Opened 2 years ago
Closed 2 years ago
#9976 closed defect (fixed)
Fetching PDB biounit shows error in status line
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.5.2-x86_64-i386-64bit
ChimeraX Version: 1.7.dev202309121847 (2023-09-12 18:47:21 UTC)
Description
Fetching pdbe_bio 6ts0 says in the secondary status line (right side): "Error fetching 6ts0 bioassembly 2".
I believe this is because there is only 1 bioassembly but the code does not know how many there are and just tries to keep reading additional ones until it gets an error. Elaine reported this.
Log:
Could not find tool "Tabbed Toolbar"
UCSF ChimeraX version: 1.7.dev202309121847 (2023-09-12)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 6ts0 fromDatabase pdbe_bio ignoreCache true
Summary of feedback from opening 6ts0 fetched from pdbe_bio
---
warnings | Atom H is not in the residue template for SER /A:6
Atom H is not in the residue template for SER /AA:6
Atom H is not in the residue template for SER /AB:6
Atom H is not in the residue template for SER /AC:6
Atom H is not in the residue template for SER /AD:6
4 messages similar to the above omitted
Too many hydrogens missing from residue template(s) to warn about
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
notes | Fetching compressed 6ts0 bioassembly 1 from
https://www.ebi.ac.uk/pdbe/static/entry/download/6ts0-assembly-1.cif.gz
Combining 4 symmetry atoms into HOH /MA:415 O
Combining 4 symmetry atoms into FE /FA:205 FE
Combining 4 symmetry atoms into HOH /MA:318 O
Combining 3 symmetry atoms into FE /HM:207 FE
Combining 3 symmetry atoms into FE /HA:207 FE
Combining 3 symmetry atoms into FE /HB:207 FE
Combining 3 symmetry atoms into FE /HO:207 FE
Combining 3 symmetry atoms into FE /EM:204 FE
11 messages similar to the above omitted
Combining 4 symmetry atoms into HOH /ME:415 O
Combining 4 symmetry atoms into FE /FE:205 FE
Combining 4 symmetry atoms into HOH /ME:318 O
Combining 4 symmetry atoms into HOH /MI:415 O
Combining 4 symmetry atoms into FE /FI:205 FE
7 messages similar to the above omitted
Combining 3 symmetry atoms into HOH /MC:449 O
Combining 3 symmetry atoms into HOH /MN:449 O
Combining 3 symmetry atoms into HOH /ML:449 O
Combining 3 symmetry atoms into HOH /M:449 O
Combining 3 symmetry atoms into FE /JC:209 FE
11 messages similar to the above omitted
Combining 4 symmetry atoms into HOH /M:318 O
Combining 4 symmetry atoms into FE /F:205 FE
Combining 4 symmetry atoms into HOH /M:415 O
6ts0 bioassembly 1 title:
Crystal structure of human L ferritin (HuLf) triple variant E60A-E61A-E64A
Fe(III)-loaded for 30 minutes [more info...]
Chain information for 6ts0 bioassembly 1 #1
---
Chain | Description
A AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW |
Ferritin light chain
Non-standard residues in 6ts0 bioassembly 1 #1
---
CD — (CD)
FE — (FE)
O — (O)
6ts0 bioassembly 1 mmCIF Assemblies
---
1| author_defined_assembly
Opened 1 biological assemblies for 6ts0
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OpenGL version: 4.1 ATI-4.14.1
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
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Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Reporter: | changed from to |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Fetching PDB biounit shows error in status line |
comment:2 by , 2 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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Fixed.
As suspected, ChimeraX does not know how many bioassemblies there are and just keeps fetching files with higher suffix numbers until an error occurs. Made that error not appear in the status line.