JAL-2465: No mapping generated for 3D Structures loaded in Jmol via URL
Activity
CR-JAL-63 0
- Details
- Objectives
- General Comments 0
- Unresolved
- Resolved
- Number of files included: 33
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jalview
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src
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MCview
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- File AppletPDBCanvas.java 0 Remove
- File AppletPDBCanvas.java 0 Remove
- File AppletPDBCanvas.java 0 Remove
- File PDBCanvas.java 0 Remove
- File PDBCanvas.java 0 Remove
- File PDBCanvas.java 0 Remove
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jalview
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ext
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jmol
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- File JalviewJmolBinding.java 0 Remove
- File JalviewJmolBinding.java 0 Remove
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rbvi/chimera
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- File JalviewChimeraBinding.java 0 Remove
- File JalviewChimeraBinding.java 0 Remove
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jmol
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gui
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- File AppJmol.java 0 Remove
- File AppJmol.java 0 Remove
- File AppVarnaBinding.java 0 Remove
- File AppVarnaBinding.java 0 Remove
- File ChimeraViewFrame.java 0 Remove
- File ChimeraViewFrame.java 0 Remove
- File StructureViewerBase.java 0 Remove
- File StructureViewerBase.java 0 Remove
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javascript
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- File MouseOverStructureListener.java 0 Remove
- File MouseOverStructureListener.java 0 Remove
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structure
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- File StructureListener.java 0 Remove
- File StructureListener.java 0 Remove
- File StructureSelectionManager.java 0 Remove
- File StructureSelectionManager.java 0 Remove
- File StructureSelectionManager.java 0 Remove
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structures/models
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- File AAStructureBindingModel.java 0 Remove
- File AAStructureBindingModel.java 0 Remove
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ext
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MCview
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test/jalview
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ext
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jmol
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- File JmolViewerTest.java 0 Remove
- File JmolViewerTest.java 0 Remove
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rbvi/chimera
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- File JalviewChimeraView.java 0 Remove
- File JalviewChimeraView.java 0 Remove
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jmol
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structures/models
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- File AAStructureBindingModelTest.java 0 Remove
- File AAStructureBindingModelTest.java 0 Remove
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ext
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src
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Participant | Role | Time Spent | Comments | Latest Comment |
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Total | 8m | 0 |
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Linked Issue:
JAL-2465
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Objectives
I initially thought this bug was specific to Phyre2 model structures, however further tracking shows it happens for all structures and also affects version 2.10.1.
Follow the steps below to reproduce bug:
- set structure viewer to JMOL
- load any 3D structure file from URL e.g. http://www.ebi.ac.uk/pdbe/entry-files/pdb1a70.ent
- view the 3D structure for the added sequence from Cached Option of the Structure Chooser
Outcome:
Jmol launches and displays the structure - however, no mapping is generated hence the displayed structure is grayed out and cannot communicate with the alignment window.
With Chimera, mapping is created successfully.
Branches in review
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/src/MCview/AppletPDBCanvas.java
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/src/MCview/AppletPDBCanvas.java
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/src/MCview/AppletPDBCanvas.java
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/src/MCview/PDBCanvas.java
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/src/MCview/PDBCanvas.java
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/src/MCview/PDBCanvas.java
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/src/jalview/.../jmol/JalviewJmolBinding.java
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/src/jalview/.../jmol/JalviewJmolBinding.java
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/src/.../chimera/JalviewChimeraBinding.java
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/src/.../chimera/JalviewChimeraBinding.java
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/src/jalview/gui/AppJmol.java
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/src/jalview/gui/AppJmol.java
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/src/jalview/gui/AppVarnaBinding.java
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/src/jalview/gui/AppVarnaBinding.java
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/src/jalview/gui/ChimeraViewFrame.java
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/src/jalview/gui/ChimeraViewFrame.java
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/src/jalview/gui/StructureViewerBase.java
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/src/jalview/gui/StructureViewerBase.java
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/src/.../javascript/MouseOverStructureListener.java
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/src/.../javascript/MouseOverStructureListener.java
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/src/.../structure/StructureListener.java
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/src/.../structure/StructureListener.java
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/src/.../structure/StructureSelectionManager.java
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/src/.../structure/StructureSelectionManager.java
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/src/.../structure/StructureSelectionManager.java
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/src/.../models/AAStructureBindingModel.java
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/src/.../models/AAStructureBindingModel.java
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/test/jalview/ext/jmol/JmolViewerTest.java
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/test/jalview/ext/jmol/JmolViewerTest.java
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/test/.../chimera/JalviewChimeraView.java
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/test/.../chimera/JalviewChimeraView.java
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/test/.../models/AAStructureBindingModelTest.java
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/test/.../models/AAStructureBindingModelTest.java
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