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Type: Bug
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Status: Closed
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Priority: Blocker
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Resolution: Fixed
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Affects Version/s: 1.19
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Fix Version/s: 1.20
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Component/s: Basic-Other, Basic-Protein
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Story Points:5
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Tests Type:GUI automatic
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Sprint:DEV-02/12/2015
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Affect Type:Userdefined
The issue must be fixed and tested until Nov. 18!!
In the current UGENE version names of chains, loaded from a PDB file, are numerical. This is incorrect. The names are available in the PDB format and must be used in the UGENE GUI - use chain identifier field from the "ATOM" records.
For details see the use cases below, the attached screenshots, and the format specification:
http://www.wwpdb.org/docs/documentation/file-format/PDB_format_1996.pdf (p.174 - the chapter about "ATOM")
Use case 1:
- Open a PDB file with several "MOLECULE" records (e.g. 1FDL).
Expected state: The correct chain names are shown in the Project View and in each single-sequence view of the Sequence View. - Open an annotation node in the Annotations Editor to see its qualifiers.
Expected state: There is "molecule_name" filed. It has a correct molecule name, read from the PDB file header, NOT the chain name. - Select "Structural Alignment > Align With" item in the context menu.
Expected state:- The correct chain names are available in the "Chain" menu.
Use case 2:
The same as UC1, but use a PDB file with molecules that have several chains, i.e. the comma-separated list of chain identifiers (e.g. 3INS).
- relates to
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UGENE-4975 Incorrect loading of chain identifiers from MMDB files
- Closed