Details
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Type: Bug
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Status: Resolved
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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: None
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Component/s: Structures
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Labels:
Description
Regression on PDB import functionality - originally noticed when trying to view PDB structures for ENSEMBL locus view.
1. Import 4uj3 via PDB fetcher
--> successful in 2.9.0b2 - fails in 2.9.1 develop
2. View [cached] structure for all chains
--> 2.9.0b2
. cached view results in chains mapped as extracted from file. Unmapped regions are insertions (presumably)
3. I tried saving a project from 2.9.0b2 and importing it to 2.9.1 develop (attached).
--> Project imported in to 2.9.1 fine
4. Repeat step 2: view cached structure
--> 2.9.1 develop - fails to get chain mapping correct
Console output:
Could not get source DB Ref
Could not get source DB Ref
Getting mapping for: 4UJ3|A : seq- PDB|4uj3|4UJ3|A
Getting mapping for: 4UJ3|B : seq- PDB|4uj3|4UJ3|B
Getting mapping for: 4UJ3|C : seq- PDB|4uj3|4UJ3|C
Could not get source DB Ref
Could not get source DB Ref
Could not get source DB Ref
Could not get source DB Ref
Could not get source DB Ref
Getting mapping for: 4UJ3|D : seq- PDB|4uj3|4UJ3|D
Getting mapping for: 4UJ3|E : seq- PDB|4uj3|4UJ3|E
Getting mapping for: 4UJ3|F : seq- PDB|4uj3|4UJ3|F
Getting mapping for: 4UJ3|G : seq- PDB|4uj3|4UJ3|G
Could not get source DB Ref
Could not get source DB Ref
Could not get source DB Ref
Could not get source DB Ref
Could not get source DB Ref
Getting mapping for: 4UJ3|H : seq- PDB|4uj3|4UJ3|H
Getting mapping for: 4UJ3|I : seq- PDB|4uj3|4UJ3|I
Getting mapping for: 4UJ3|J : seq- PDB|4uj3|4UJ3|J
Getting mapping for: 4UJ3|K : seq- PDB|4uj3|4UJ3|K
Getting mapping for: 4UJ3|L : seq- PDB|4uj3|4UJ3|L
Could not get source DB Ref
Could not get source DB Ref
Could not get source DB Ref
Could not get source DB Ref
Could not get source DB Ref
Getting mapping for: 4UJ3|M : seq- PDB|4uj3|4UJ3|M
Getting mapping for: 4UJ3|N : seq- PDB|4uj3|4UJ3|N
Getting mapping for: 4UJ3|O : seq- PDB|4uj3|4UJ3|O
Getting mapping for: 4UJ3|P : seq- PDB|4uj3|4UJ3|P
Getting mapping for: 4UJ3|Q : seq- PDB|4uj3|4UJ3|Q
Could not get source DB Ref
Could not get source DB Ref
Could not get source DB Ref
Could not get source DB Ref
Could not get source DB Ref
Could not get source DB Ref
Getting mapping for: 4UJ3|R : seq- PDB|4uj3|4UJ3|R
Getting mapping for: 4UJ3|S : seq- PDB|4uj3|4UJ3|S
Getting mapping for: 4UJ3|T : seq- PDB|4uj3|4UJ3|T
Getting mapping for: 4UJ3|U : seq- PDB|4uj3|4UJ3|U
Getting mapping for: 4UJ3|V : seq- PDB|4uj3|4UJ3|V
Getting mapping for: 4UJ3|W : seq- PDB|4uj3|4UJ3|W
Getting mapping for: 4UJ3|X : seq- PDB|4uj3|4UJ3|X
network: Connecting socket://127.0.0.1:61367 with proxy=DIRECT
Could not get source DB Ref
View mapping shows chain/chain mapping has been corrupted:
Sequence ⟷ Structure mapping details
Method: inferred with Needleman & Wunsch alignment
PDB Sequence is :
Sequence = RDDEYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDGKTIKAQIWDTAGLERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEIYRIVSQK
No of residues = 176
Score = 8790
Length of alignment = 175
Sequence PDB|4uj3|4UJ3|D : 5 - 179 (Sequence length = 175)
Sequence 4UJ3|A : 4 - 179 (Sequence length = 176)
Attachments
Issue Links
- depends on
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JAL-1803 PDB chain id not saved in Jalview project
- Closed