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.jav >>>a:269) >>>at >>>java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java: >>>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 > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 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
