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  • Assemble: a tool to construct and study RNA architectures - Support tickets

    Submit | Open tickets | Closed tickets

    [ Ticket #1087 ] Can't open up PDB files at all
    Date:
    05/25/09 00:54
    Submitted by:
    Capegreenie08
    Assigned to:
    unset
    Category:
    Unset
    Priority:
    5
    Ticket group:
    Unset
    Resolution:
    Unset
    Summary:
    Can't open up PDB files at all
    Original submission:
    Whenever I attempt to open up a PDB file the following error message pops up.

    The RNAVIEW service is not able to process your request effectively.

    Error
    Message: fr.unistra.ibmc.paradise.goloka.core.analysis.AnalysisException: java.lang.NullPointerException: null
    Level: SEVERE

    Stack Trace:
    java.lang.NullPointerException: null
    fr.unistra.ibmc.paradise.goloka.core.features.AbstractParadiseFeature.annotates(AbstractParadiseFeature.java:111)
    fr.unistra.ibmc.paradise.goloka.core.features.StructuralFeatureFactory.createHelix(StructuralFeatureFactory.java:108)
    fr.unistra.ibmc.paradise.goloka.core.features.StructuralFeatureFactory.copyHelix(StructuralFeatureFactory.java:79)
    fr.unistra.ibmc.paradise.goloka.core.features.StructuralFeatureFactory.copySubFeaturesToSecondaryStructure(StructuralFeatureFactory.java:220)
    fr.unistra.ibmc.paradise.goloka.core.features.StructuralFeatureFactory.copySecondaryStructure(StructuralFeatureFactory.java:199)
    fr.unistra.ibmc.paradise.goloka.services.analysis.rnaview.RnaviewAnalysis.run(RnaviewAnalysis.java:108)
    fr.unistra.ibmc.paradise.goloka.services.analysis.RequestBehaviour$1AnalysisWorker.doInBackground(RequestBehaviour.java:81)
    org.jdesktop.swingworker.SwingWorker$1.call(Unknown Source)
    java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:269)
    java.util.concurrent.FutureTask.run(FutureTask.java:123)
    org.jdesktop.swingworker.SwingWorker.run(Unknown Source)
    java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:650)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:675)
    java.lang.Thread.run(Thread.java:613)



    Does anyone know how to get this to work properly. I'm using Assemble on Mac OSX vers 10.5.7.
    Thanks
    ~Adrián
    Please log in to add comments and receive followups via email.
    Followups
    Comment Date By
    I am also having the same problem, but I'm running Ubuntu 8.04 (Hardy Heron), Linux kernel 2.6.24. 06/23/09 14:27 szaheer
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