#324 Unable to load file of PDB entry "1SOM"

v10
closed-fixed
Miguel
5
2005-11-28
2005-09-14
Rolf Huehne
No

Version 10.00.36 and 10.00.00 are unable to load the
PDB file of PDB entry "1SOM".

The error occurs independently of the method to provide
the file (opened directly using the application or by
specifying an URL that sends the original PDB file to
the applet).

The java console shows the following messages:

FileManager.openFile(http://www.fli-leibniz.de/cgi-bin/idb_send.pl?CODE=1SOM)
SmarterJmolAdapter:The Resolver thinks:Pdb
java.lang.NullPointerException
at
org.jmol.adapter.smarter.AtomSetCollectionReader.parseToken(AtomSetCollectionReader.java:224)
at
org.jmol.adapter.smarter.PdbReader.formul(PdbReader.java:437)
at
org.jmol.adapter.smarter.PdbReader.readAtomSetCollection(PdbReader.java:95)
at
org.jmol.adapter.smarter.Resolver.resolve(Resolver.java:60)
at
org.jmol.adapter.smarter.SmarterJmolAdapter.openBufferedReader(SmarterJmolAdapter.java:56)
at
org.jmol.viewer.FileManager$FileOpenThread.openReader(FileManager.java:350)
at
org.jmol.viewer.FileManager$FileOpenThread.openInputStream(FileManager.java:343)
at
org.jmol.viewer.FileManager$FileOpenThread.run(FileManager.java:320)
at
org.jmol.viewer.FileManager.openFile(FileManager.java:89)
at org.jmol.viewer.Viewer.openFile(Viewer.java:982)
at org.jmol.viewer.Eval.load(Eval.java:1682)
at
org.jmol.viewer.Eval.instructionDispatchLoop(Eval.java:351)
at org.jmol.viewer.Eval.script(Eval.java:1813)
at
org.jmol.viewer.Eval.instructionDispatchLoop(Eval.java:366)
at org.jmol.viewer.Eval.run(Eval.java:291)
at java.lang.Thread.run(Thread.java:534)
error opening
http://www.fli-leibniz.de/cgi-bin/idb_send.pl?CODE=1SOM
java.lang.NullPointerException

Discussion

  • Miguel
    Miguel
    2005-11-28

    Logged In: YES
    user_id=1050060

    Good bug report.

    Problem was caused by an unusual formula entry in 1SOM.pdb

    FORMUL 4 DUM 10()

    Note that there are no elements in the formula.

    Jmol will now handle this without crashing. Checked in to
    cvs with 10.00.44

     
  • Miguel
    Miguel
    2005-11-28

    • status: open --> closed-fixed