Details
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Type:
Bug
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Status: Open
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Priority:
Blocker
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Resolution: Unresolved
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Affects Version/s: None
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Fix Version/s: None
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Component/s: Structures
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Labels:None
Description
Steps to reproduce:
1. import and view LGUL_HUMAN
2. Use 3d structure chooser to view available alphafold and pdbe structures.
3. Select a PDBe filter like 'Most bound molecules' from drop down.
4. then pick an alphafold structure from the list
5. Try to retreive/view the structure
Exceptions are seen like:
Exception in thread "Thread-44" java.lang.IllegalArgumentException: Identifier not found
at java.desktop/javax.swing.table.DefaultTableColumnModel.getColumnIndex(DefaultTableColumnModel.java:283)
at java.desktop/javax.swing.JTable.getColumn(JTable.java:2548)
at jalview.gui.structurechooser.PDBStructureChooserQuerySource.collectSelectedRows(PDBStructureChooserQuerySource.java:352)
at jalview.gui.StructureChooser$8.run(StructureChooser.java:1264)
at java.base/java.lang.Thread.run(Thread.java:829)
The 'fetch structure' routine uses the getStructures method from the picked filter from the dropdown to decide how to retrieve structures, since no pdbId is available for an alphafold structure.
Needs a bit of reworking of the structure selection GUI model to fix this.
1. import and view LGUL_HUMAN
2. Use 3d structure chooser to view available alphafold and pdbe structures.
3. Select a PDBe filter like 'Most bound molecules' from drop down.
4. then pick an alphafold structure from the list
5. Try to retreive/view the structure
Exceptions are seen like:
Exception in thread "Thread-44" java.lang.IllegalArgumentException: Identifier not found
at java.desktop/javax.swing.table.DefaultTableColumnModel.getColumnIndex(DefaultTableColumnModel.java:283)
at java.desktop/javax.swing.JTable.getColumn(JTable.java:2548)
at jalview.gui.structurechooser.PDBStructureChooserQuerySource.collectSelectedRows(PDBStructureChooserQuerySource.java:352)
at jalview.gui.StructureChooser$8.run(StructureChooser.java:1264)
at java.base/java.lang.Thread.run(Thread.java:829)
The 'fetch structure' routine uses the getStructures method from the picked filter from the dropdown to decide how to retrieve structures, since no pdbId is available for an alphafold structure.
Needs a bit of reworking of the structure selection GUI model to fix this.