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