CR-JAL-109
JAL-2777: Exceptions and superposition failure when viewing PDB files with empty...
Details
Participant | Role | Time Spent | Comments | Latest Comment |
---|---|---|---|---|
Author | 7m | 2 | oops - this is the wrong issue number :q | |
Reviewer - 93% reviewed | 7m | 2 | Not quite sure what the FeatureSettings changes were fixi... | |
Total | 14m | 4 |
- Linked Issue:
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Objectives
PDB files produced by modelling tools often lack PDB chain codes (like the one attached). Importing these to view in Chimera yields the following exception:
Time for creating model: 68 ms
Exception in thread "Thread-132" java.lang.NullPointerException
at java.util.Collections.sort(Collections.java:175)
at jalview.ext.rbvi.chimera.AtomSpecModel.getAtomSpec(AtomSpecModel.java:130)
at jalview.ext.rbvi.chimera.ChimeraCommands.buildColourCommands(ChimeraCommands.java:121)
at jalview.ext.rbvi.chimera.ChimeraCommands.getColourBySequenceCommand(ChimeraCommands.java:75)
at jalview.ext.rbvi.chimera.JalviewChimeraBinding.getColourBySequenceCommands(JalviewChimeraBinding.java:701)
at jalview.structures.models.AAStructureBindingModel.colourBySequence(AAStructureBindingModel.java:814)
at jalview.gui.JalviewChimeraBindingModel.updateColours(JalviewChimeraBindingModel.java:90)
at jalview.gui.ChimeraViewFrame.run(ChimeraView...
Not quite sure what the FeatureSettings changes were fixing - doesn't look like it was anything referred to in the bug report. Difficult to review/test without knowing that.