'Sequence' object has no attribute 'structure'

[daysehuang20@…]

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

[pett]

Essentially a duplicate of #7851