Hi
Using 11.1.42
Not sure if it's a bug, since other files don't give this error.
Using either
a) load =1GIX
or
b) load "F:/1GIXmodl.pdb" (a cut-down version of the above file, with just 2 of
the tRNA
molecules)
after calling "hbonds calculate" the model freezes and Jmol is unresponsive.
Java console gives:
(The thread number given in the error seems to change every time.)
FileManager opening F:/1GIXmodl.pdb
The Resolver thinks Pdb
openFile(F:/1GIXmodl.pdb)80 ms
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
Exception in thread "Thread-10" java.lang.NullPointerException
at org.jmol.modelset.ModelSet.addHydrogenBond(Unknown Source)
at org.jmol.modelset.Model.addHydrogenBond(Unknown Source)
at org.jmol.modelsetbio.NucleicPolymer.lookForHbonds(Unknown Source)
at org.jmol.modelsetbio.NucleicPolymer.calcHydrogenBonds(Unknown Source)
at org.jmol.modelset.Model.calcHydrogenBonds(Unknown Source)
at org.jmol.modelset.Mmset.calcHydrogenBonds(Unknown Source)
at org.jmol.modelset.ModelSet.autoHbond(Unknown Source)
at org.jmol.modelset.ModelManager.autoHbond(Unknown Source)
at org.jmol.viewer.Viewer.autoHbond(Unknown Source)
at org.jmol.viewer.Viewer.autoHbond(Unknown Source)
at org.jmol.viewer.Eval.hbond(Unknown Source)
at org.jmol.viewer.Eval.instructionDispatchLoop(Unknown Source)
at org.jmol.viewer.Eval.runEval(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)
-------------------------------------------------------------------------
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
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
