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  1. Jalview
  2. JAL-1941

Exception when retrieving RnaView RNA secondary structure

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    Details

    • Type: Bug
    • Status: In Progress
    • Priority: Critical
    • Resolution: Unresolved
    • Affects Version/s: 2.9.0b2
    • Fix Version/s: None
    • Component/s: Dev and Dep, na
    • Labels:
      None
    • Urgency:
      Urgent

      Description

      To reproduce:
      1. Install Jalview from InstallAnywhere and launch.
      2. open console.
      3. Use PDB fetcher to retrieve 2GIS. Ensure 'Process structure with RNAView service' is checked in your Structure preferences.
      3. only temperature (if selected) wil be shown on retrieved structure.

      Two problems.
      1. No RNA secondary structure.
      2. A second Temperature annotation row can be added with 'Add Reference Annotation' - this might be due to the PDB annotation processing code being interrupted when the exception below is raised.

      The console shows the following issue - looks like a library is missing in the installAnywhere classpath:
      Annotate3D
      Exceptions when dealing with RNA in pdb file
      java.lang.reflect.InvocationTargetException
      at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
      at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
      at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
      at java.lang.reflect.Method.invoke(Method.java:483)
      at MCview.PDBfile.processPdbFileWithAnnotate3d(PDBfile.java:450)
      at MCview.PDBfile.predictSecondaryStructure(PDBfile.java:253)
      at MCview.PDBfile.parse(PDBfile.java:216)
      at jalview.io.AlignFile.doParse(AlignFile.java:169)
      at MCview.PDBfile.<init>(PDBfile.java:83)
      at jalview.io.AppletFormatAdapter.readFile(AppletFormatAdapter.java:280)
      at jalview.io.FormatAdapter.readFile(FormatAdapter.java:311)
      at jalview.ws.dbsources.Pdb.getSequenceRecords(Pdb.java:134)
      at jalview.gui.SequenceFetcher.run(SequenceFetcher.java:579)
      at java.lang.Thread.run(Thread.java:745)
      Caused by: java.io.IOException: Unexpected exception when handling RNAML translation of PDB data
      at jalview.ws.jws1.Annotate3D.getRNAMLFor(Annotate3D.java:108)
      ... 14 more
      Caused by: java.lang.NoClassDefFoundError: org/apache/james/mime4j/message/Body
      at java.lang.ClassLoader.defineClass1(Native Method)
      ...

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              Assignee:
              jprocter Jim Procter
              Reporter:
              jprocter Jim Procter
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                Dates

                Created:
                Updated: