Plain sequence in structure associations

[jae-hun.jeoung@…]

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

[pett]

Hi Jae-Hun,

Thanks for reporting this problem. I cannot reproduce it myself using some simple test files. Perhaps if you provided copies of your YjiL-AF-W8T7F9-F1-model_v4.pdb and YjiL-AF-W8T7F9-F1-model_v4.pdb files I might have better luck. I can promise to keep the files confidential if that is an issue.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab