Destruction of status bar during session restore: wrapped C/C++ object of type QScreen has been deleted

[maru.jaimegarza@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/maru/Desktop/Models/from40_148_isolde_v10.pdb

Chain information for from40_148_isolde_v10.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
  

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> hide atoms

> show cartoons

> select /B:96

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select add /A:14

32 atoms, 31 bonds, 2 residues, 1 model selected  

> select add /F:45

54 atoms, 52 bonds, 3 residues, 1 model selected  

> select add /D:401

73 atoms, 70 bonds, 4 residues, 1 model selected  

> select add /C:656

89 atoms, 85 bonds, 5 residues, 1 model selected  

> select add /F:224

111 atoms, 106 bonds, 6 residues, 1 model selected  

> select add /G:588

131 atoms, 126 bonds, 7 residues, 1 model selected  

> select up

2227 atoms, 2231 bonds, 132 residues, 1 model selected  

> select up

26741 atoms, 26967 bonds, 1637 residues, 1 model selected  

> select add /H:440

26763 atoms, 26988 bonds, 1638 residues, 1 model selected  

> select up

26872 atoms, 27100 bonds, 1644 residues, 1 model selected  

> select up

28125 atoms, 28365 bonds, 1722 residues, 1 model selected  

> color sel dark gray

> select clear

Drag select of 122 residues  

> select up

2131 atoms, 2150 bonds, 130 residues, 1 model selected  

> color sel #b8b0ddff

> select clear

Drag select of 210 residues  

> select up

3865 atoms, 3909 bonds, 248 residues, 1 model selected  

> select up

7326 atoms, 7408 bonds, 459 residues, 1 model selected  

> select up

35535 atoms, 35855 bonds, 2189 residues, 1 model selected  

> select down

7326 atoms, 7408 bonds, 459 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel medium purple

> select clear

Drag select of 121 residues  

> select up

2131 atoms, 2150 bonds, 130 residues, 1 model selected  

> color sel #b8b0ddff

> select clear

> open /Users/maru/Downloads/1wao_cat.pdb

Summary of feedback from opening /Users/maru/Downloads/1wao_cat.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA 3 28
LYS 3 32 1 5  
Start residue of secondary structure not found: HELIX 2 2 ALA 3 35 LYS 3 42 1
8  
Start residue of secondary structure not found: HELIX 3 3 TYR 3 44 PHE 3 50 1
7  
Start residue of secondary structure not found: HELIX 4 4 ILE 3 63 TYR 3 72 1
10  
Start residue of secondary structure not found: HELIX 5 5 CYS 3 77 ALA 3 85 1
9  
4 messages similar to the above omitted  
Cannot find LINK/SSBOND residue MN (601 )  
Cannot find LINK/SSBOND residue MN (601 )  
Cannot find LINK/SSBOND residue MN (601 )  
Cannot find LINK/SSBOND residue MN (601 )  
Cannot find LINK/SSBOND residue MN (602 )  
2 messages similar to the above omitted  
  
1wao_cat.pdb title:  
PP5 structure [more info...]  
  
Chain information for 1wao_cat.pdb #2  
---  
Chain | Description  
3 | serine/threonine protein phosphatase 5  
  

> mmaker #2 to #1

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 from40_148_isolde_v10.pdb, chain E (#1) with 1wao_cat.pdb, chain 3
(#2), sequence alignment score = 2029.5  
RMSD between 262 pruned atom pairs is 1.137 angstroms; (across all 323 pairs:
1.890)  
  

> select #2/3:482

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

166 atoms, 170 bonds, 23 residues, 1 model selected  

> select up

2717 atoms, 2781 bonds, 341 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel medium purple

> select clear

> select add #2/3:499

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select add #2/3:497

9 atoms, 7 bonds, 2 residues, 1 model selected  

> select add #2/3:498

14 atoms, 11 bonds, 3 residues, 1 model selected  

> select add #2/3:496

22 atoms, 18 bonds, 4 residues, 1 model selected  

> select add #2/3:495

31 atoms, 26 bonds, 5 residues, 1 model selected  

> select add #2/3:494

39 atoms, 33 bonds, 6 residues, 1 model selected  

> select add #2/3:493

47 atoms, 40 bonds, 7 residues, 1 model selected  

> select add #2/3:492

54 atoms, 46 bonds, 8 residues, 1 model selected  

> select add #2/3:491

62 atoms, 53 bonds, 9 residues, 1 model selected  

> select add #2/3:490

67 atoms, 57 bonds, 10 residues, 1 model selected  

> select add #2/3:488

72 atoms, 61 bonds, 11 residues, 1 model selected  

> select add #2/3:489

84 atoms, 73 bonds, 12 residues, 1 model selected  

> select add #2/3:487

92 atoms, 80 bonds, 13 residues, 1 model selected  

> select add #2/3:486

99 atoms, 87 bonds, 14 residues, 1 model selected  

> select subtract #2/3:486

92 atoms, 80 bonds, 13 residues, 1 model selected  

> select subtract #2/3:487

84 atoms, 73 bonds, 12 residues, 1 model selected  

> select subtract #2/3:488

79 atoms, 69 bonds, 11 residues, 1 model selected  

> color sel #ff2600ff

> select clear

> ui tool show "Side View"

> ui tool show "Side View"

> select #2/3:484

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

166 atoms, 170 bonds, 23 residues, 1 model selected  

> select up

2717 atoms, 2781 bonds, 341 residues, 1 model selected  

> select subtract #2/3:499

2712 atoms, 2777 bonds, 340 residues, 1 model selected  

> select subtract #2/3:498

2707 atoms, 2773 bonds, 339 residues, 1 model selected  

> select subtract #2/3:497

2703 atoms, 2770 bonds, 338 residues, 1 model selected  

> select subtract #2/3:496

2695 atoms, 2763 bonds, 337 residues, 1 model selected  

> select add #1/C:652

2717 atoms, 2784 bonds, 338 residues, 2 models selected  

> select subtract #1/C:652

2695 atoms, 2763 bonds, 337 residues, 1 model selected  

> select subtract #2/3:492

2688 atoms, 2757 bonds, 336 residues, 1 model selected  

> select subtract #2/3:491

2680 atoms, 2750 bonds, 335 residues, 1 model selected  

> select subtract #2/3:493

2672 atoms, 2743 bonds, 334 residues, 1 model selected  

> select subtract #2/3:494

2664 atoms, 2736 bonds, 333 residues, 1 model selected  

> select subtract #2/3:495

2655 atoms, 2728 bonds, 332 residues, 1 model selected  

> select subtract #2/3:490

2650 atoms, 2724 bonds, 331 residues, 1 model selected  

> select subtract #2/3:489

2638 atoms, 2712 bonds, 330 residues, 1 model selected  

> select subtract #2/3:488

2633 atoms, 2708 bonds, 329 residues, 1 model selected  

> select subtract #2/3:487

2625 atoms, 2701 bonds, 328 residues, 1 model selected  

> select subtract #2/3:486

2618 atoms, 2694 bonds, 327 residues, 1 model selected  

> select subtract #2/3:485

2609 atoms, 2686 bonds, 326 residues, 1 model selected  

> select add #2/3:485

2618 atoms, 2694 bonds, 327 residues, 1 model selected  

> select subtract #2/3:485

2609 atoms, 2686 bonds, 326 residues, 1 model selected  

> select subtract #2/3:484

2602 atoms, 2680 bonds, 325 residues, 1 model selected  

> select subtract #2/3:483

2594 atoms, 2673 bonds, 324 residues, 1 model selected  

> select subtract #2/3:482

2587 atoms, 2666 bonds, 323 residues, 1 model selected  

> cartoon hide sel

> select #1/G:609

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select up

163 atoms, 162 bonds, 10 residues, 1 model selected  

> select up

1723 atoms, 1743 bonds, 106 residues, 1 model selected  

> color sel #cf3a5eff

> select #1/H:451

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select up

318 atoms, 320 bonds, 20 residues, 1 model selected  

> select up

1384 atoms, 1398 bonds, 85 residues, 1 model selected  

> color sel #cf3a5eff

> select clear

> save /Users/maru/Desktop/grayALL_PP5color.png width 847 height 623
> supersample 4 transparentBackground true

> open /Users/maru/Downloads/6xlg.pdb

6xlg.pdb title:  
Full-length HSC82 In complex with two AHA1 CTD In the presence of atpgammas
[more info...]  
  
Chain information for 6xlg.pdb #3  
---  
Chain | Description  
A B | atp-dependent molecular chaperone HSC82  
C D | activator OF HSP90 atpase protein 1  
  
Non-standard residues in 6xlg.pdb #3  
---  
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate);adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)  
K — potassium ion  
MG — magnesium ion  
  

> open /Users/maru/Desktop/Models/from40_148_isolde_v10.pdb

Chain information for from40_148_isolde_v10.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
  

> view clip false

> mmaker #3 to #1

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 from40_148_isolde_v10.pdb, chain D (#1) with 6xlg.pdb, chain B
(#3), sequence alignment score = 1453.7  
RMSD between 319 pruned atom pairs is 1.071 angstroms; (across all 397 pairs:
1.566)  
  

> close #4

Alignment identifier is 1/A  
Alignment identifier is 1/B  
Alignment identifier is 1/C  
Alignment identifier is 1/D  
Alignment identifier is 1/E  
Alignment identifier is 1/F  
Alignment identifier is 1/G  
Alignment identifier is 1/H  
Alignment identifier is 2/3  
Alignment identifier is 1  
Alignment identifier is 2  

> select #3/A-B:282

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3/A-B:282

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3/A-B:281

14 atoms, 12 bonds, 2 residues, 1 model selected  

> select #3/A-B:281

14 atoms, 12 bonds, 2 residues, 1 model selected  

> open /Users/maru/Downloads/2cg9.pdb

2cg9.pdb title:  
Crystal structure of an HSP90-SBA1 closed chaperone complex [more info...]  
  
Chain information for 2cg9.pdb #4  
---  
Chain | Description  
A B | atp-dependent molecular chaperone HSP82  
X Y | Co-chaperone protein SBA1  
  
Non-standard residues in 2cg9.pdb #4  
---  
ATP — adenosine-5'-triphosphate  
  

> mmaker #4 to #1

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 from40_148_isolde_v10.pdb, chain D (#1) with 2cg9.pdb, chain B
(#4), sequence alignment score = 1342.4  
RMSD between 331 pruned atom pairs is 1.017 angstroms; (across all 402 pairs:
1.785)  
  

> close #3

> select #4

11906 atoms, 12124 bonds, 9 pseudobonds, 1459 residues, 2 models selected  
Alignment identifier is 1  
Alignment identifier is 2  

> select clear

> select #4/A-B:282

12 atoms, 10 bonds, 2 residues, 1 model selected  

> select #4/A-B:282

12 atoms, 10 bonds, 2 residues, 1 model selected  

> color sel red

> select #4/A-B:297

12 atoms, 10 bonds, 2 residues, 1 model selected  

> select #4/A-B:297-298

28 atoms, 26 bonds, 4 residues, 1 model selected  

> select #4/A-B:297

12 atoms, 10 bonds, 2 residues, 1 model selected  

> select #4/A-B:297

12 atoms, 10 bonds, 2 residues, 1 model selected  

> color sel red

> select #4/B:334

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #4/B:334

6 atoms, 5 bonds, 1 residue, 1 model selected  

> color sel red

> select #4/A-B:379

12 atoms, 10 bonds, 2 residues, 1 model selected  

> color sel red

> select #4/A-B:450

12 atoms, 10 bonds, 2 residues, 1 model selected  

> select #4/A-B:450

12 atoms, 10 bonds, 2 residues, 1 model selected  

> color sel red

> hide #!4 models

> show #!4 models

> hide #2 models

> hide #1 models

> select #4/A-B:456

12 atoms, 10 bonds, 2 residues, 1 model selected  

> select #4/A-B:456

12 atoms, 10 bonds, 2 residues, 1 model selected  

> color sel red

> select #4/A-B:485

12 atoms, 10 bonds, 2 residues, 1 model selected  

> select #4/A-B:485

12 atoms, 10 bonds, 2 residues, 1 model selected  

> color sel red

> select #4/A-B:533

14 atoms, 12 bonds, 2 residues, 1 model selected  

> select #4/A-B:533

14 atoms, 12 bonds, 2 residues, 1 model selected  

> color sel red

> color sel red

> show #2 models

> hide #2 models

> show #1 models

> select add #1/G:609

24 atoms, 21 bonds, 3 residues, 2 models selected  

> select add #1/F:39

48 atoms, 44 bonds, 4 residues, 2 models selected  

> select up

1178 atoms, 1180 bonds, 79 residues, 2 models selected  

> select up

16016 atoms, 16244 bonds, 1594 residues, 2 models selected  

> select down

1178 atoms, 1180 bonds, 79 residues, 2 models selected  

> select add #1/G:589

1195 atoms, 1196 bonds, 80 residues, 2 models selected  

> select down

1195 atoms, 1196 bonds, 80 residues, 2 models selected  

> select up

1329 atoms, 1331 bonds, 88 residues, 2 models selected  

> select up

16016 atoms, 16244 bonds, 1594 residues, 2 models selected  

> select down

1329 atoms, 1331 bonds, 88 residues, 2 models selected  

> select add #1/G:571

1346 atoms, 1347 bonds, 89 residues, 2 models selected  

> select up

1605 atoms, 1610 bonds, 105 residues, 2 models selected  

> select up

16016 atoms, 16244 bonds, 1594 residues, 2 models selected  

> hide sel cartoons

> show sel cartoons

> select clear

> select add #1/A:220

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select add #1/F:39

48 atoms, 46 bonds, 2 residues, 1 model selected  

> select add #1/G:637

67 atoms, 64 bonds, 3 residues, 1 model selected  

> select add #1/H:463

84 atoms, 80 bonds, 4 residues, 1 model selected  

> select up

1412 atoms, 1418 bonds, 83 residues, 1 model selected  

> select up

10847 atoms, 10946 bonds, 667 residues, 1 model selected  

> hide sel cartoons

> select add #1/C:278

10859 atoms, 10957 bonds, 668 residues, 1 model selected  

> select up

10895 atoms, 10993 bonds, 670 residues, 1 model selected  

> select up

17835 atoms, 17991 bonds, 1089 residues, 1 model selected  

> hide sel cartoons

> select add #1/B:12

17850 atoms, 18005 bonds, 1090 residues, 1 model selected  

> select add #1/B:167

17874 atoms, 18028 bonds, 1091 residues, 1 model selected  

> select up

18005 atoms, 18161 bonds, 1100 residues, 1 model selected  

> select up

21158 atoms, 21341 bonds, 1300 residues, 1 model selected  

> hide sel cartoons

> select add #1/D:523

21175 atoms, 21357 bonds, 1301 residues, 1 model selected  

> select up

21319 atoms, 21503 bonds, 1310 residues, 1 model selected  

> select up

28125 atoms, 28365 bonds, 1722 residues, 1 model selected  

> hide sel cartoons

> ui mousemode right label

> label delete residues

> label delete residues

> label delete residues

> label #4/A:456

> label #4/A:450

> label #4/B:652

> label #4/B:485

> label #4/B:533

> label #4/A:533

> label #4/B:282

> label #4/B:297

> label #4/A:297

> label #4/A:282

> ui mousemode right "move label"

> ui mousemode right label

> label delete residues

> label #4/A:450

> label delete residues

> label delete residues

> label #4/A:456

> label #4/A:450

> label #4/A:485

> label #4/B:450

> label #4/A:533

> label #4/B:456

> ui mousemode right "move label"

> save /Users/maru/Desktop/yHsp90_Phospho.png width 1094 height 623
> supersample 3

> select #4/A-B:485

12 atoms, 10 bonds, 2 residues, 1 model selected  

> select #4/A-B:485

12 atoms, 10 bonds, 2 residues, 1 model selected  

> color sel orange red

> color sel magenta

> save /Users/maru/Desktop/S485affectedByPpt1-.png width 1094 height 623
> supersample 3

> select #4/A-B:379

12 atoms, 10 bonds, 2 residues, 1 model selected  

> select #4/A-B:379

12 atoms, 10 bonds, 2 residues, 1 model selected  

> select #1

35535 atoms, 35855 bonds, 2189 residues, 1 model selected  

> hide #!4 models

> show sel cartoons

> select clear

> select #1/G:608

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

163 atoms, 162 bonds, 10 residues, 1 model selected  

> select up

1723 atoms, 1743 bonds, 106 residues, 1 model selected  

> select up

35535 atoms, 35855 bonds, 2189 residues, 1 model selected  

> select down

1723 atoms, 1743 bonds, 106 residues, 1 model selected  

> select add #1/H:451

1740 atoms, 1759 bonds, 107 residues, 1 model selected  

> select up

2041 atoms, 2063 bonds, 126 residues, 1 model selected  

> select up

3107 atoms, 3141 bonds, 191 residues, 1 model selected  

> color sel dark gray

> select clear

> select add #1/C:410

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

421 atoms, 421 bonds, 24 residues, 1 model selected  

> select up

6988 atoms, 7045 bonds, 422 residues, 1 model selected  
Alignment identifier is 1/C  

> select #1/C:452

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1/C:452

11 atoms, 10 bonds, 1 residue, 1 model selected  

> color sel red

> select #1/A:220

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select up

54 atoms, 53 bonds, 3 residues, 1 model selected  

> select up

3429 atoms, 3456 bonds, 217 residues, 1 model selected  
Alignment identifier is 1/A  

> select #1/A:57

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1/A:57

11 atoms, 10 bonds, 1 residue, 1 model selected  

> color sel red

> select #1/A:62

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1/A:62

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1/A:59

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #1/A:59-60

26 atoms, 25 bonds, 2 residues, 1 model selected  

> select #1/A:59

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #1/A:59

14 atoms, 13 bonds, 1 residue, 1 model selected  

> color sel red

> select #1/A:62

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1/A:62

11 atoms, 10 bonds, 1 residue, 1 model selected  

> color sel red

> select #1/A:66

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1/A:66

11 atoms, 10 bonds, 1 residue, 1 model selected  

> color sel red

> select #1/A:84

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #1/A:84

14 atoms, 13 bonds, 1 residue, 1 model selected  

> color sel red

> select #1/A:205

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1/A:205

11 atoms, 10 bonds, 1 residue, 1 model selected  

> color sel red

> select #1/A:225

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select #1/A:225

12 atoms, 11 bonds, 1 residue, 1 model selected  

> color sel red

> select clear

> save /Users/maru/Desktop/hHsp90B_Phospho.png width 1001 height 623
> supersample 3

> open /Users/maru/Desktop/FigureStructureImages/Fig4_redo/wPeptide.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 679, in restore  
self.reset()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/manager.py", line 252, in reset_state  
alignment._destroy()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 603, in _destroy  
self._notify_observers(self.NOTE_DESTROYED, None)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 652, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 474, in alignment_notification  
self.delete()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 512, in delete  
ToolInstance.delete(self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 154, in delete  
self.session.ui.remove_tool(self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 345, in remove_tool  
self.main_window.remove_tool(tool_instance)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 725, in remove_tool  
tw._destroy()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2049, in _destroy  
self.__toolkit.destroy()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2189, in destroy  
sbar.destroy()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/statusbar.py", line 51, in destroy  
v.delete()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 438, in delete  
self.make_current()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 478, in make_current  
return self._opengl_context.make_current()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 99, in make_current  
qc = self._initialize_context()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context  
qc.setScreen(self._screen)  
RuntimeError: wrapped C/C++ object of type QScreen has been deleted  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 679, in restore  
self.reset()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/manager.py", line 252, in reset_state  
alignment._destroy()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 603, in _destroy  
self._notify_observers(self.NOTE_DESTROYED, None)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 652, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 474, in alignment_notification  
self.delete()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 512, in delete  
ToolInstance.delete(self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 154, in delete  
self.session.ui.remove_tool(self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 345, in remove_tool  
self.main_window.remove_tool(tool_instance)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 725, in remove_tool  
tw._destroy()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2049, in _destroy  
self.__toolkit.destroy()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2189, in destroy  
sbar.destroy()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/statusbar.py", line 51, in destroy  
v.delete()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 438, in delete  
self.make_current()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 478, in make_current  
return self._opengl_context.make_current()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 99, in make_current  
qc = self._initialize_context()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context  
qc.setScreen(self._screen)  
RuntimeError: wrapped C/C++ object of type QScreen has been deleted  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 261, in event  
_open_dropped_file(self.session, event.file())  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1812, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 179, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 422, in collated_open  
return func(*func_args, **func_kw)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 982, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 721, in restore  
self.reset()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/manager.py", line 252, in reset_state  
alignment._destroy()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 603, in _destroy  
self._notify_observers(self.NOTE_DESTROYED, None)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 652, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 474, in alignment_notification  
self.delete()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 512, in delete  
ToolInstance.delete(self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 154, in delete  
self.session.ui.remove_tool(self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 345, in remove_tool  
self.main_window.remove_tool(tool_instance)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 725, in remove_tool  
tw._destroy()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2049, in _destroy  
self.__toolkit.destroy()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2189, in destroy  
sbar.destroy()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/statusbar.py", line 51, in destroy  
v.delete()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 438, in delete  
self.make_current()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 478, in make_current  
return self._opengl_context.make_current()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 99, in make_current  
qc = self._initialize_context()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context  
qc.setScreen(self._screen)  
RuntimeError: wrapped C/C++ object of type QScreen has been deleted  
  
RuntimeError: wrapped C/C++ object of type QScreen has been deleted  
  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context  
qc.setScreen(self._screen)  
  
See log for complete Python traceback.  
  

> open /Users/maru/Desktop/FigureStructureImages/Fig4_redo/wPeptide.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 679, in restore  
self.reset()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 679, in restore  
self.reset()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 261, in event  
_open_dropped_file(self.session, event.file())  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1812, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 179, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 422, in collated_open  
return func(*func_args, **func_kw)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 982, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 721, in restore  
self.reset()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
  
See log for complete Python traceback.  
  

> open /Users/maru/Desktop/FigureStructureImages/Fig4_redo/wPeptide_2.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 679, in restore  
self.reset()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 679, in restore  
self.reset()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 261, in event  
_open_dropped_file(self.session, event.file())  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1812, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 179, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 422, in collated_open  
return func(*func_args, **func_kw)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 982, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 721, in restore  
self.reset()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
  
See log for complete Python traceback.  
  

> open /Users/maru/Desktop/FigureStructureImages/Fig4_redo/wPeptide_2.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 679, in restore  
self.reset()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 679, in restore  
self.reset()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/dialog.py", line 155, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 179, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 422, in collated_open  
return func(*func_args, **func_kw)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 982, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 721, in restore  
self.reset()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
  
See log for complete Python traceback.  
  

> open /Users/maru/Desktop/FigureStructureImages/Fig4_redo/fig4redo.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 679, in restore  
self.reset()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 679, in restore  
self.reset()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 261, in event  
_open_dropped_file(self.session, event.file())  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1812, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 179, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 422, in collated_open  
return func(*func_args, **func_kw)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 982, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 721, in restore  
self.reset()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 71.7.1
OpenGL renderer: Apple M1
OpenGL vendor: AppleHardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro17,1
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 4 MB
      Memory: 16 GB

Software:

    System Software Overview:

      System Version: macOS 11.6 (20G165)
      Kernel Version: Darwin 20.6.0
      Time since boot: 16 days 21:52

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Resolution: 2880 x 1800
          UI Looks like: 1440 x 900 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.16.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.2.2
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0

[Eric Pettersen]

Hi Maria,

Thanks for reporting this problem. It has been fixed in newer releases, so if you upgrade to the current version of ChimeraX you won't run into it anymore.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab