Details
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Type:
Bug
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Status: Open
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Priority:
Major
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Resolution: Unresolved
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Affects Version/s: 2.10.0
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Fix Version/s: 2.11.0
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Component/s: Structures
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Labels:
Description
1. Import 3A6S
2. note both chains have start-end numbering of 1-129 - the end number is derived from RESNUM for last residue in chain.
3. open a structure view, and open the structure mapping report
4. note also that chains have a mapped range between sequence and structure of 1-129
The problem comes if one tries to use this data to locate positions in the alignment - programmatically or otherwise. e.g. use Find to locate position 128 in either alignment will simply highlight the last residue, because both sequences are shorter than 128 amino acids. This is dissonant because both sequence's ends are stated to be 129 !
Suggested action ? Jalview should set the 'end' to the real 'end' number for the sequence as it is manipulated in Jalview, rather than the numerical label assigned to the last residue via the PDB ResNum field.
2. note both chains have start-end numbering of 1-129 - the end number is derived from RESNUM for last residue in chain.
3. open a structure view, and open the structure mapping report
4. note also that chains have a mapped range between sequence and structure of 1-129
The problem comes if one tries to use this data to locate positions in the alignment - programmatically or otherwise. e.g. use Find to locate position 128 in either alignment will simply highlight the last residue, because both sequences are shorter than 128 amino acids. This is dissonant because both sequence's ends are stated to be 129 !
Suggested action ? Jalview should set the 'end' to the real 'end' number for the sequence as it is manipulated in Jalview, rather than the numerical label assigned to the last residue via the PDB ResNum field.
Attachments
Issue Links
- depends on
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JAL-2007 Use PDBe numbering for sequences extracted from PDB files
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- In Progress
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- related with
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- Closed
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- Closed
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- Closed
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- Closed
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