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Opened 3 years ago
Closed 3 years ago
#7852 closed defect (duplicate)
'Sequence' object has no attribute 'structure'
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sequence | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5.dev202210150056 (2022-10-15 00:56:37 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.5.dev202210150056 (2022-10-15)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show AlphaFold
Populating font family aliases took 909 ms. Replace uses of missing font
family "Monospace" with one that exists to avoid this cost.
> alphafold predict
> RSHQVVSGQSLSQKAVNMNRYMMRHRPMYSNMYRTGRKYRGVMEPMSRMTMDFQGRYMDSQGRMVDPRYYDYGRCHDYDRYYGRSMFNYGPNMDGQRYGGWMDFPERYMDMSGYQMDMHGRWMDSQGRYCNPMGHSWSNRQGYYPGSNYGRNMFNPERYMDMSGYQMDMQGRWMDMGGRHVNPFSHSMYGRNMFNPSY
Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.
> alphafold predict
> RSHQVVSGQSLSQKAVNMNRYMMRHRPMYSNMYRTGRKYRGVMEPMSRMTMDFQGRYMDSQGRMVDPRYYDYGRCHDYDRYYGRSMFNYGPNMDGQRYGGWMDFPERYMDMSGYQMDMHGRWMDSQGRYCNPMGHSWSNRQGYYPGSNYGRNMFNPERYMDMSGYQMDMQGRWMDMGGRHVNPFSHSMYGRNMFNPSY
Running AlphaFold prediction
AlphaFold prediction finished
Results in /Users/daysehuang/Downloads/ChimeraX/AlphaFold/prediction_1
> open
> /Users/daysehuang/Downloads/ChimeraX/AlphaFold/prediction_1/best_model.pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
> save /Users/daysehuang/Desktop/EXAM.pdb relModel #1
> open /Users/daysehuang/Downloads/7xtm.pdb
7xtm.pdb title:
Crystal structure of the C-terminal domain of bombyx mori N-
acetylglucosaminyltransferase IV [more info...]
Chain information for 7xtm.pdb #2
---
Chain | Description
A B | α-1,3-mannosyl-glycoprotein 4-β-N- acetylglucosaminyltransferase A-like
isoform X2
Non-standard residues in 7xtm.pdb #2
---
EDO — 1,2-ethanediol (ethylene glycol)
MES — 2-(N-morpholino)-ethanesulfonic acid
> open /Users/daysehuang/Downloads/7xtn.pdb
7xtn.pdb title:
Crystal structure of the C-terminal domain of bombyx mori N-
acetylglucosaminyltransferase IV In complex with N-acetylglucosamine [more
info...]
Chain information for 7xtn.pdb #3
---
Chain | Description
A B | α-1,3-mannosyl-glycoprotein 4-β-N- acetylglucosaminyltransferase A-like
isoform X2
Non-standard residues in 7xtn.pdb #3
---
EDO — 1,2-ethanediol (ethylene glycol)
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
> open /Users/daysehuang/Downloads/5vcu.pdb
5vcu.pdb title:
Crystal structure of ras-related C3 botulinum toxin substrate 1 isoform X2
from naegleria fowleri In complex with GDP [more info...]
Chain information for 5vcu.pdb #4
---
Chain | Description
A B | nafoa.00927.A
Non-standard residues in 5vcu.pdb #4
---
GDP — guanosine-5'-diphosphate
MG — magnesium ion
> close session
> open /Users/daysehuang/Desktop/EXAM.pdb format pdb
Chain information for EXAM.pdb #1
---
Chain | Description
A | No description available
> open /Users/daysehuang/Downloads/5vcu.pdb
5vcu.pdb title:
Crystal structure of ras-related C3 botulinum toxin substrate 1 isoform X2
from naegleria fowleri In complex with GDP [more info...]
Chain information for 5vcu.pdb #2
---
Chain | Description
A B | nafoa.00927.A
Non-standard residues in 5vcu.pdb #2
---
GDP — guanosine-5'-diphosphate
MG — magnesium ion
> close session
> open /Users/daysehuang/Desktop/EXAM.pdb format pdb
Chain information for EXAM.pdb #1
---
Chain | Description
A | No description available
> color white
> undo
> set bgColor white
> set bgColor #ffffff00
> color bfactor pallete alphafold
> color byattribute bfactor pallete alphafold
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> colorbfactoralletealphafold
Unknown command: colorbfactoralletealphafold
> color bfactor pallete alphafold
> color byattribute bfactor pallete alphafold
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color bfactor alphafold
> color byattribute bfactor alphafold
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color bfactor
1669 atoms, 198 residues, atom bfactor range 23.6 to 74
> open /Users/daysehuang/Downloads/5vcu.pdb
5vcu.pdb title:
Crystal structure of ras-related C3 botulinum toxin substrate 1 isoform X2
from naegleria fowleri In complex with GDP [more info...]
Chain information for 5vcu.pdb #2
---
Chain | Description
A B | nafoa.00927.A
Non-standard residues in 5vcu.pdb #2
---
GDP — guanosine-5'-diphosphate
MG — magnesium ion
> ui tool show Matchmaker
> matchmaker #!2 to #1 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker EXAM.pdb, chain A (#1) with 5vcu.pdb, chain A (#2), sequence
alignment score = 13.9
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: EXAM.pdb #1/A, 5vcu.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 11 pruned atom pairs is 0.459 angstroms; (across all 25 pairs:
11.491)
> close session
> open /Users/daysehuang/Desktop/EXAM.pdb format pdb
Chain information for EXAM.pdb #1
---
Chain | Description
A | No description available
> color bfactor
1669 atoms, 198 residues, atom bfactor range 23.6 to 74
> save "/Users/daysehuang/Downloads/bfactor exam.pdb" relModel #1
> open /Users/daysehuang/Downloads/4yzn.pdb
4yzn.pdb title:
Humanized ROCO4 bound to compound 19 [more info...]
Chain information for 4yzn.pdb #2
---
Chain | Description | UniProt
A | RAS OF complex proteins AND C-terminal OF ROC 4 | ROCO4_DICDI
Non-standard residues in 4yzn.pdb #2
---
4K5 —
(4-{[4-(cyclopropylamino)-5-(trifluoromethyl)pyrimidin-2-yl]amino}-2-fluoro-5-methoxyphenyl)(morpholin-4-yl)methanone
> ui tool show Matchmaker
> matchmaker #1 to #2 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4yzn.pdb, chain A (#2) with EXAM.pdb, chain A (#1), sequence
alignment score = 16.1
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: EXAM.pdb #1/A, 4yzn.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 8 pruned atom pairs is 1.604 angstroms; (across all 56 pairs:
32.822)
> save /Users/daysehuang/Downloads/ex.pdb
> close session
> open "/Users/daysehuang/Downloads/5845 (1).txt"
Unrecognized file suffix '.txt'
> ui tool show AlphaFold
> alphafold predict
> >5845|UncharacterizedProt|Doryteuthispealeii|ChromatophoreRSHQVVSGQSLSQKAVNMNRYMMRHRPMYSNMYRTGRKYRGVMEPMSRMTMDFQGRYMDSQGRMVDPRYYDYGRCHDYDRYYGRSMFNYGPNMDGQRYGGWMDFPERYMDMSGYQMDMHGRWMDSQGRYCNPMGHSWSNRQGYYPGSNYGRNMFNPERYMDMSGYQMDMQGRWMDMGGRHVNPFSHSMYGRNMFNPSY
Missing or invalid "sequences" argument: Sequences argument
">5845|UncharacterizedProt|Doryteuthispealeii|ChromatophoreRSHQVVSGQSLSQKAVNMNRYMMRHRPMYSNMYRTGRKYRGVMEPMSRMTMDFQGRYMDSQGRMVDPRYYDYGRCHDYDRYYGRSMFNYGPNMDGQRYGGWMDFPERYMDMSGYQMDMHGRWMDSQGRYCNPMGHSWSNRQGYYPGSNYGRNMFNPERYMDMSGYQMDMQGRWMDMGGRHVNPFSHSMYGRNMFNPSY"
is not a chain specifier, alignment id, UniProt id, or sequence characters
> alphafold predict
> RSHQVVSGQSLSQKAVNMNRYMMRHRPMYSNMYRTGRKYRGVMEPMSRMTMDFQGRYMDSQGRMVDPRYYDYGRCHDYDRYYGRSMFNYGPNMDGQRYGGWMDFPERYMDMSGYQMDMHGRWMDSQGRYCNPMGHSWSNRQGYYPGSNYGRNMFNPERYMDMSGYQMDMQGRWMDMGGRHVNPFSHSMYGRNMFNPSY
Running AlphaFold prediction
AlphaFold prediction finished
Results in /Users/daysehuang/Downloads/ChimeraX/AlphaFold/prediction_2
> open
> /Users/daysehuang/Downloads/ChimeraX/AlphaFold/prediction_2/best_model.pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
> save "/Users/daysehuang/Downloads/exam 2.pdb" relModel #1
> open /Users/daysehuang/Desktop/EXAM.pdb
Chain information for EXAM.pdb #2
---
Chain | Description
A | No description available
> close session
> open "/Users/daysehuang/Downloads/bfactor exam.pdb" format pdb
Chain information for bfactor exam.pdb #1
---
Chain | Description
A | No description available
> close session
> open /Users/daysehuang/Desktop/EXAM.pdb format pdb
Chain information for EXAM.pdb #1
---
Chain | Description
A | No description available
> set bgColor white
> color bfactor
1669 atoms, 198 residues, atom bfactor range 23.6 to 74
> ui tool show "Model Loops"
> ui tool show "Blast Protein"
> ui tool show AlphaFold
> alphafold predict
> RSHQVVSGQSLSQKAVNMNRYMMRHRPMYSNMYRTGRKYRGVMEPMSRMTMDFQGRYMDSQGRMVDPRYYDYGRCHDYDRYYGRSMFNYGPNMDGQRYGGWMDFPERYMDMSGYQMDMHGRWMDSQGRYCNPMGHSWSNRQGYYPGSNYGRNMFNPERYMDMSGYQMDMQGRWMDMGGRHVNPFSHSMYGRNMFNPSY
Running AlphaFold prediction
AlphaFold prediction finished
Results in /Users/daysehuang/Downloads/ChimeraX/AlphaFold/prediction_3
> open
> /Users/daysehuang/Downloads/ChimeraX/AlphaFold/prediction_3/best_model.pdb
Chain information for best_model.pdb #2
---
Chain | Description
A | No description available
> close session
> open
> /Users/daysehuang/Downloads/ChimeraX/AlphaFold/prediction_3/best_model.pdb
> format pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
> close session
> open /Users/daysehuang/Desktop/EXAM.pdb format pdb
Chain information for EXAM.pdb #1
---
Chain | Description
A | No description available
> ui tool show Rotamers
> ui tool show "Modeller Comparative"
> open "/Users/daysehuang/Downloads/4yzn (1).pdb"
4yzn (1).pdb title:
Humanized ROCO4 bound to compound 19 [more info...]
Chain information for 4yzn (1).pdb #2
---
Chain | Description | UniProt
A | RAS OF complex proteins AND C-terminal OF ROC 4 | ROCO4_DICDI
Non-standard residues in 4yzn (1).pdb #2
---
4K5 —
(4-{[4-(cyclopropylamino)-5-(trifluoromethyl)pyrimidin-2-yl]amino}-2-fluoro-5-methoxyphenyl)(morpholin-4-yl)methanone
> ui tool show "Modeller Comparative"
> open /Users/daysehuang/Downloads/rcsb_pdb_4YZN.fasta
Summary of feedback from opening
/Users/daysehuang/Downloads/rcsb_pdb_4YZN.fasta
---
notes | Alignment identifier is rcsb_pdb_4YZN.fasta
Associated 4yzn (1).pdb chain A to 4YZN_1|Chain A|Probable serine/threonine-
protein kinase roco4|Dictyostelium discoideum (44689) with 0 mismatches
Opened 1 sequences from rcsb_pdb_4YZN.fasta
> select #2/A:1019-1244
1764 atoms, 1803 bonds, 1 pseudobond, 221 residues, 2 models selected
> select #2/A:1289-1292
32 atoms, 31 bonds, 4 residues, 1 model selected
> select #2/A:1019-1292
2161 atoms, 2211 bonds, 1 pseudobond, 269 residues, 2 models selected
> ui tool show "Modeller Comparative"
> modeller comparative rcsb_pdb_4YZN.fasta:1 numModels 5 fast false multichain
> true hetPreserve false hydrogens false waterPreserve false
Webservices job id: V865GU9CQD8JVC6J
> ui tool show Matchmaker
Modeller job (ID V865GU9CQD8JVC6J) finished
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4yzn (1).pdb, chain A (#2) with 4YZN_1_Chain_A_P, chain A (#),
sequence alignment score = 1437.4
RMSD between 268 pruned atom pairs is 0.205 angstroms; (across all 269 pairs:
0.241)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4yzn (1).pdb, chain A (#2) with 4YZN_1_Chain_A_P, chain A (#),
sequence alignment score = 1431.4
RMSD between 268 pruned atom pairs is 0.211 angstroms; (across all 269 pairs:
0.411)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4yzn (1).pdb, chain A (#2) with 4YZN_1_Chain_A_P, chain A (#),
sequence alignment score = 1431.4
RMSD between 268 pruned atom pairs is 0.266 angstroms; (across all 269 pairs:
0.315)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4yzn (1).pdb, chain A (#2) with 4YZN_1_Chain_A_P, chain A (#),
sequence alignment score = 1446.4
RMSD between 269 pruned atom pairs is 0.201 angstroms; (across all 269 pairs:
0.201)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4yzn (1).pdb, chain A (#2) with 4YZN_1_Chain_A_P, chain A (#),
sequence alignment score = 1446.4
RMSD between 268 pruned atom pairs is 0.231 angstroms; (across all 269 pairs:
0.305)
Associated 4YZN_1_Chain_A_P chain A to 4YZN_1|Chain A|Probable
serine/threonine-protein kinase roco4|Dictyostelium discoideum (44689) with 0
mismatches
[Repeated 4 time(s)] Chain information for 4YZN_1_Chain_A_P
---
Chain | Description
3.1/A 3.2/A 3.3/A 3.4/A 3.5/A | No description available
> matchmaker #1 to #2 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4yzn (1).pdb, chain A (#2) with EXAM.pdb, chain A (#1), sequence
alignment score = 16.1
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: EXAM.pdb #1/A, 4yzn (1).pdb
#2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 8 pruned atom pairs is 1.604 angstroms; (across all 56 pairs:
32.822)
> close session
> open /Users/daysehuang/Desktop/EXAM.pdb format pdb
Chain information for EXAM.pdb #1
---
Chain | Description
A | No description available
> open /Users/daysehuang/Downloads/2kdl.pdb
2kdl.pdb title:
NMR structures of GA95 and GB95, two designed proteins with 95% sequence
identity but different folds and functions [more info...]
Chain information for 2kdl.pdb
---
Chain | Description
2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A 2.10/A 2.11/A 2.12/A
2.13/A 2.14/A 2.15/A 2.16/A 2.17/A 2.18/A 2.19/A 2.20/A | designed protein
> close session
> open /Users/daysehuang/Desktop/EXAM.pdb format pdb
Chain information for EXAM.pdb #1
---
Chain | Description
A | No description available
> open "/Users/daysehuang/Downloads/4yzn (1).pdb"
4yzn (1).pdb title:
Humanized ROCO4 bound to compound 19 [more info...]
Chain information for 4yzn (1).pdb #2
---
Chain | Description | UniProt
A | RAS OF complex proteins AND C-terminal OF ROC 4 | ROCO4_DICDI
Non-standard residues in 4yzn (1).pdb #2
---
4K5 —
(4-{[4-(cyclopropylamino)-5-(trifluoromethyl)pyrimidin-2-yl]amino}-2-fluoro-5-methoxyphenyl)(morpholin-4-yl)methanone
Associated 4yzn (1).pdb chain A to 4YZN_1|Chain A|Probable serine/threonine-
protein kinase roco4|Dictyostelium discoideum (44689) with 0 mismatches
> ui tool show Matchmaker
> matchmaker #1 to #2 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4yzn (1).pdb, chain A (#2) with EXAM.pdb, chain A (#1), sequence
alignment score = 16.1
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: EXAM.pdb #1/A, 4yzn (1).pdb
#2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 8 pruned atom pairs is 1.604 angstroms; (across all 56 pairs:
32.822)
> select #1/A:13
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:1241
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:1241-1246 #1/A:13-18
98 atoms, 97 bonds, 12 residues, 2 models selected
MatchMaker Alignment [ID: 1] region 4yzn (1).pdb, chain A..EXAM.pdb, chain A
[236-241] RMSD: 1.641
> color bfactor
4076 atoms, 682 residues, atom bfactor range 6.83 to 95.5
Traceback (most recent call last):
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/D742CF37-B63D-420F-BC64-8D68F51A5C80/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/D742CF37-B63D-420F-BC64-8D68F51A5C80/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq_view/seq_canvas.py", line 1864, in update_swatches
assoc_structures = set([chain.structure for chain in aseq.match_maps.keys()])
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/D742CF37-B63D-420F-BC64-8D68F51A5C80/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq_view/seq_canvas.py", line 1864, in <listcomp>
assoc_structures = set([chain.structure for chain in aseq.match_maps.keys()])
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes done":
AttributeError: 'Sequence' object has no attribute 'structure'
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/D742CF37-B63D-420F-BC64-8D68F51A5C80/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq_view/seq_canvas.py", line 1864, in
assoc_structures = set([chain.structure for chain in aseq.match_maps.keys()])
See log for complete Python traceback.
> undo
Traceback (most recent call last):
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/D742CF37-B63D-420F-BC64-8D68F51A5C80/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/D742CF37-B63D-420F-BC64-8D68F51A5C80/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq_view/seq_canvas.py", line 1864, in update_swatches
assoc_structures = set([chain.structure for chain in aseq.match_maps.keys()])
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/D742CF37-B63D-420F-BC64-8D68F51A5C80/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq_view/seq_canvas.py", line 1864, in <listcomp>
assoc_structures = set([chain.structure for chain in aseq.match_maps.keys()])
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes done":
AttributeError: 'Sequence' object has no attribute 'structure'
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/D742CF37-B63D-420F-BC64-8D68F51A5C80/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq_view/seq_canvas.py", line 1864, in
assoc_structures = set([chain.structure for chain in aseq.match_maps.keys()])
See log for complete Python traceback.
Traceback (most recent call last):
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/D742CF37-B63D-420F-BC64-8D68F51A5C80/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/D742CF37-B63D-420F-BC64-8D68F51A5C80/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq_view/seq_canvas.py", line 1864, in update_swatches
assoc_structures = set([chain.structure for chain in aseq.match_maps.keys()])
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/D742CF37-B63D-420F-BC64-8D68F51A5C80/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq_view/seq_canvas.py", line 1864, in <listcomp>
assoc_structures = set([chain.structure for chain in aseq.match_maps.keys()])
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes done":
AttributeError: 'Sequence' object has no attribute 'structure'
File
"/private/var/folders/5h/mtfx85j94sz_9m0yb9_x38hc0000gn/T/AppTranslocation/D742CF37-B63D-420F-BC64-8D68F51A5C80/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq_view/seq_canvas.py", line 1864, in
assoc_structures = set([chain.structure for chain in aseq.match_maps.keys()])
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-16.5.9
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,4
Processor Name: Quad-Core Intel Core i5
Processor Speed: 1.4 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 1731.100.130.0.0 (iBridge: 19.16.14243.0.0,0)
Software:
System Software Overview:
System Version: macOS 11.6.5 (20G527)
Kernel Version: Darwin 20.6.0
Time since boot: 3 days 22:02
Graphics/Displays:
Intel Iris Plus Graphics 645:
Chipset Model: Intel Iris Plus Graphics 645
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea6
Revision ID: 0x0001
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.0.8
Babel: 2.10.3
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.43.2
ChimeraX-AtomicLibrary: 8.0.2
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5.dev202210150056
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.2
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.3
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.1.1
filelock: 3.7.1
fonttools: 4.37.4
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.0.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 4.11.1
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.3
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
prompt-toolkit: 3.0.31
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.4
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.2.1
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.5.1
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.12
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.9.0
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Sequence |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → 'Sequence' object has no attribute 'structure' |
comment:2 by , 3 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Essentially a duplicate of #7851