Details
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Type: Improvement
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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: 2.11.3.0, 2.11.4.0
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Fix Version/s: 2.12
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Component/s: file format issue, Structures
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Labels:None
Description
Jalview should be able to autodetect AlphafoldDB structures imported directly since they include text like the following in the TITLE and REMARK lines:
HEADER 01-JUN-22
TITLE ALPHAFOLD MONOMER V2.0 PREDICTION FOR TRIOSEPHOSPHATE ISOMERASE
..
Licensing can be obtained from the REMARK:
REMARK 1 ACADEMIC AND COMMERCIAL PURPOSES, UNDER CC-BY 4.0 LICENCE.
Finally, 'UNP' refers to the Uniprot accession:
DBREF XXXX A 1 253 UNP A0Q8C4 TPIS_FRATN 1 253
So importing a pdb file like this should yield a sequence annotated with temperature factor interpreted as PLDDT automatically, and a database cross-reference to uniprot with the stated accession.
HEADER 01-JUN-22
TITLE ALPHAFOLD MONOMER V2.0 PREDICTION FOR TRIOSEPHOSPHATE ISOMERASE
..
Licensing can be obtained from the REMARK:
REMARK 1 ACADEMIC AND COMMERCIAL PURPOSES, UNDER CC-BY 4.0 LICENCE.
Finally, 'UNP' refers to the Uniprot accession:
DBREF XXXX A 1 253 UNP A0Q8C4 TPIS_FRATN 1 253
So importing a pdb file like this should yield a sequence annotated with temperature factor interpreted as PLDDT automatically, and a database cross-reference to uniprot with the stated accession.