CR-JAL-63 JAL-2465: No mapping generated for 3D Structures loaded in Jmol via URL

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JAL-2465: No mapping generated for 3D Structures loaded in Jmol via URL

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Number of files included: 33

jalview 0
- Folder src 0
  - Folder MCview 0
    - 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
  - Folder jalview 0
    - Folder ext 0
      - Folder jmol 0
        
        File JalviewJmolBinding.java 0 Remove
        
        File JalviewJmolBinding.java 0 Remove
      - Folder rbvi/chimera 0
        
        File JalviewChimeraBinding.java 0 Remove
        
        File JalviewChimeraBinding.java 0 Remove
    - Folder gui 0
      - 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
    - Folder javascript 0
      - File MouseOverStructureListener.java 0 Remove
      - File MouseOverStructureListener.java 0 Remove
    - Folder structure 0
      - 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
    - Folder structures/models 0
      - File AAStructureBindingModel.java 0 Remove
      - File AAStructureBindingModel.java 0 Remove
- Folder test/jalview 0
  - Folder ext 0
    - Folder jmol 0
      - File JmolViewerTest.java 0 Remove
      - File JmolViewerTest.java 0 Remove
    - Folder rbvi/chimera 0
      - File JalviewChimeraView.java 0 Remove
      - File JalviewChimeraView.java 0 Remove
  - Folder structures/models 0
    - File AAStructureBindingModelTest.java 0 Remove
    - File AAStructureBindingModelTest.java 0 Remove

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Participant	Role	Time Spent	Comments
Tochukwu Charles N Ofoegbu	Author	5m
Kira Mourão	Reviewer - 90% reviewed	3m
Total		8m	0

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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Issues Raised From Comments

Key	Summary	State	Assignee

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CR-JAL-63

JAL-2465: No mapping generated for 3D Structures loaded in Jmol via URL

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JAL-2465: No mapping generated for 3D Structures loaded in Jmol via URL

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