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Opened 14 months ago
Closed 14 months ago
#15815 closed defect (fixed)
'AtomicStructure' object has no attribute '_alt_loc_changes_handler'
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.5-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/lichinghsiao/Desktop/Abeta_chimera_graphs/J84/phenix96/model_and_map/model_and_map_1.cxs
Opened postprocess_masked.mrc as #1, grid size 300,300,300, pixel 0.83, shown
at level 0.00448, step 1, values float32
Log from Thu Jun 20 18:01:49 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/lichinghsiao/Desktop/Abeta_chimera_graphs/J84/phenix96/model_and_map/model_and_map_1.cxs
Opened postprocess_masked.mrc as #1, grid size 300,300,300, pixel 0.83, shown
at level 0.00448, step 1, values float32
Log from Thu Jun 20 16:37:24 2024 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/lichinghsiao/Desktop/relionD723_new/PostProcess/job091/postprocess_masked.mrc
Opened postprocess_masked.mrc as #1, grid size 300,300,300, pixel 0.83, shown
at level 0.000538, step 2, values float32
> volume #1 step 1
> open
> /Users/lichinghsiao/Desktop/phenix_D723_trimer_J84/RealSpaceRefine_96/edit_all拷貝_real_space_refined_096.pdb
Chain information for edit_all拷貝_real_space_refined_096.pdb #2
---
Chain | Description
A B C D E | No description available
BA BB BC BD BE | No description available
CA CB CC CD CE | No description available
45 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> show cartoons
> hide atoms
> volume #1 level 0.0047
> turn x 180 models #1-2
> turn z 5 models #1-2
[Repeated 6 time(s)]
> volume #1 level 0.00448
> ui tool show "Hide Dust"
> surface dust #1 size 4.98
> surface undust #1
> surface dust #1 size 4.98
> surface dust #1 size 1
> surface dust #1 size 1.9
> surface dust #1 size 1.98
> surface undust #1
> surface dust #1 size 1.98
> surface dust #1 size 1.9
> surface dust #1 size 11.95
> hide #!1 models
> style stick
Changed 3855 atom styles
> show atoms
Drag select of 220 atoms, 63 residues, 191 bonds
> select up
479 atoms, 476 bonds, 70 residues, 1 model selected
> select up
518 atoms, 521 bonds, 70 residues, 1 model selected
> select up
1094 atoms, 1110 bonds, 149 residues, 1 model selected
> select up
1255 atoms, 1275 bonds, 170 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark salmon
Drag select of 110 atoms, 42 residues, 81 bonds
> select up
319 atoms, 311 bonds, 48 residues, 1 model selected
> select up
358 atoms, 358 bonds, 48 residues, 1 model selected
> select up
663 atoms, 668 bonds, 91 residues, 1 model selected
> select up
1595 atoms, 1625 bonds, 210 residues, 1 model selected
> select up
3855 atoms, 3900 bonds, 530 residues, 1 model selected
> select down
1595 atoms, 1625 bonds, 210 residues, 1 model selected
> color sel dark sea green
Drag select of 125 atoms, 38 residues, 110 bonds
> select up
390 atoms, 395 bonds, 48 residues, 1 model selected
> select up
995 atoms, 1000 bonds, 140 residues, 1 model selected
> select up
3855 atoms, 3900 bonds, 530 residues, 1 model selected
> select down
995 atoms, 1000 bonds, 140 residues, 1 model selected
> color sel cornflower blue
Drag select of 10 atoms
> color sel yellow
> select clear
> show #!1 models
> ui tool show "Surface Color"
> ui tool show "Color Zone"
> color zone #1 near #2 distance 4.98
> color zone #1 near #2 distance 5.08
> color zone #1 near #2 distance 5.18
> color zone #1 near #2 distance 5.28
> color zone #1 near #2 distance 5.38
> color zone #1 near #2 distance 5.48
> color zone #1 near #2 distance 5.58
> color zone #1 near #2 distance 5.68
> color zone #1 near #2 distance 5.78
> color zone #1 near #2 distance 5.88
> color zone #1 near #2 distance 5.98
> color zone #1 near #2 distance 6.08
> color zone #1 near #2 distance 6.18
> color zone #1 near #2 distance 6.28
> color zone #1 near #2 distance 6.38
> color zone #1 near #2 distance 6.48
> color zone #1 near #2 distance 6.1
> color zone #1 near #2 distance 18.09
> color zone #1 near #2 distance 18.36
> color zone #1 near #2 distance 39.81
> color single #1
> color zone #1 near #2 distance 21
> color single #1
> color zone #1 near #2 distance 11.58
> view orient
> ui tool show "Side View"
> select clear
> view orient
[Repeated 2 time(s)]
> ui mousemode right clip
> hide #!2 models
> show #!2 models
> hide #!1 models
> view orient
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> select /CB:5
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:18
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /CA:4
11 atoms, 11 bonds, 1 residue, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select add /B:17
19 atoms, 18 bonds, 2 residues, 1 model selected
> select up
21 atoms, 19 bonds, 3 residues, 1 model selected
> select up
28 atoms, 26 bonds, 3 residues, 1 model selected
> select up
147 atoms, 150 bonds, 16 residues, 1 model selected
> select up
769 atoms, 780 bonds, 104 residues, 1 model selected
> select clear
> select add /?:7@O
1 atom, 1 residue, 1 model selected
> select add /?:8@O
2 atoms, 2 residues, 1 model selected
> select add /CB:37
6 atoms, 3 bonds, 3 residues, 1 model selected
> select add /B:18
13 atoms, 9 bonds, 4 residues, 1 model selected
> select add /BB:25
17 atoms, 12 bonds, 5 residues, 1 model selected
> select up
127 atoms, 125 bonds, 19 residues, 1 model selected
> select up
771 atoms, 780 bonds, 106 residues, 1 model selected
> select up
779 atoms, 780 bonds, 114 residues, 1 model selected
> select up
3855 atoms, 3900 bonds, 530 residues, 1 model selected
> select down
779 atoms, 780 bonds, 114 residues, 1 model selected
> select down
771 atoms, 780 bonds, 106 residues, 1 model selected
> select ~sel & ##selected
3084 atoms, 3120 bonds, 1 pseudobond, 424 residues, 2 models selected
> hide sel atoms
> undo
> hide sel atoms
[Repeated 2 time(s)]
> show sel atoms
> select clear
> select add /?:7@O
1 atom, 1 residue, 1 model selected
> select add /?:8@O
2 atoms, 2 residues, 1 model selected
> select add /B:18
9 atoms, 6 bonds, 3 residues, 1 model selected
> select add /CB:41
17 atoms, 13 bonds, 4 residues, 1 model selected
> select add /BB:25
21 atoms, 16 bonds, 5 residues, 1 model selected
> select up
114 atoms, 112 bonds, 16 residues, 1 model selected
> select up
771 atoms, 780 bonds, 106 residues, 1 model selected
> select up
779 atoms, 780 bonds, 114 residues, 1 model selected
> select down
771 atoms, 780 bonds, 106 residues, 1 model selected
> select ~sel & ##selected
3084 atoms, 3120 bonds, 1 pseudobond, 424 residues, 2 models selected
> hide sel atoms
[Repeated 1 time(s)]
> show sel atoms
> hide sel atoms
> hide sel cartoons
> show #!1 models
> volume splitbyzone #1
Opened postprocess_masked.mrc 0 as #3.1, grid size 300,300,300, pixel 0.83,
shown at level 0.00448, step 1, values float32
Opened postprocess_masked.mrc 1 as #3.2, grid size 300,300,300, pixel 0.83,
shown at level 0.00448, step 1, values float32
Opened postprocess_masked.mrc 2 as #3.3, grid size 300,300,300, pixel 0.83,
shown at level 0.00448, step 1, values float32
Opened postprocess_masked.mrc 3 as #3.4, grid size 300,300,300, pixel 0.83,
shown at level 0.00448, step 1, values float32
Opened postprocess_masked.mrc 4 as #3.5, grid size 300,300,300, pixel 0.83,
shown at level 0.00448, step 1, values float32
> hide #!3 models
> show #!3 models
> close #3#3.1-5
Drag select of 439 atoms, 104 residues, 1 pseudobonds, 364 bonds
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume splitbyzone #1
Opened postprocess_masked.mrc 0 as #3.1, grid size 300,300,300, pixel 0.83,
shown at level 0.00448, step 1, values float32
Opened postprocess_masked.mrc 1 as #3.2, grid size 300,300,300, pixel 0.83,
shown at level 0.00448, step 1, values float32
Opened postprocess_masked.mrc 2 as #3.3, grid size 300,300,300, pixel 0.83,
shown at level 0.00448, step 1, values float32
Opened postprocess_masked.mrc 3 as #3.4, grid size 300,300,300, pixel 0.83,
shown at level 0.00448, step 1, values float32
Opened postprocess_masked.mrc 4 as #3.5, grid size 300,300,300, pixel 0.83,
shown at level 0.00448, step 1, values float32
> select clear
> hide #!3.1 models
> hide #!3 models
> hide #!3.2 models
> hide #!3.3 models
> hide #!3.4 models
> hide #!3.5 models
> close #3#3.1-5
> show #!1 models
> hide #!1 models
> view orient
> ui tool show "Surface Zone"
> surface zone #1 nearAtoms #2 distance 4.98
[Repeated 1 time(s)]
> show #!1 models
> surface zone #1 nearAtoms #2 distance 4.88
> surface zone #1 nearAtoms #2 distance 4.78
> surface zone #1 nearAtoms #2 distance 4.68
> surface zone #1 nearAtoms #2 distance 4.58
> surface zone #1 nearAtoms #2 distance 4.48
> surface zone #1 nearAtoms #2 distance 4.38
> surface zone #1 nearAtoms #2 distance 4.28
> surface zone #1 nearAtoms #2 distance 4.18
> surface zone #1 nearAtoms #2 distance 4.08
> surface zone #1 nearAtoms #2 distance 3.98
> surface zone #1 nearAtoms #2 distance 3.88
> surface zone #1 nearAtoms #2 distance 3.78
> surface zone #1 nearAtoms #2 distance 3.68
> surface zone #1 nearAtoms #2 distance 3.58
> surface zone #1 nearAtoms #2 distance 3.48
> surface zone #1 nearAtoms #2 distance 3.38
> surface zone #1 nearAtoms #2 distance 3.28
> surface zone #1 nearAtoms #2 distance 3.18
> surface zone #1 nearAtoms #2 distance 3.08
> surface zone #1 nearAtoms #2 distance 2.98
> surface zone #1 nearAtoms #2 distance 2.88
> surface zone #1 nearAtoms #2 distance 2.78
> surface zone #1 nearAtoms #2 distance 2.68
> surface zone #1 nearAtoms #2 distance 2.58
> surface zone #1 nearAtoms #2 distance 2.48
> surface zone #1 nearAtoms #2 distance 2.38
> surface zone #1 nearAtoms #2 distance 2.28
> surface zone #1 nearAtoms #2 distance 2.18
> surface zone #1 nearAtoms #2 distance 2.08
> surface zone #1 nearAtoms #2 distance 1.98
> surface zone #1 nearAtoms #2 distance 1.88
> surface zone #1 nearAtoms #2 distance 1.78
> surface zone #1 nearAtoms #2 distance 1.68
> surface zone #1 nearAtoms #2 distance 1.58
> surface zone #1 nearAtoms #2 distance 1.48
> surface zone #1 nearAtoms #2 distance 1.38
> surface zone #1 nearAtoms #2 distance 1.28
> surface zone #1 nearAtoms #2 distance 1.18
> surface zone #1 nearAtoms #2 distance 1.08
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!1 models
Drag select of 439 atoms, 104 residues, 1 pseudobonds, 364 bonds
> surface zone #1 nearAtoms sel distance 1.08
> show #!1 models
> surface zone #1 nearAtoms sel distance 1.14
> surface zone #1 nearAtoms sel distance 1.68
> surface zone #1 nearAtoms sel distance 1.79
> surface zone #1 nearAtoms sel distance 2.18
> surface zone #1 nearAtoms sel distance 2.14
> surface zone #1 nearAtoms sel distance 2.01
> set bgColor white
> surface zone #1 nearAtoms sel distance 2.14
> surface zone #1 nearAtoms sel distance 3.64
> surface zone #1 nearAtoms sel distance 3.88
> surface zone #1 nearAtoms sel distance 3.36
> surface zone #1 nearAtoms sel distance 3.7
> surface zone #1 nearAtoms sel distance 2.07
> transparency (#!2 & sel) 80
> select clear
> transparency 80
> hide cartoons
> graphics silhouettes true
No atoms selected for zoning
[Repeated 1 time(s)]
> hide #!1 models
Drag select of 771 atoms, 1 pseudobonds, 780 bonds
> show #!1 models
> surface zone #1 nearAtoms sel distance 2.64
> surface dust #1 size 12.35
> undo
> surface dust #1 size 12.35
> surface undust #1
> show #!1 models
> surface dust #1 size 12.35
> surface dust #1 size 12.77
> surface dust #1 size 68.04
> surface zone #1 nearAtoms sel distance 2.64
> surface zone #1 nearAtoms sel distance 2.04
> surface zone #1 nearAtoms sel distance 2.07
> surface zone #1 nearAtoms sel distance 2.25
> select clear
> ui tool show "Color Zone"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui tool show "Surface Zone"
> hide #!1 models
Drag select of 771 atoms, 1 pseudobonds, 780 bonds
> show #!1 models
> surface zone #1 nearAtoms #2 distance 2.31
> surface zone #1 nearAtoms #2 distance 1.94
> undo
> redo
> surface zone #1 nearAtoms #2 distance 1.91
> surface zone #1 nearAtoms #2 distance 2.34
> surface zone #1 nearAtoms sel distance 2.34
> surface zone #1 nearAtoms sel distance 2.36
> surface zone #1 nearAtoms sel distance 2.07
> surface zone #1 nearAtoms sel distance 2.18
> surface zone #1 nearAtoms sel distance 1.85
> surface zone #1 nearAtoms sel distance 1.88
> surface zone #1 nearAtoms sel distance 1.68
> select clear
> save
> /Users/lichinghsiao/Desktop/Abeta_chimera_graphs/J84/phenix96/model_and_map/model_and_map_1.cxs
——— End of log from Thu Jun 20 16:37:24 2024 ———
opened ChimeraX session
> hide #!2 models
> show #!2 models
> hide #!1 models
Drag select of 771 atoms, 1 pseudobonds, 780 bonds
> select ~sel & ##selected
3084 atoms, 3120 bonds, 1 pseudobond, 424 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> altlocs show
Drag select of 3 atoms, 3 bonds
> select up
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
22 atoms, 22 bonds, 2 residues, 2 models selected
> color sel dark salmon
> select clear
> show #!1 models
> ui tool show "Surface Zone"
> surface zone #1 nearAtoms #2 distance 1.68
> hide #!1 models
> select clear
> open
> /Users/lichinghsiao/Desktop/phenix_D723_trimer_J84/RealSpaceRefine_96/edit_all拷貝_real_space_refined_096.pdb
Chain information for edit_all拷貝_real_space_refined_096.pdb #3
---
Chain | Description
A B C D E | No description available
BA BB BC BD BE | No description available
CA CB CC CD CE | No description available
45 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!2 models
> show #!3 cartoons
> hide #!3 atoms
> select #3/D:40
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #3/BD:19
18 atoms, 17 bonds, 2 residues, 1 model selected
> select add #3/CD:31
26 atoms, 24 bonds, 3 residues, 1 model selected
> select up
94 atoms, 93 bonds, 12 residues, 1 model selected
> select up
769 atoms, 780 bonds, 104 residues, 1 model selected
> style sel stick
Changed 769 atom styles
> show sel atoms
[Repeated 1 time(s)]
> select clear
> show #!3 atoms
> style #!3 stick
Changed 3855 atom styles
> select add #3/BD:31
8 atoms, 8 bonds, 1 residue, 1 model selected
> select add #3/CD:30
13 atoms, 12 bonds, 2 residues, 1 model selected
> select add #3/?:3@O
14 atoms, 12 bonds, 3 residues, 1 model selected
> select add #3/?:4@O
15 atoms, 12 bonds, 4 residues, 1 model selected
> select up
17 atoms, 12 bonds, 5 residues, 1 model selected
> select up
23 atoms, 18 bonds, 5 residues, 1 model selected
> select up
66 atoms, 61 bonds, 11 residues, 1 model selected
> select up
771 atoms, 780 bonds, 106 residues, 1 model selected
> select up
779 atoms, 780 bonds, 114 residues, 1 model selected
> select down
771 atoms, 780 bonds, 106 residues, 1 model selected
> select ~sel & ##selected
3084 atoms, 3120 bonds, 2 pseudobonds, 424 residues, 2 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> matchmaker 3 to 2
Missing or invalid "matchAtoms" argument: invalid atoms specifier
> matchmaker #3 to #2
Specify a single 'to' model only
> matchmaker model #3 to #2
Missing or invalid "matchAtoms" argument: invalid atoms specifier
> matchAtoms model #3 to #2
Unknown command: matchAtoms model #3 to #2
> matchmaker #3 to #2
Specify a single 'to' model only
> matchmaker #3 to 2
Invalid "to" argument: invalid atoms specifier
> matchmaker #3 to #2
Specify a single 'to' model only
> matchmaker model #3 to model #2
Missing or invalid "matchAtoms" argument: invalid atoms specifier
> mmaker #3 to #2
Specify a single 'to' model only
> ui tool show "Fit in Map"
> show #!2 models
> select add #3
771 atoms, 780 bonds, 106 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.71281,0.57109,-0.40713,19.576,0.69899,-0.62608,0.34559,64.577,-0.057531,-0.53092,-0.84547,310.56
> view matrix models
> #3,0.82291,0.56643,-0.044513,-40.543,0.56114,-0.82251,-0.092785,162.09,-0.089168,0.051375,-0.99469,263.98
> view matrix models
> #3,0.82324,0.56545,-0.050449,-39.693,0.56169,-0.8242,-0.072101,159.53,-0.082349,0.03102,-0.99612,265.77
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.82324,0.56545,-0.050449,-39.697,0.56169,-0.8242,-0.072101,162.99,-0.082349,0.03102,-0.99612,265.58
> view matrix models
> #3,0.82324,0.56545,-0.050449,-40.525,0.56169,-0.8242,-0.072101,164,-0.082349,0.03102,-0.99612,265.59
> hide sel cartoons
> show sel atoms
> view matrix models
> #3,0.82324,0.56545,-0.050449,-41.021,0.56169,-0.8242,-0.072101,164.1,-0.082349,0.03102,-0.99612,265.62
> view matrix models
> #3,0.82324,0.56545,-0.050449,-41.004,0.56169,-0.8242,-0.072101,164.13,-0.082349,0.03102,-0.99612,265.62
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.86524,0.5002,-0.03409,-40.464,0.49543,-0.86345,-0.094884,179.88,-0.076897,0.065208,-0.9949,260.7
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.86524,0.5002,-0.03409,-40.493,0.49543,-0.86345,-0.094884,179.45,-0.076897,0.065208,-0.9949,258.18
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.8434,0.50432,-0.18532,-18.652,0.51587,-0.8565,0.016929,161.58,-0.15019,-0.10988,-0.98253,286.46
> view matrix models
> #3,0.862,0.50643,-0.022115,-42.399,0.50686,-0.86174,0.022507,162.58,-0.0076592,-0.03061,-0.9995,261.77
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.862,0.50643,-0.022115,-42.252,0.50686,-0.86174,0.022507,162.5,-0.0076592,-0.03061,-0.9995,262.76
> select clear
> matchmaker #3 to #2
Specify a single 'to' model only
> hide #!3 models
> open
> /Users/lichinghsiao/Desktop/Abeta_chimera_graphs/J84/phenix96/model_and_map/1plain_test.pdb
Summary of feedback from opening
/Users/lichinghsiao/Desktop/Abeta_chimera_graphs/J84/phenix96/model_and_map/1plain_test.pdb
---
warnings | Start residue of secondary structure not found: SHEET 4 4 1 LYSBE 16 ALABE 21 0
Start residue of secondary structure not found: SHEET 5 5 1 VALBE 24 ASNBE 27
0
Start residue of secondary structure not found: SHEET 6 6 1 ALABE 30 ILEBE 32
0
Start residue of secondary structure not found: SHEET 7 7 1 VALBE 39 ILEBE 41
0
Start residue of secondary structure not found: SHEET 8 8 1 GLUCE 3 ARGCE 5 0
4 messages similar to the above omitted
Chain information for 1plain_test.pdb #4
---
Chain | Description
BE | No description available
CE | No description available
E | No description available
9 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select #4/E:16
9 atoms, 8 bonds, 1 residue, 1 model selected
> close #4
> open
> /Users/lichinghsiao/Desktop/phenix_D723_trimer_J84/RealSpaceRefine_96/edit_all拷貝_real_space_refined_096.pdb
Chain information for edit_all拷貝_real_space_refined_096.pdb #4
---
Chain | Description
A B C D E | No description available
BA BB BC BD BE | No description available
CA CB CC CD CE | No description available
45 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> show #2.2.1.1-2#!2,4 cartoons
> hide #2.2.1.1-2#!2,4 atoms
> turn x 180 models #4
> turn z 5 models #4
[Repeated 3 time(s)]
> undo
[Repeated 1 time(s)]
> close #4
> undo
[Repeated 1 time(s)]Undo failed, probably because structures have been
modified.
> undo
Undo failed, probably because structures have been modified.
> select clear
[Repeated 4 time(s)]
> hide #2.2.1.1-2#!2 atoms
> hide #2.2.1.1-2#!2 cartoons
[Repeated 1 time(s)]
> show #2.2.1.1-2#!2 atoms
> select clear
> select add #2
793 atoms, 802 bonds, 1 pseudobond, 108 residues, 6 models selected
> save
> /Users/lichinghsiao/Desktop/Abeta_chimera_graphs/J84/phenix96/model_and_map/1plain_test.pdb
> selectedOnly true
> open
> /Users/lichinghsiao/Desktop/Abeta_chimera_graphs/J84/phenix96/model_and_map/1plain_test.pdb
Chain information for 1plain_test.pdb #4
---
Chain | Description
BE | No description available
CE | No description available
E | No description available
9 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide sel cartoons
> style sel stick
Changed 793 atom styles
> select clear
> hide #2.2.1.1-2#!2,4 cartoons
> show #2.2.1.1-2#!2,4 atoms
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> show #!2 models
> close #4
> open
> /Users/lichinghsiao/Desktop/phenix_D723_trimer_J84/RealSpaceRefine_96/edit_all拷貝_real_space_refined_096.pdb
Chain information for edit_all拷貝_real_space_refined_096.pdb #4
---
Chain | Description
A B C D E | No description available
BA BB BC BD BE | No description available
CA CB CC CD CE | No description available
45 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!2 models
> show #!4 cartoons
> hide #!4 atoms
> select #4/D:40
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> show sel atoms
> select clear
> style #!4 stick
Changed 3855 atom styles
> show #!4 atoms
> select #4/D:40
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #4/CD:40
14 atoms, 13 bonds, 2 residues, 1 model selected
> select add #4/?:3@O
15 atoms, 13 bonds, 3 residues, 1 model selected
> select add #4/?:4@O
16 atoms, 13 bonds, 4 residues, 1 model selected
> select up
18 atoms, 13 bonds, 5 residues, 1 model selected
> select up
23 atoms, 18 bonds, 5 residues, 1 model selected
> select up
71 atoms, 66 bonds, 12 residues, 1 model selected
> select up
771 atoms, 780 bonds, 106 residues, 1 model selected
> select up
779 atoms, 780 bonds, 114 residues, 1 model selected
> select down
771 atoms, 780 bonds, 106 residues, 1 model selected
> select ~sel & ##selected
3084 atoms, 3120 bonds, 2 pseudobonds, 424 residues, 2 models selected
> delete atoms (#!4 & sel)
> delete bonds (#!4 & sel)
> altlocs show
> hide #4.2.1.1-2#!4 cartoons
> show #4.2.1.1-2#!4 atoms
> select clear
Drag select of 6 atoms, 6 bonds
> size sel stickRadius +.1
Changed 7 bond radii
> select clear
> view orient
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> hide #!2.2 models
> show #!2.2 models
> matchmaker #3 to #2.2
Specify a single 'to' model only
> matchmaker #3 to #2.1
No 'to' model specified
> matchmaker #3 to #2
Specify a single 'to' model only
> hide #!3 models
> show #2.1 models
> hide #2.1 models
Drag select of 12 atoms, 12 bonds
> select up
13 atoms, 13 bonds, 2 residues, 2 models selected
> size sel stickRadius +.1
Changed 13 bond radii
> color sel dark salmon
> select clear
> close #3
> close #4
> show #!1 models
> hide #!1 models
Drag select of 8 atoms, 8 bonds
> select add #!2.2.1.1/B:19@CD2
9 atoms, 12 bonds, 2 residues, 2 models selected
> color (#2.2.1.1.1.1.1#!2.2.1.1 & sel) dark gray
> undo
> select clear
Drag select of 12 atoms, 12 bonds
> color (#2.2.1.1.1.1.1#!2.2.1.1 & sel) gray
> color (#2.2.1.1.1.1.1 & sel) gray
> select clear
> select add #!2/B:19@CB
1 atom, 1 bond, 1 residue, 2 models selected
> color (#2.2.1.1.1.1.1#!2 & sel) gray
> undo
> color sel gray
> undo
> select clear
Drag select of 28 atoms, 31 bonds
> color sel dark salmon
> select clear
[Repeated 1 time(s)]
> select add #!2.2.1.1/B:19@CE1
1 atom, 1 bond, 1 residue, 2 models selected
> select add #!2.2.1.1/B:19@CZ
2 atoms, 2 bonds, 1 residue, 2 models selected
> select add #!2.2.1.1/B:19@CE2
3 atoms, 4 bonds, 1 residue, 2 models selected
> select add #!2.2.1.1/B:19@CD2
4 atoms, 5 bonds, 1 residue, 2 models selected
> select add #!2.2.1.1/B:19@CD1
5 atoms, 5 bonds, 1 residue, 2 models selected
> select add #!2.2.1.1/B:19@CG
6 atoms, 7 bonds, 1 residue, 2 models selected
> color (#2.2.1.1.1.1.1#!2.2.1.1 & sel) gray
> select clear
[Repeated 2 time(s)]
> select add #!2.2.1.1/B:19@CG
1 atom, 2 bonds, 1 residue, 1 model selected
> color (#2.2.1.1.1.1.1#!2.2.1.1 & sel) gray
> select add #!2/B:19@CB
2 atoms, 3 bonds, 2 residues, 3 models selected
> color sel gray
> undo
> select clear
> select #2.2.1.1.1.1.1/B:19@CB
1 atom, 1 residue, 1 model selected
> color (#2.2.1.1.1.1.1#!2.2.1.1 & sel) gray
> select clear
Drag select of 17 bonds, 12 atoms
> select add #!2/B:19@CG
13 atoms, 16 bonds, 3 residues, 4 models selected
> select subtract #!2/B:19@CG
12 atoms, 16 bonds, 2 residues, 4 models selected
> color (#2.2.1.1.1.1.1#2.2.1.2.1.1.1#!2.2.1.1-2 & sel) gray
> select clear
> view orient
> addh
Summary of feedback from adding hydrogens to multiple structures
---
notes | No usable SEQRES records for edit_all拷貝_real_space_refined_096.pdb (#2) chain B; guessing termini instead
No usable SEQRES records for edit_all拷貝_real_space_refined_096.pdb (#2) chain
BB; guessing termini instead
No usable SEQRES records for edit_all拷貝_real_space_refined_096.pdb (#2) chain
CB; guessing termini instead
Chain-initial residues that are actual N termini:
edit_all拷貝_real_space_refined_096.pdb #!2/B GLY 9,
edit_all拷貝_real_space_refined_096.pdb #!2/BB GLN 15,
edit_all拷貝_real_space_refined_096.pdb #!2/CB ASP 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
edit_all拷貝_real_space_refined_096.pdb #!2/B ALA 42,
edit_all拷貝_real_space_refined_096.pdb #!2/BB ALA 42,
edit_all拷貝_real_space_refined_096.pdb #!2/CB ALA 42
Chain-final residues that are not actual C termini:
22 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
829 hydrogens added
> select H
817 atoms, 110 residues, 5 models selected
> select subtract #!2/?:7@H2
816 atoms, 110 residues, 5 models selected
> select subtract #!2/?:7@H1
815 atoms, 109 residues, 5 models selected
> select subtract #!2/?:8@H2
814 atoms, 109 residues, 5 models selected
> select subtract #!2/?:8@H1
813 atoms, 108 residues, 5 models selected
> delete atoms sel
> delete bonds sel
> select O
147 atoms, 110 residues, 5 models selected
> color sel red
> select N
133 atoms, 108 residues, 5 models selected
> color sel medium blue
> select S
3 atoms, 3 residues, 1 model selected
> color sel yellow
> select clear
> show #!1 models
> save
> /Users/lichinghsiao/Desktop/Abeta_chimera_graphs/J84/phenix96/model_and_map/model_and_map_1.cxs
> view orient
> windowsize 1000 800
> save
> /Users/lichinghsiao/Desktop/Abeta_chimera_graphs/J84/phenix96/model_and_map/model_and_map_1.png
> width 3000 height 2400 supersample 4
> hide #!1 models
Drag select of 2 atoms, 1 bonds
Drag select of 3 atoms, 2 bonds
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Drag select of 3 atoms, 3 bonds
[Repeated 1 time(s)]
> select up
13 atoms, 9 bonds, 4 residues, 1 model selected
> select up
32 atoms, 28 bonds, 4 residues, 1 model selected
> style sel sphere
Changed 32 atom styles
> size sel atomRadius -.8
Changed 32 atom radii
> select clear
> show #!1 models
> save
> /Users/lichinghsiao/Desktop/Abeta_chimera_graphs/J84/phenix96/model_and_map/model_and_map_1.png
> width 3000 height 2400 supersample 4
> save
> /Users/lichinghsiao/Desktop/Abeta_chimera_graphs/J84/phenix96/model_and_map/model_and_map_1.cxs
——— End of log from Thu Jun 20 18:01:49 2024 ———
opened ChimeraX session
> open
> /Users/lichinghsiao/Desktop/Abeta_chimera_graphs/J84/phenix96/model_and_map/model_and_map.cxs
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.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-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/altlocs.py", line 301, in _models_closed_cb
self.destroy()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
Error processing trigger "remove models":
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.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-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/altlocs.py", line 301, in _models_closed_cb
self.destroy()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
Error processing trigger "remove models":
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.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-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/altlocs.py", line 301, in _models_closed_cb
self.destroy()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
Error processing trigger "remove models":
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Unable to restore session, resetting.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 723, in restore
self.reset()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 552, in reset
sm.reset_state(container, self)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/altlocs.py", line 356, in reset_state
self.destroy()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 723, in restore
self.reset()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 552, in reset
sm.reset_state(container, self)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/altlocs.py", line 356, in reset_state
self.destroy()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 334, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 131, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 213, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 514, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 484, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 37, in open
return cxs_open(session, data, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 1027, in open
session.restore(stream, path=path, resize_window=resize_window,
combine=combine)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 765, in restore
self.reset()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 552, in reset
sm.reset_state(container, self)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/altlocs.py", line 356, in reset_state
self.destroy()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> open
> /Users/lichinghsiao/Desktop/Abeta_chimera_graphs/J84/phenix96/model_and_map/model_and_map_1.cxs
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.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-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/altlocs.py", line 305, in _models_closed_cb
self.destroy()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
Error processing trigger "remove models":
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.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-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/altlocs.py", line 305, in _models_closed_cb
self.destroy()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
Error processing trigger "remove models":
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.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-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/altlocs.py", line 305, in _models_closed_cb
self.destroy()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
Error processing trigger "remove models":
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Unable to restore session, resetting.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 723, in restore
self.reset()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 552, in reset
sm.reset_state(container, self)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/altlocs.py", line 356, in reset_state
self.destroy()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 723, in restore
self.reset()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 552, in reset
sm.reset_state(container, self)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/altlocs.py", line 356, in reset_state
self.destroy()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 334, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 131, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 213, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 514, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 484, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 37, in open
return cxs_open(session, data, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 1027, in open
session.restore(stream, path=path, resize_window=resize_window,
combine=combine)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 765, in restore
self.reset()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 552, in reset
sm.reset_state(container, self)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/altlocs.py", line 356, in reset_state
self.destroy()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
AttributeError: 'AtomicStructure' object has no attribute
'_alt_loc_changes_handler'
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/altlocs.py", line 172, in destroy
alt_loc_s._alt_loc_changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac14,2
Model Number: MLXY3TA/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 8422.141.2
OS Loader Version: 8422.141.2
Software:
System Software Overview:
System Version: macOS 13.5 (22G74)
Kernel Version: Darwin 22.6.0
Time since boot: 17天23小時27分鐘
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL P2717H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
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: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
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: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
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-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
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: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
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: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 14 months ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → 'AtomicStructure' object has no attribute '_alt_loc_changes_handler' |
comment:2 by , 14 months ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
Note:
See TracTickets
for help on using tickets.
Fix: https://github.com/RBVI/ChimeraX/commit/f39b8392e6b756e930f8d577f9553fd36a56fa33