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Opened 21 months ago
Last modified 21 months ago
#14547 feedback defect
Plain sequence in structure associations
| 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-14.2.1-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
> camera ortho
> cofr centerOfView
> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true
Saved volume settings
> mousemode rightMode clip
> mousemode alt rightMode "contour level"
> mousemode alt leftMode "move picked models"
> alias cofron cofr centerofview showpivot true
> alias cofroff cofr centerofview showpivot false
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias cootmode surface cap false; surface style solid; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; size ballscale 0.1; size
> stickradius 0.07; transparency 70; cofr centerofview; clip near -10 far 10
> position cofr; color ##~num_residues cornflower blue
> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; size ballscale 0.1; size
> stickradius 0.07; cofr centerofview; clip near -10 far 10 position cofr;
> color ##~num_residues #3d60ffff; transparency 50
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000;
> marker #10000 position cofr; sel ~sel; surface zone ##~num_residues
> nearAtoms sel distance 15; close #10000
> alias map_unsphere surface unzone ##~num_residues
> alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5;
> lighting soft
> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000
> alias showmaps surface unzone ##~num_residues
> alias caps_off surface cap false
> alias caps_on surface cap true
> alias selbetween ks ri
> buttonpanel Shortcuts rows 3 columns 4
> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add Model_Panel command "tool show Models"
> buttonpanel Shortcuts add Log command "tool show Log"
> buttonpanel Shortcuts add default_disp command default_mol_display
> buttonpanel Shortcuts add map_sphere command map_sphere_15
> buttonpanel Shortcuts add map_unsphere command map_unsphere
> buttonpanel Shortcuts add cofron command cofron
> buttonpanel Shortcuts add cofroff command cofroff
> buttonpanel Shortcuts add cootmode command cootmode
> buttonpanel Shortcuts add mark_cofr command "marker #10000 position cofr"
> buttonpanel Shortcuts add hidemaps command hidemaps
> buttonpanel Shortcuts add showmaps command showmaps
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/adminjh/Documents/ChimeraX/DCCP+R/Class-
> II/Alphafold/Models&maps/YjiL-AF-W8T7F9-F1-model_v4.pdb
YjiL-AF-W8T7F9-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for yjil (W8T7F9) [more info...]
Chain information for YjiL-AF-W8T7F9-F1-model_v4.pdb #1
---
Chain | Description | UniProt
A | YJIL | W8T7F9_PEPAC 1-261
> set bgColor white
> graphics silhouettes true
> lighting soft
> open /Users/adminjh/Documents/ChimeraX/DCCP+R/Class-
> II/Alphafold/Models&maps/AMPPNP-GH_CHXR.pdb
Summary of feedback from opening
/Users/adminjh/Documents/ChimeraX/DCCP+R/Class-
II/Alphafold/Models&maps/AMPPNP-GH_CHXR.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Date 2017-06-14 Time 13:13:50 CEST +0200 (1497438830.19 s)
Ignored bad PDB record found on line 2
REMARK PHENIX refinement
Ignored bad PDB record found on line 4
REMARK ****************** INPUT FILES AND LABELS
******************************
Ignored bad PDB record found on line 5
REMARK Reflections:
Ignored bad PDB record found on line 6
REMARK file name : /Volumes/Data/xtal/data/CHX-
R_complex/bessy_030215/108_1_1/108_1_1_F.mtz
41 messages similar to the above omitted
Cannot find LINK/SSBOND residue SO4 (423 )
Cannot find LINK/SSBOND residue SO4 (424 )
Cannot find LINK/SSBOND residue SO4 (425 )
Cannot find LINK/SSBOND residue SO4 (426 )
Cannot find LINK/SSBOND residue SO4 (246 )
Chain information for AMPPNP-GH_CHXR.pdb #2
---
Chain | Description
G H | No description available
> mmaker #1 to #2
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 AMPPNP-GH_CHXR.pdb, chain H (#2) with YjiL-
AF-W8T7F9-F1-model_v4.pdb, chain A (#1), sequence alignment score = 598.3
RMSD between 169 pruned atom pairs is 0.883 angstroms; (across all 242 pairs:
2.969)
> open /Users/adminjh/Documents/ChimeraX/DCCP+R/Class-
> II/Alphafold/Models&maps/YjiL-AF-W8T7F9-F1-model_v4.pdb
YjiL-AF-W8T7F9-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for yjil (W8T7F9) [more info...]
Chain information for YjiL-AF-W8T7F9-F1-model_v4.pdb #3
---
Chain | Description | UniProt
A | YJIL | W8T7F9_PEPAC 1-261
> mmaker #3 to #2/G
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 AMPPNP-GH_CHXR.pdb, chain G (#2) with YjiL-
AF-W8T7F9-F1-model_v4.pdb, chain A (#3), sequence alignment score = 597.7
RMSD between 173 pruned atom pairs is 0.952 angstroms; (across all 242 pairs:
3.036)
> show #1:Cys
> show #3:Cys
> color byattribute seq_conservation palette cyanmaroon range -1.4,1.4
No known/registered numeric attribute seq_conservation
> color byattribute seq_conservation protein palette cyanmaroon range -1.4,1.4
> noValueColor yellow
No known/registered numeric attribute seq_conservation
> color byattribute seq_conservation protein palette cyanmaroon range -1.4,1.4
> noValueColor yellow
No known/registered numeric attribute seq_conservation
> show ::seq_conservation>1.8
> label ::seq_conservation>1.8
> ui tool show "Show Sequence Viewer"
> sequence chain #2/G #2/H
Alignment identifier is 1
Window position QRect(1431,1349 575x226) outside any known screen, using
primary screen
QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x6000037bc930, name="DELL U3223QE") screenTo: QScreen(0x6000037bc930,
name="DELL U3223QE") wdgScreen: QScreen(0x6000037bc930, name="DELL U3223QE")
orgWdgScreen QScreen(0x0)
[Repeated 182 time(s)]
> color byattribute seq_conservation
8052 atoms, 1406 residues, atom seq_conservation range 100 to 100
> color byattribute seq_conservation palette blue:red:yellow
8052 atoms, 1406 residues, atom seq_conservation range 100 to 100
> color byattribute seq_conservation palette cyanmaroon
8052 atoms, 1406 residues, atom seq_conservation range 100 to 100
> color byattribute seq_conservation palette cyanmaroon range -1.4,1.4
8052 atoms, 1406 residues, atom seq_conservation range 100 to 100
> color byattribute seq_conservation protein palette cyanmaroon range -1.4,1.4
7564 atoms, 1008 residues, atom seq_conservation range 100 to 100
> color byattribute seq_conservation protein palette cyanmaroon range -1.4,1.4
> noValueColor yellow
7564 atoms, 1008 residues, atom seq_conservation range 100 to 100
> hide protein
> show ::seq_conservation>1.8
> label ::seq_conservation>1.8
> label height 1.3
> hide label
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> ~label
> close session
> open /Users/adminjh/Documents/ChimeraX/DCCP+R/Class-
> II/Alphafold/Models&maps/YjiL-AF-W8T7F9-F1-model_v4.pdb
YjiL-AF-W8T7F9-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for yjil (W8T7F9) [more info...]
Chain information for YjiL-AF-W8T7F9-F1-model_v4.pdb #1
---
Chain | Description | UniProt
A | YJIL | W8T7F9_PEPAC 1-261
> open /Users/adminjh/Documents/ChimeraX/DCCP+R/Class-
> II/Alphafold/Models&maps/AMPPNP-G_CHXR.pdb
Chain information for AMPPNP-G_CHXR.pdb #2
---
Chain | Description
G | No description available
> mmaker #1 to #2
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 AMPPNP-G_CHXR.pdb, chain G (#2) with YjiL-
AF-W8T7F9-F1-model_v4.pdb, chain A (#1), sequence alignment score = 597.7
RMSD between 173 pruned atom pairs is 0.952 angstroms; (across all 242 pairs:
3.036)
> color byattribute seq_conservation protein palette cyanmaroon range -1.4,1.4
All 'seq_conservation' values are None
> color byattribute seq_conservation protein palette cyanmaroon range -1.4,1.4
> noValueColor yellow
All 'seq_conservation' values are None
> color byattribute seq_conservation protein palette cyanmaroon
All 'seq_conservation' values are None
> color byattribute seq_conservation palette blue:red:yellow
All 'seq_conservation' values are None
> open /Users/adminjh/Documents/ChimeraX/DCCP+R/Class-
> II/Alphafold/Models&maps/clustalo-I20240206-144227-0446-95664545-p1m-out.txt
Unrecognized file suffix '.txt'
> open /Users/adminjh/Documents/ChimeraX/DCCP+R/Class-
> II/Alphafold/Models&maps/clustalo-I20240206-144227-0446-95664545-p1m-out.aln
Cannot open files: Syntax error in ALN file
'clustalo-I20240206-144227-0446-95664545-p1m-out.aln': First non-blank line
does not start with 'CLUSTAL'
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> ui tool show "Show Sequence Viewer"
> sequence chain #2/G
Alignment identifier is 2/G
> ui tool show "Modeller Comparative"
> modeller comparative 1/A:1 2/G:1 numModels 5 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false
No Modeller license key provided. Get a license key by registering at the
Modeller web site.
> modeller comparative 1/A:1 2/G:1 numModels 5 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false
Webservices job id: NGYPXVY0R2VWTFEB
> ui tool show "Modeller Comparative"
> modeller comparative 1/A:1 2/G:1 numModels 5 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false
Webservices job id: NUOIVVQ2HA7UF8YD
Modeller job (ID NGYPXVY0R2VWTFEB) 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 YjiL-AF-W8T7F9-F1-model_v4.pdb, chain A (#1) with target, chain A
(#), sequence alignment score = 1289.6
RMSD between 261 pruned atom pairs is 0.181 angstroms; (across all 261 pairs:
0.181)
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 YjiL-AF-W8T7F9-F1-model_v4.pdb, chain A (#1) with target, chain A
(#), sequence alignment score = 1303.4
RMSD between 261 pruned atom pairs is 0.149 angstroms; (across all 261 pairs:
0.149)
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 YjiL-AF-W8T7F9-F1-model_v4.pdb, chain A (#1) with target, chain A
(#), sequence alignment score = 1289.6
RMSD between 261 pruned atom pairs is 0.152 angstroms; (across all 261 pairs:
0.152)
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 YjiL-AF-W8T7F9-F1-model_v4.pdb, chain A (#1) with target, chain A
(#), sequence alignment score = 1292.6
RMSD between 261 pruned atom pairs is 0.195 angstroms; (across all 261 pairs:
0.195)
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 YjiL-AF-W8T7F9-F1-model_v4.pdb, chain A (#1) with target, chain A
(#), sequence alignment score = 1299.8
RMSD between 261 pruned atom pairs is 0.169 angstroms; (across all 261 pairs:
0.169)
Associated target chain A to chain A with 0 mismatches
[Repeated 4 time(s)]Associated target chain A to chain G with 138 mismatches
and/or gaps
[Repeated 4 time(s)] Chain information for target
---
Chain | Description
3.1/A 3.2/A 3.3/A 3.4/A 3.5/A | No description available
> color byattribute seq_conservation palette blue:red:yellow
13732 atoms, 2046 residues, atom seq_conservation range 100 to 100
Modeller job (ID NUOIVVQ2HA7UF8YD) 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 YjiL-AF-W8T7F9-F1-model_v4.pdb, chain A (#1) with target, chain A
(#), sequence alignment score = 1289.6
RMSD between 261 pruned atom pairs is 0.181 angstroms; (across all 261 pairs:
0.181)
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 YjiL-AF-W8T7F9-F1-model_v4.pdb, chain A (#1) with target, chain A
(#), sequence alignment score = 1303.4
RMSD between 261 pruned atom pairs is 0.149 angstroms; (across all 261 pairs:
0.149)
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 YjiL-AF-W8T7F9-F1-model_v4.pdb, chain A (#1) with target, chain A
(#), sequence alignment score = 1289.6
RMSD between 261 pruned atom pairs is 0.152 angstroms; (across all 261 pairs:
0.152)
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 YjiL-AF-W8T7F9-F1-model_v4.pdb, chain A (#1) with target, chain A
(#), sequence alignment score = 1292.6
RMSD between 261 pruned atom pairs is 0.195 angstroms; (across all 261 pairs:
0.195)
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 YjiL-AF-W8T7F9-F1-model_v4.pdb, chain A (#1) with target, chain A
(#), sequence alignment score = 1299.8
RMSD between 261 pruned atom pairs is 0.169 angstroms; (across all 261 pairs:
0.169)
Associated target chain A to chain A with 0 mismatches
[Repeated 4 time(s)]Associated target chain A to chain G with 138 mismatches
and/or gaps
[Repeated 4 time(s)] Chain information for target
---
Chain | Description
4.1/A 4.2/A 4.3/A 4.4/A 4.5/A | No description available
> close #3
> color byattribute seq_conservation
13732 atoms, 2046 residues, atom seq_conservation range 100 to 100
> ui tool show "Show Sequence Viewer"
> sequence chain #4.1/A
Alignment identifier is 4.1/A
> ui tool show "Show Sequence Viewer"
> close #4
> mmaker #1 to #2
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 AMPPNP-G_CHXR.pdb, chain G (#2) with YjiL-
AF-W8T7F9-F1-model_v4.pdb, chain A (#1), sequence alignment score = 597.7
RMSD between 173 pruned atom pairs is 0.952 angstroms; (across all 242 pairs:
3.036)
> select sequence #1
Nothing selected
>
Unknown command: sequence #1
>
Incomplete command: sequence
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> view #1 clip false
> sequence align #1/A,#2/G program clustalOmega
Alignment identifier is 1
Associated YjiL-AF-W8T7F9-F1-model_v4.pdb chain A to chain A with 0 mismatches
Associated AMPPNP-G_CHXR.pdb chain G to chain G with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Webservices job id: 2A6HD1WHH9LMNT2Q
> color byattribute seq_conservation protein palette cyanmaroon range -1.4,1.4
> noValueColor yellow
3782 atoms, 504 residues, atom seq_conservation range -0.845 to 1.18
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/seq_canvas.py", line 1881, in update_swatches
assoc_structures = set([chain.structure for chain in aseq.match_maps.keys()])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/seq_canvas.py", line 1881, 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
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/seq_canvas.py", line 1881, 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
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/seq_canvas.py", line 1881, in update_swatches
assoc_structures = set([chain.structure for chain in aseq.match_maps.keys()])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/seq_canvas.py", line 1881, 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
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/seq_canvas.py", line 1881, in
assoc_structures = set([chain.structure for chain in aseq.match_maps.keys()])
^^^^^^^^^^^^^^^
See log for complete Python traceback.
> color byattribute seq_conservation protein palette cyanmaroon range -1.4,1.4
3782 atoms, 504 residues, atom seq_conservation range -0.845 to 1.18
> color byattribute seq_conservation palette cyanmaroon range -1.4,1.4
4062 atoms, 741 residues, atom seq_conservation range -0.845 to 1.18
> color byattribute seq_conservation palette darkcyan:gray:yellow
4062 atoms, 741 residues, atom seq_conservation range -0.845 to 1.18
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/seq_canvas.py", line 1881, in update_swatches
assoc_structures = set([chain.structure for chain in aseq.match_maps.keys()])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/seq_canvas.py", line 1881, 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
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/seq_canvas.py", line 1881, 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
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/seq_canvas.py", line 1881, in update_swatches
assoc_structures = set([chain.structure for chain in aseq.match_maps.keys()])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/seq_canvas.py", line 1881, 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
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/seq_canvas.py", line 1881, 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
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/seq_canvas.py", line 1881, in update_swatches
assoc_structures = set([chain.structure for chain in aseq.match_maps.keys()])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/seq_canvas.py", line 1881, 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
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/seq_canvas.py", line 1881, 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
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/seq_canvas.py", line 1881, in update_swatches
assoc_structures = set([chain.structure for chain in aseq.match_maps.keys()])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/seq_canvas.py", line 1881, 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
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/seq_canvas.py", line 1881, in
assoc_structures = set([chain.structure for chain in aseq.match_maps.keys()])
^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.2
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: Mac14,7
Model Number: Z16R000QGD/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 10151.61.4
OS Loader Version: 10151.61.4
Software:
System Software Overview:
System Version: macOS 14.2.1 (23C71)
Kernel Version: Darwin 23.2.0
Time since boot: 33 days, 7 hours, 54 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U3223QE:
Resolution: 6016 x 3384
UI Looks like: 3008 x 1692 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-Cytoscape: 0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
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-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-OpenCommands: 1.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-PICKLUSTER: 0.2
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-QScore: 1.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
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: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
Send2Trash: 1.8.2
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 21 months ago
| Component: | Unassigned → Sequence |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Plain sequence in structure associations |
comment:2 by , 21 months ago
| Status: | accepted → feedback |
|---|
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Hi Jae-Hun,
--Eric