__ destroyed Jmol applet jmolApplet0__6949575859348389__ initializing AppletRegistry.checkIn(jmolApplet0__6949575859348389__) urlImage=jar:http://chemapps.stolaf.edu/jmol/docs/examples-11/JmolApplet0.ja r!/jmol75x29x8.gif 1734 script command tokens applet context: -applet appletDocumentBase=http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm appletCodeBase=http://chemapps.stolaf.edu/jmol/docs/examples-11/ (C) 2009 Jmol Development Jmol Version: 12.1.31 2011-01-17 00:12 java.vendor: Sun Microsystems Inc. java.version: 1.6.0_21 os.name: Windows 7 memory: 6.3/16.3 processors available: 2 useCommandThread: false appletId:jmolApplet0__6949575859348389__ defaults = "Jmol" backgroundColor = "#000033" errorCallback = "errorCallback" hoverCallback = "showmsg" measureCallback = "measureCallback" messageCallback = "showmsg" pickCallback = "showpick" scriptCallback = "scriptCallback" language=en_US defaultDirectory = "data" FileManager.getAtomSetCollectionFromFile(caffeine.xyz) FileManager opening http://chemapps.stolaf.edu/jmol/docs/examples-11/data/caffeine.xyz The Resolver thinks Xyz openFile(caffeine.xyz): 1983 ms reading 24 atoms ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false 1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. Default Van der Waals type for model set to Babel 24 atoms created Time to autoBond: 17 ms ModelSet: autobonding; use autobond=false to not generate bonds automatically Jmol applet jmolApplet0__6949575859348389__ destroyed Jmol applet jmolApplet0__345997870461704__ initializing AppletRegistry.checkIn(jmolApplet0__345997870461704__) applet context: -applet appletDocumentBase=http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm appletCodeBase=http://chemapps.stolaf.edu/jmol/docs/examples-11/ (C) 2009 Jmol Development Jmol Version: 12.1.31 2011-01-17 00:12 java.vendor: Sun Microsystems Inc. java.version: 1.6.0_21 os.name: Windows 7 memory: 3.0/16.3 processors available: 2 useCommandThread: false appletId:jmolApplet0__345997870461704__ urlImage=jar:http://chemapps.stolaf.edu/jmol/docs/examples-11/JmolApplet0.ja r!/jmol75x29x8.gif defaults = "Jmol" backgroundColor = "#000033" errorCallback = "errorCallback" hoverCallback = "showmsg" measureCallback = "measureCallback" messageCallback = "showmsg" pickCallback = "showpick" scriptCallback = "scriptCallback" language=en_US defaultDirectory = "data" FileManager.getAtomSetCollectionFromFile(caffeine.xyz) FileManager opening http://chemapps.stolaf.edu/jmol/docs/examples-11/data/caffeine.xyz The Resolver thinks Xyz openFile(caffeine.xyz): 143 ms reading 24 atoms ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false 1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. Default Van der Waals type for model set to Babel 24 atoms created Time to autoBond: 1 ms ModelSet: autobonding; use autobond=false to not generate bonds automatically Jmol applet jmolApplet0__345997870461704__ destroyed java.net.MalformedURLException: no protocol: JmolApplet0.jar at java.net.URL.<init>(Unknown Source) at java.net.URL.<init>(Unknown Source) at sun.plugin.util.GrayBoxPainter.setProgressFilter(Unknown Source) at sun.plugin2.applet.Plugin2Manager.setupGrayBoxPainter(Unknown Source) at sun.plugin2.applet.Plugin2Manager.access$600(Unknown Source) at sun.plugin2.applet.Plugin2Manager$AppletExecutionRunnable.run(Unknown Source) at java.lang.Thread.run(Unknown Source) exception: name. java.lang.IllegalArgumentException: name at sun.plugin2.applet.Applet2ClassLoader.addJar(Unknown Source) at sun.plugin2.applet.Applet2Manager.loadJarFiles(Unknown Source) at sun.plugin2.applet.Plugin2Manager$AppletExecutionRunnable.run(Unknown Source) at java.lang.Thread.run(Unknown Source) Exception: java.lang.IllegalArgumentException: name -- Otis Rothenberger Department of Chemistry Illinois State University Normal, IL 61790-4160 http://chemagic.org
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