Beautiful - explained the problem AND fixed the problem AND removed some extraneous scripting to boot. All in one step. THANKS!
Dean On 6/8/07 11:33 PM, "Bob Hanson" <[EMAIL PROTECTED]> wrote: > I think this system uses multiple threads, and the first thread has hit: > >> connect (all) (all) delete; >> > and is in the process of deleting the bonds when another thread starts > rendering the picture. So the first thread has cleared some bonds that > the renderer thread needs. > I'll look into it. > > You might consider instead of the above to > > set autobond false > data ..... > > Then there is less chance of such a thing happening. > > Bob > > >> connect (atomno=001) (atomno=002 ) AROMATIC >> create;connect (atomno=002) (atomno=003 ) AROMATIC create;connect >> (atomno=003) (atomno=004 ) AROMATIC create;connect (atomno=004) (atomno=005 >> ) AROMATIC create;connect (atomno=005) (atomno=006 ) AROMATIC create;connect >> (atomno=006) (atomno=001 ) AROMATIC create;connect (atomno=001) (atomno=007 >> ) SINGLE create;connect (atomno=002) (atomno=008 ) SINGLE create;connect >> (atomno=003) (atomno=009 ) SINGLE create;connect (atomno=004) (atomno=010 ) >> SINGLE create;connect (atomno=005) (atomno=011 ) SINGLE create;connect >> (atomno=006) (atomno=012 ) SINGLE create; >> set perspectiveDepth off; center all >> set echo bottom left; font echo 15 sansserif italic; color echo gray; echo >> Point Group = D6h >> >> As I said before, however, I can only produce the error sporadically and >> only on OS X. In general I can load several molecules successfully before I >> get this error. It doesn't seem to be a memory issue, however. Let me know >> if you want me to put up an example page (it's currently just running >> locally). >> >> Dean >> >> >> On 6/8/07 10:39 PM, "Bob Hanson" <[EMAIL PROTECTED]> wrote: >> >> >> >>> Dean, please send me the script. I'd like to fix this. >>> >>> Dean Johnston wrote: >>> >>> >>> >>>> I¹m getting an odd (and hard to reproduce) crash with the Jmol applet >>>> (Firefox or Safari on OS X, version 11.1.48_dev). I try and load an >>>> inline model and sporadically get the error listed below. It seems to >>>> always be in the middle of creating the new bonds (my page creates all >>>> the bonds manually from a connection list) after the molecule loads. >>>> >>>> For some reason I never get the same error under Windows (Firefox or IE). >>>> >>>> If it¹s any help, my earlier version of the page that uses the 11.1.22 >>>> applet does not produce the same error. >>>> >>>> Dean Johnston >>>> >>>> --------------------------- >>>> FileManager.openStringInline() >>>> The Resolver thinks Xyz >>>> ModelSet: haveSymmetry:false haveUnitcells:false 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 >>>> data "model molecule" >>>> |12|molecule|C -1.2125 -0.7000 0.0000|C -1.2125 0.7000 0.0000|C 0.0000 >>>> 1.4000 0.0000|C 1.2124 0.7000 0.0000|C 1.2124 -0.7000 0.0000|C 0.0000 >>>> -1.4000 0.0000|H -2.1478 -1.2400 0.0000|H -2.1478 1.2400 0.0000|H >>>> 0.0000 2.4800 0.0000|H 2.1477 1.2400 0.0000|H 2.1477 -1.2400 0.0000|H >>>> 0.0000 -2.4800 0.0000| >>>> 12 bonds deleted >>>> 1 new bonds; 0 modified >>>> 1 new bonds; 0 modified >>>> 1 new bonds; 0 modified >>>> 1 new bonds; 0 modified >>>> 1 new bonds; 0 modified >>>> Exception in thread "AWT-EventQueue-8" java.lang.NullPointerException >>>> at org.jmol.shape.Sticks.setModelClickability(Unknown Source) >>>> at org.jmol.modelset.ModelSet.setModelVisibility(Unknown Source) >>>> at org.jmol.modelset.ModelManager.setModelVisibility(Unknown Source) >>>> at org.jmol.viewer.Viewer.setModelVisibility(Unknown Source) >>>> at org.jmol.viewer.Viewer.renderScreenImage(Unknown Source) >>>> at org.jmol.applet.Jmol.update(Unknown Source) >>>> at org.jmol.applet.Jmol.update(Unknown Source) >>>> at org.jmol.appletwrapper.AppletWrapper.update(Unknown Source) >>>> at sun.awt.RepaintArea.updateComponent(RepaintArea.java:267) >>>> at sun.awt.RepaintArea.paint(RepaintArea.java:233) >>>> at apple.awt.ComponentModel.handleEvent(ComponentModel.java:251) >>>> at apple.awt.MyCPanel.handleEvent(MyCPanel.java:97) >>>> at java.awt.Component.dispatchEventImpl(Component.java:4097) >>>> at java.awt.Container.dispatchEventImpl(Container.java:2068) >>>> at java.awt.Component.dispatchEvent(Component.java:3869) >>>> at java.awt.EventQueue.dispatchEvent(EventQueue.java:463) >>>> at jep.MySimpleEventQueue.dispatchEvent(MySimpleEventQueue.java:59) >>>> at >>>> java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.j >>>> av >>>> a:269) >>>> at >>>> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.jav >>>> a: >>>> 190) >>>> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:184) >>>> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:176) >>>> at java.awt.EventDispatchThread.run(EventDispatchThread.java:110) >>>> 1 new bonds; 0 modified >>>> 1 new bonds; 0 modified >>>> 1 new bonds; 0 modified >>>> 1 new bonds; 0 modified >>>> 1 new bonds; 0 modified >>>> 1 new bonds; 0 modified >>>> 1 new bonds; 0 modified >>>> perspectivedepth = false >>>> >>>> ------------------------------------------------------------------------ >>>> >>>> ------------------------------------------------------------------------- >>>> This SF.net email is sponsored by DB2 Express >>>> Download DB2 Express C - the FREE version of DB2 express and take >>>> control of your XML. No limits. Just data. Click to get it now. >>>> http://sourceforge.net/powerbar/db2/ >>>> >>>> ------------------------------------------------------------------------ >>>> >>>> _______________________________________________ >>>> Jmol-users mailing list >>>> Jmol-users@lists.sourceforge.net >>>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>>> >>>> >>>> >>>> >> >> >> >> ------------------------------------------------------------------------- >> This SF.net email is sponsored by DB2 Express >> Download DB2 Express C - the FREE version of DB2 express and take >> control of your XML. No limits. Just data. Click to get it now. >> http://sourceforge.net/powerbar/db2/ >> _______________________________________________ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
