Details
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Type: Bug
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Status: Closed
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Priority: Major
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Resolution: Fixed
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Affects Version/s: 2.10.2b1, 2.10.2b2, 2.10.3
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Fix Version/s: 2.10.4
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Component/s: Structures
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Labels:None
Description
Importing and showing PDB Entries with jumps in RESNUM fields (e.g. 4im2) yields a structure where C-terminal residues do not receive a feature colour and are not labelled / or side-chains made visible when moused over in the alignment view.
added 4im2_missing.pdb to examples/testdata to demonstrate this. Issue is only seen with SIFTS mappings enabled - plain N&W mappings work fine. Removing the HEADER line from the PDB file, triggers N&W mapping only, so issue is definitely in the SIFTS mapping routine.
Rather than fix the SIFTS mapping routine (which works fine for Uniprot<>PDB sequence relationships), in this case the problem is that sequences extracted from coordinate files (PDB, mmCIF, whatever) shouldn't need SIFTS mappings, so that code should never execute in those cases. Recommended fix is to recognise and create 1:1 mappings (by NW or otherwise) for sequences extracted from files corresponding to PDB entries (ie those which may also yield a SIFTS file).
added 4im2_missing.pdb to examples/testdata to demonstrate this. Issue is only seen with SIFTS mappings enabled - plain N&W mappings work fine. Removing the HEADER line from the PDB file, triggers N&W mapping only, so issue is definitely in the SIFTS mapping routine.
Rather than fix the SIFTS mapping routine (which works fine for Uniprot<>PDB sequence relationships), in this case the problem is that sequences extracted from coordinate files (PDB, mmCIF, whatever) shouldn't need SIFTS mappings, so that code should never execute in those cases. Recommended fix is to recognise and create 1:1 mappings (by NW or otherwise) for sequences extracted from files corresponding to PDB entries (ie those which may also yield a SIFTS file).
Attachments
Issue Links
- related with
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JAL-2224 Structure's extracted sequence's start/end numbering misleading
- Open
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JAL-2780 PDB entries with negative residue numbers are incorrectly annotated
- Closed
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JAL-2007 Use PDBe numbering for sequences extracted from PDB files
- In Progress
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JAL-2902 programmatic control of structure chooser dialog for an alignment view
- Closed