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#7355 closed defect (can't reproduce)

Save dead dock widget shown state in session

Reported by:	chimerax-bug-report@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	UI	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        macOS-10.15.3-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/basem/Downloads/example1 (27).pdb"

Chain information for example1 (27).pdb #1  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/basem/Downloads/test_8289a.result/test_8289a_unrelaxed_rank_1_model_5.pdb

Chain information for test_8289a_unrelaxed_rank_1_model_5.pdb #2  
---  
Chain | Description  
A | No description available  
  

> preset cartoons/nucleotides cylinders/stubs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> lighting soft

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> select #2

5184 atoms, 5276 bonds, 640 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,-51.881,0,1,0,-26.524,0,0,1,-19.473

> view matrix models #2,1,0,0,-68.927,0,1,0,-24.049,0,0,1,4.8241

> open /Users/basem/Downloads/7n3o.pdb

7n3o.pdb title:  
Cryo-em structure of the CAS12K-sgRNA complex [more info...]  
  
Chain information for 7n3o.pdb #3  
---  
Chain | Description  
A | CAS12K  
B | single guide RNA  
  

> mmaker #2 to #3

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 7n3o.pdb, chain A (#3) with
test_8289a_unrelaxed_rank_1_model_5.pdb, chain A (#2), sequence alignment
score = 2034.9  
RMSD between 296 pruned atom pairs is 1.177 angstroms; (across all 454 pairs:
2.689)  
  

> select #3

8295 atoms, 8922 bonds, 7 pseudobonds, 676 residues, 2 models selected  

> preset cartoons/nucleotides cylinders/stubs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> mmaker #1 to #3

No chains in match structure example1 (27).pdb #1 compatible with BLOSUM-62
similarity matrix  

> select #2

5184 atoms, 5276 bonds, 640 residues, 1 model selected  

> view matrix models
> #2,0.46796,0.67887,-0.56582,150.09,-0.83662,0.13401,-0.53114,154.08,-0.28475,0.72193,0.63066,129.8

> view matrix models
> #2,0.46796,0.67887,-0.56582,159.67,-0.83662,0.13401,-0.53114,167.51,-0.28475,0.72193,0.63066,134.25

> select #1

6886 atoms, 7425 bonds, 215 residues, 1 model selected  

> mmaker #1 to #3

No chains in match structure example1 (27).pdb #1 compatible with BLOSUM-62
similarity matrix  

> view matrix models #1,1,0,0,27.328,0,1,0,-17.266,0,0,1,15.156

> view matrix models #1,1,0,0,19.565,0,1,0,-11.405,0,0,1,52.491

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.87008,-0.45551,-0.18834,1.7771,0.47947,0.69351,0.53773,-3.928,-0.11432,-0.55817,0.82181,32.241

> view matrix models
> #1,0.68013,0.022022,-0.73276,-1.6497,0.46319,0.76185,0.45281,-4.6462,0.56823,-0.64738,0.50796,19.363

> view matrix models
> #1,0.85661,-0.26858,-0.44055,-0.88741,0.48251,0.71946,0.49956,-4.4006,0.18279,-0.6405,0.74589,27.322

> view matrix models
> #1,0.69618,-0.6974,-0.17016,-3.8881,0.66059,0.5296,0.53212,-8.7518,-0.28099,-0.48286,0.82939,34.771

> view matrix models
> #1,0.76703,-0.37969,0.51721,25.516,0.13378,0.88303,0.44985,-0.84202,-0.62751,-0.27586,0.7281,37.849

> view matrix models
> #1,0.68098,-0.72953,0.063643,2.4453,0.63029,0.62815,0.45624,-8.385,-0.37282,-0.27058,0.88758,42.392

> view matrix models
> #1,-0.33419,-0.80423,-0.49146,-14.888,0.89947,-0.11638,-0.4212,-55.599,0.28154,-0.58282,0.76227,29.121

> view matrix models
> #1,0.82611,-0.34285,-0.44721,-3.0927,0.33354,0.93717,-0.10232,-16.717,0.45419,-0.064636,0.88856,46.657

> view matrix models
> #1,0.91552,0.17981,-0.35985,13.511,-0.11441,0.97399,0.19561,-6.0522,0.38566,-0.13791,0.91228,45.448

> ui tool show "Show Sequence Viewer"

> sequence chain #3/A

Alignment identifier is 3/A  

> sequence chain #2/A

Alignment identifier is 2/A  

> select
> #3/A:13-25,27-42,44-51,55-69,76-102,318-338,364-369,379-406,413-430,476-481,485-505,518-538,551-567,570-585,589-605,618-637

2168 atoms, 2195 bonds, 270 residues, 1 model selected  

> select #3/A:1

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

> select #3/A:1-4

31 atoms, 30 bonds, 4 residues, 1 model selected  

> select #3/A:1

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

> select #3/A:1-11

87 atoms, 86 bonds, 11 residues, 1 model selected  
No model chosen to save relative to  

> save /Users/basem/Downloads/cas12k_new.cxs

> color sel #c6e0e1ff

> select #2/A:1

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

> select #2/A:1-11

87 atoms, 86 bonds, 11 residues, 1 model selected  

> color sel #c6e0e1ff

> select #2/A:93-94

20 atoms, 21 bonds, 2 residues, 1 model selected  

> select #2/A:12-94

698 atoms, 716 bonds, 83 residues, 1 model selected  

> color sel #0d9df4ff

> select #2/A:277

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

> select #2/A:277-280

27 atoms, 27 bonds, 4 residues, 1 model selected  

> select #2/A:277

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

> select #2/A:277-378

853 atoms, 875 bonds, 102 residues, 1 model selected  

> color sel #c6e0e1ff

> select #2/A:380-381

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

> select #2/A:380-443

517 atoms, 525 bonds, 64 residues, 1 model selected  

> color sel #662d90ff

> select #2/A:443-444

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

> select #2/A:444-484

306 atoms, 309 bonds, 41 residues, 1 model selected  

> color sel #fe2a4eff

> select #2/A:485

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

> select #2/A:485-506

199 atoms, 203 bonds, 22 residues, 1 model selected  

> select #2/A:485-506

199 atoms, 203 bonds, 22 residues, 1 model selected  

> select #2/A:484-485

20 atoms, 20 bonds, 2 residues, 1 model selected  

> select #2/A:485-508

215 atoms, 219 bonds, 24 residues, 1 model selected  

> color sel #63c7b2ff

> select #2/A:509

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

> select #2/A:509-510

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

> select #2/A:477-478

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

> select #2/A:477-484

64 atoms, 63 bonds, 8 residues, 1 model selected  

> color sel #63c7b2ff

> select #2/A:509-510

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

> select #2/A:509-640

1044 atoms, 1059 bonds, 132 residues, 1 model selected  

> color sel #fe2a4eff

> select #2/A:114

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

> select #2/A:114-268

1226 atoms, 1240 bonds, 155 residues, 1 model selected  

> select #2/A:118

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

> select #2/A:118-218

798 atoms, 805 bonds, 101 residues, 1 model selected  

> select #2/A:101-102

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

> select #2/A:101-273

1381 atoms, 1397 bonds, 173 residues, 1 model selected  

> select #2/A:101-273

1381 atoms, 1397 bonds, 173 residues, 1 model selected  

> select #2/A:276-277

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select #2/A:101-277

1415 atoms, 1431 bonds, 177 residues, 1 model selected  

> select #2/A:101-102

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

> select #2/A:101-281

1445 atoms, 1463 bonds, 181 residues, 1 model selected  

> select #2/A:282

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

> select #2/A:101-282

1452 atoms, 1471 bonds, 182 residues, 1 model selected  

> select #2/A:103-104

20 atoms, 19 bonds, 2 residues, 1 model selected  

> select #2/A:103-286

1470 atoms, 1490 bonds, 184 residues, 1 model selected  

> select #2/A:96-97

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

> select #2/A:97-281

1482 atoms, 1500 bonds, 185 residues, 1 model selected  

> select #2/A:95-96

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

> select #2/A:96-282

1494 atoms, 1513 bonds, 187 residues, 1 model selected  

> select #2/A:101

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

> select #2/A:101-282

1452 atoms, 1471 bonds, 182 residues, 1 model selected  

> select #2/A:95

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

> select #2/A:95-282

1502 atoms, 1521 bonds, 188 residues, 1 model selected  

> select #2/A:277

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

> select #2/A:228-277

393 atoms, 399 bonds, 50 residues, 1 model selected  

> select #2/A:278

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

> select #2/A:239-278

309 atoms, 314 bonds, 40 residues, 1 model selected  

> color sel #003162ff

> select #2/A:118

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

> select #2/A:118-119

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #2/A:166-216

405 atoms, 411 bonds, 51 residues, 1 model selected  

> select #2/A:115-216

800 atoms, 806 bonds, 102 residues, 1 model selected  

> select #2/A:63

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

> select #2/A:13-63

426 atoms, 436 bonds, 51 residues, 1 model selected  

> select #2/A:68

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

> select #2/A:68-119

446 atoms, 455 bonds, 52 residues, 1 model selected  

> select #2/A:425

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

> select #2/A:425-475

390 atoms, 399 bonds, 51 residues, 1 model selected  

> select #2/A:527

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

> select #2/A:527-577

395 atoms, 398 bonds, 51 residues, 1 model selected  

> select #2/A:475

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

> select #2/A:475-526

442 atoms, 449 bonds, 52 residues, 1 model selected  

> select #2/A:637

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

> select #2/A:431-637

1648 atoms, 1678 bonds, 207 residues, 1 model selected  

> select #2/A:377-427

406 atoms, 408 bonds, 51 residues, 1 model selected  

> select #2/A:276-427

1249 atoms, 1274 bonds, 152 residues, 1 model selected  

> select #2/A:276

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

> select #2/A:276-326

422 atoms, 434 bonds, 51 residues, 1 model selected  

> select #2/A:327

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

> select #2/A:327-428

838 atoms, 850 bonds, 102 residues, 1 model selected  

> select #2/A:378

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

> select #2/A:328-378

426 atoms, 435 bonds, 51 residues, 1 model selected  

> select #2/A:379

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

> select #2/A:379-428

401 atoms, 403 bonds, 50 residues, 1 model selected  

> color sel #662d90ff

> select
> #2/A:3-11,283-285,291-295,301-305,314-316,349-357,370-378,447-452,460-465,470-475,542-546,607-611

566 atoms, 564 bonds, 71 residues, 1 model selected  

> save /Users/basem/Downloads/cas12k_new.cxs

> mmaker #1 to #3

No chains in match structure example1 (27).pdb #1 compatible with BLOSUM-62
similarity matrix  

> mmaker #2 to #3

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 7n3o.pdb, chain A (#3) with
test_8289a_unrelaxed_rank_1_model_5.pdb, chain A (#2), sequence alignment
score = 2034.9  
RMSD between 296 pruned atom pairs is 1.177 angstroms; (across all 454 pairs:
2.689)  
  

> select #2

5184 atoms, 5276 bonds, 640 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.46796,0.67887,-0.56582,165.02,-0.83662,0.13401,-0.53114,162.77,-0.28475,0.72193,0.63066,115.42

> ~select #2

Nothing selected  

> select #2

5184 atoms, 5276 bonds, 640 residues, 1 model selected  

> view matrix models
> #2,0.46796,0.67887,-0.56582,174.82,-0.83662,0.13401,-0.53114,168.15,-0.28475,0.72193,0.63066,120.68

> ~select #2

Nothing selected  

> open
> /Users/basem/Downloads/tnsb_4a8de.result/tnsb_4a8de_unrelaxed_rank_1_model_3.pdb

Chain information for tnsb_4a8de_unrelaxed_rank_1_model_3.pdb #4  
---  
Chain | Description  
A | No description available  
  

> select #4

4607 atoms, 4692 bonds, 573 residues, 1 model selected  

> view matrix models #4,1,0,0,74.453,0,1,0,251.15,0,0,1,24.375

> preset cartoons/nucleotides cylinders/stubs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> ~select #4

Nothing selected  

> open /Users/basem/Downloads/7pik.pdb

7pik.pdb title:  
Cryo-em structure of E. Coli TNSB In complex with right end fragment of TN7
transposon [more info...]  
  
Chain information for 7pik.pdb #5  
---  
Chain | Description  
A B C D E | transposon TN7 transposition protein TNSB  
K | right end fragment of TN7 transposon  
L | right end fragment of TN7 transposon  
  

> select #5

15475 atoms, 16088 bonds, 10 pseudobonds, 1750 residues, 2 models selected  

> preset cartoons/nucleotides cylinders/stubs

Changed 15475 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> ~select #5

Nothing selected  

> mmaker #4 to #5

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 7pik.pdb, chain B (#5) with
tnsb_4a8de_unrelaxed_rank_1_model_3.pdb, chain A (#4), sequence alignment
score = 472.1  
RMSD between 90 pruned atom pairs is 1.158 angstroms; (across all 416 pairs:
33.634)  
  

> select #4

4607 atoms, 4692 bonds, 573 residues, 1 model selected  

> view matrix models
> #4,0.33324,-0.90569,-0.26206,274.64,0.20283,-0.20257,0.95803,139.93,-0.92077,-0.37241,0.1162,300.45

> view matrix models
> #4,0.33324,-0.90569,-0.26206,279.72,0.20283,-0.20257,0.95803,139.79,-0.92077,-0.37241,0.1162,299.25

> mmaker #4 to #5

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 7pik.pdb, chain B (#5) with
tnsb_4a8de_unrelaxed_rank_1_model_3.pdb, chain A (#4), sequence alignment
score = 472.1  
RMSD between 90 pruned atom pairs is 1.158 angstroms; (across all 416 pairs:
33.634)  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #4/A

Alignment identifier is 4/A  

> sequence chain #5/A

Alignment identifier is 5/A  

> sequence chain #5/B

Alignment identifier is 5/B  

> sequence chain #5/C

Alignment identifier is 5/C  

> sequence chain #5/D

Alignment identifier is 5/D  

> sequence chain #5/E

Alignment identifier is 5/E  

> sequence chain #5/K

Alignment identifier is 5/K  

> sequence chain #5/L

Alignment identifier is 5/L  

> select #4/A:1

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

> select #4/A:1-35

270 atoms, 271 bonds, 35 residues, 1 model selected  

> select #4/A:573

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select #4/A:547-573

231 atoms, 237 bonds, 27 residues, 1 model selected  

> select #4/A:518

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #4/A:488-518

262 atoms, 262 bonds, 31 residues, 1 model selected  

> select
> #4/A:34-47,52-66,70-88,103-116,125-139,147-167,243-254,261-263,289-298,308-328,337-339,344-347,352-367,380-386,398-403,431-433,478-491,497-513,517-534,564-571

1962 atoms, 1972 bonds, 240 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> open "/Users/basem/Downloads/tnsC_1e5a1.result
> (1)/tnsC_1e5a1_unrelaxed_rank_1_model_3.pdb"

Chain information for tnsC_1e5a1_unrelaxed_rank_1_model_3.pdb #6  
---  
Chain | Description  
A | No description available  
  

> select #6

2197 atoms, 2225 bonds, 276 residues, 1 model selected  

> view matrix models #6,1,0,0,27.961,0,1,0,3.8729,0,0,1,218.64

> open /Users/basem/Downloads/7m99.pdb

7m99.pdb title:  
Atpgs bound TNSC filament from shcast system [more info...]  
  
Chain information for 7m99.pdb #7  
---  
Chain | Description  
A B C D E F G H | TNSC  
I | DNA (5'- D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')  
J | DNA (5'- D(P*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*A)-3')  
  
Non-standard residues in 7m99.pdb #7  
---  
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate);adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)  
MG — magnesium ion  
  

> select #7

17531 atoms, 17879 bonds, 17 pseudobonds, 2108 residues, 2 models selected  

> view matrix models #7,1,0,0,-66.844,0,1,0,-134.97,0,0,1,109.62

> view matrix models #7,1,0,0,-65.03,0,1,0,-142.35,0,0,1,120.81

> preset cartoons/nucleotides cylinders/stubs

Changed 17307 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> select #6

2197 atoms, 2225 bonds, 276 residues, 1 model selected  

> mmaker #6 to #7

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 7m99.pdb, chain H (#7) with
tnsC_1e5a1_unrelaxed_rank_1_model_3.pdb, chain A (#6), sequence alignment
score = 1045.7  
RMSD between 248 pruned atom pairs is 1.044 angstroms; (across all 257 pairs:
1.179)  
  

> view matrix models
> #6,-0.14605,0.61561,-0.7744,71.686,0.41902,-0.67061,-0.61213,85.714,-0.89615,-0.41389,-0.16002,361.38

> open /Users/basem/Downloads/7m99.pdb

7m99.pdb title:  
Atpgs bound TNSC filament from shcast system [more info...]  
  
Chain information for 7m99.pdb #8  
---  
Chain | Description  
A B C D E F G H | TNSC  
I | DNA (5'- D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')  
J | DNA (5'- D(P*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*A)-3')  
  
Non-standard residues in 7m99.pdb #8  
---  
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate);adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)  
MG — magnesium ion  
  

> preset cartoons/nucleotides cylinders/stubs

Changed 17307 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> select #8

17531 atoms, 17879 bonds, 17 pseudobonds, 2108 residues, 2 models selected  

> view matrix models #8,1,0,0,-62.092,0,1,0,-245.29,0,0,1,155.13

> view matrix models #8,1,0,0,-67.171,0,1,0,-265.49,0,0,1,170.62

> delete #7A

Missing or invalid "atoms" argument: invalid atoms specifier  

> mmaker #6 to #7

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 7m99.pdb, chain H (#7) with
tnsC_1e5a1_unrelaxed_rank_1_model_3.pdb, chain A (#6), sequence alignment
score = 1045.7  
RMSD between 248 pruned atom pairs is 1.044 angstroms; (across all 257 pairs:
1.179)  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #7/A

Alignment identifier is 7/A  

> sequence chain #7/B

Alignment identifier is 7/B  

> sequence chain #7/C

Alignment identifier is 7/C  

> sequence chain #7/D

Alignment identifier is 7/D  

> sequence chain #7/E

Alignment identifier is 7/E  

> sequence chain #7/F

Alignment identifier is 7/F  

> sequence chain #7/G

Alignment identifier is 7/G  

> sequence chain #7/H

Alignment identifier is 7/H  

> select
> #7/A:19-29,36-53,65-77,101-113,121-134,150-164,174-181,183-190,201-215,226-238,240-257,264-273

1287 atoms, 1294 bonds, 156 residues, 1 model selected  

> open "/Users/basem/Downloads/tnsC_1e5a1.result
> (1)/tnsC_1e5a1_unrelaxed_rank_1_model_3.pdb"

Chain information for tnsC_1e5a1_unrelaxed_rank_1_model_3.pdb #9  
---  
Chain | Description  
A | No description available  
  

> open "/Users/basem/Downloads/tnsC_1e5a1.result
> (1)/tnsC_1e5a1_unrelaxed_rank_1_model_3.pdb"

Chain information for tnsC_1e5a1_unrelaxed_rank_1_model_3.pdb #10  
---  
Chain | Description  
A | No description available  
  

> open "/Users/basem/Downloads/tnsC_1e5a1.result
> (1)/tnsC_1e5a1_unrelaxed_rank_1_model_3.pdb"

Chain information for tnsC_1e5a1_unrelaxed_rank_1_model_3.pdb #11  
---  
Chain | Description  
A | No description available  
  

> mmaker #6 to #7/A

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 7m99.pdb, chain A (#7) with
tnsC_1e5a1_unrelaxed_rank_1_model_3.pdb, chain A (#6), sequence alignment
score = 1033.1  
RMSD between 251 pruned atom pairs is 1.056 angstroms; (across all 257 pairs:
1.138)  
  

> mmaker #9 to #7/B

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 7m99.pdb, chain B (#7) with
tnsC_1e5a1_unrelaxed_rank_1_model_3.pdb, chain A (#9), sequence alignment
score = 1034.9  
RMSD between 245 pruned atom pairs is 1.044 angstroms; (across all 257 pairs:
1.162)  
  

> mmaker #10 to #7/C

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 7m99.pdb, chain C (#7) with
tnsC_1e5a1_unrelaxed_rank_1_model_3.pdb, chain A (#10), sequence alignment
score = 1036.7  
RMSD between 250 pruned atom pairs is 1.068 angstroms; (across all 257 pairs:
1.134)  
  

> mmaker #11 to #7/D

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 7m99.pdb, chain D (#7) with
tnsC_1e5a1_unrelaxed_rank_1_model_3.pdb, chain A (#11), sequence alignment
score = 1042.1  
RMSD between 248 pruned atom pairs is 1.047 angstroms; (across all 257 pairs:
1.130)  
  

> open "/Users/basem/Downloads/tnsC_1e5a1.result
> (1)/tnsC_1e5a1_unrelaxed_rank_1_model_3.pdb"

Chain information for tnsC_1e5a1_unrelaxed_rank_1_model_3.pdb #12  
---  
Chain | Description  
A | No description available  
  

> mmaker #12 to #7/E

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 7m99.pdb, chain E (#7) with
tnsC_1e5a1_unrelaxed_rank_1_model_3.pdb, chain A (#12), sequence alignment
score = 1039.7  
RMSD between 250 pruned atom pairs is 1.061 angstroms; (across all 257 pairs:
1.139)  
  

> delete #8

> open "/Users/basem/Downloads/tnsC_1e5a1.result
> (1)/tnsC_1e5a1_unrelaxed_rank_1_model_3.pdb"

Chain information for tnsC_1e5a1_unrelaxed_rank_1_model_3.pdb #8  
---  
Chain | Description  
A | No description available  
  

> mmaker #13 to #7/F

No molecules/chains to match specified  

> mmaker #13 to #7/F

No molecules/chains to match specified  

> open "/Users/basem/Downloads/tnsC_1e5a1.result
> (1)/tnsC_1e5a1_unrelaxed_rank_1_model_3.pdb"

Chain information for tnsC_1e5a1_unrelaxed_rank_1_model_3.pdb #13  
---  
Chain | Description  
A | No description available  
  

> mmaker #13 to #7/F

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 7m99.pdb, chain F (#7) with
tnsC_1e5a1_unrelaxed_rank_1_model_3.pdb, chain A (#13), sequence alignment
score = 1038.5  
RMSD between 252 pruned atom pairs is 1.073 angstroms; (across all 257 pairs:
1.132)  
  

> open "/Users/basem/Downloads/tnsC_1e5a1.result
> (1)/tnsC_1e5a1_unrelaxed_rank_1_model_3.pdb"

Chain information for tnsC_1e5a1_unrelaxed_rank_1_model_3.pdb #14  
---  
Chain | Description  
A | No description available  
  

> open "/Users/basem/Downloads/tnsC_1e5a1.result
> (1)/tnsC_1e5a1_unrelaxed_rank_1_model_3.pdb"

Chain information for tnsC_1e5a1_unrelaxed_rank_1_model_3.pdb #15  
---  
Chain | Description  
A | No description available  
  

> mmaker #14 to #7/G

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7m99.pdb, chain G (#7) with
tnsC_1e5a1_unrelaxed_rank_1_model_3.pdb, chain A (#14), sequence alignment
score = 1036.1  
RMSD between 250 pruned atom pairs is 1.063 angstroms; (across all 257 pairs:
1.142)  
  

> mmaker #15 to #7/H

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 7m99.pdb, chain H (#7) with
tnsC_1e5a1_unrelaxed_rank_1_model_3.pdb, chain A (#15), sequence alignment
score = 1045.7  
RMSD between 248 pruned atom pairs is 1.044 angstroms; (across all 257 pairs:
1.179)  
  

> hide #!7 models

> view matrix models #7,1,0,0,-86.452,0,1,0,-151.12,0,0,1,149.13

> preset cartoons/nucleotides cylinders/stubs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> view matrix models #7,1,0,0,-98.186,0,1,0,-154.83,0,0,1,140.66

> view matrix models #7,1,0,0,-98.325,0,1,0,-154.46,0,0,1,140.15

> select #15

2197 atoms, 2225 bonds, 276 residues, 1 model selected  

> ~select #15

Nothing selected  

> select #14

2197 atoms, 2225 bonds, 276 residues, 1 model selected  

> ~select #14

Nothing selected  

> select #13

2197 atoms, 2225 bonds, 276 residues, 1 model selected  

> ~select #13

Nothing selected  

> select #12

2197 atoms, 2225 bonds, 276 residues, 1 model selected  

> ~select #12

Nothing selected  

> select #11

2197 atoms, 2225 bonds, 276 residues, 1 model selected  

> ~select #11

Nothing selected  

> select #10

2197 atoms, 2225 bonds, 276 residues, 1 model selected  

> ~select #10

Nothing selected  

> select #9

2197 atoms, 2225 bonds, 276 residues, 1 model selected  

> ~select #9

Nothing selected  

> select #8

2197 atoms, 2225 bonds, 276 residues, 1 model selected  

> delete #8

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> select #7

17531 atoms, 17879 bonds, 17 pseudobonds, 2108 residues, 2 models selected  

> view matrix models #7,1,0,0,-54.264,0,1,0,-150.13,0,0,1,244.38

> hide #!7 models

> ~select #7

Nothing selected  

> select #5

15475 atoms, 16088 bonds, 10 pseudobonds, 1750 residues, 2 models selected  

> ~select #5

Nothing selected  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2149, in <lambda>  
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 626, in close_request  
tool_instance.delete()  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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.  
  

> save /Users/basem/Downloads/cas12k_new.cxs

Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 695, in take_snapshot  
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 96, in take_snapshot  
data['shown'] = self.tool_window.shown  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1983, in shown  
return self.__toolkit.shown  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2267, in shown  
return not self.dock_widget.isHidden()  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fd1902f1bb0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fd18183d2b0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save  
mgr.discovery(self._state_containers)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fd1902f1bb0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7fd18183d2b0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fd1902f1bb0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fd18183d2b0>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 695, in take_snapshot  
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 96, in take_snapshot  
data['shown'] = self.tool_window.shown  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1983, in shown  
return self.__toolkit.shown  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2267, in shown  
return not self.dock_widget.isHidden()  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fd1902f1bb0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fd18183d2b0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save  
mgr.discovery(self._state_containers)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fd1902f1bb0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7fd18183d2b0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fd1902f1bb0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fd18183d2b0>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> select #4

4607 atoms, 4692 bonds, 573 residues, 1 model selected  

> view matrix models
> #4,0.33324,-0.90569,-0.26206,325.73,0.20283,-0.20257,0.95803,188.9,-0.92077,-0.37241,0.1162,299.43

> ~select #4

Nothing selected  

> select #5

15475 atoms, 16088 bonds, 10 pseudobonds, 1750 residues, 2 models selected  

> ~select #5

Nothing selected  

> select #3

8295 atoms, 8922 bonds, 7 pseudobonds, 676 residues, 2 models selected  

> ~select #3

Nothing selected  

Back buffer dpr of 1 doesn't match <_NSViewBackingLayer: 0x60001a65c450>
contents scale of 2 - updating layer to match.  

Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x60001a65c450>
contents scale of 1 - updating layer to match.  

> select #3

8295 atoms, 8922 bonds, 7 pseudobonds, 676 residues, 2 models selected  

> ~select #3

Nothing selected  
Alignment identifier is 1/A  
Destroying pre-existing alignment with identifier 2/A  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/toolbar/tool.py", line 202, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/toolshed/info.py", line 379, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/toolshed/__init__.py", line 1285, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 1333, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 389, in try_shortcut  
self.run_shortcut(keys)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 407, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 309, in run  
f(shortcut_atoms(s))  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 1045, in show_sequence  
run(session, 'sequence chain %s' % seq_chain_spec, log = False)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 511, in run  
run_command(session, command, **kw)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/cmd.py", line 140, in seqalign_chain  
alignment = session.alignments.new_alignment([chain], ident, seq_viewer="sv",  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/manager.py", line 214, in new_alignment  
self.destroy_alignment(self._alignments[identify_as])  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/manager.py", line 108, in destroy_alignment  
alignment._destroy()  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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.  
  

> show #1-2,4,6,9-15#!3,5 surfaces

> hide #!1-6,9-15 surfaces

> open
> /Users/basem/Downloads/tniQ_6ef23.result/tniQ_6ef23_unrelaxed_rank_1_model_5.pdb

Chain information for tniQ_6ef23_unrelaxed_rank_1_model_5.pdb #8  
---  
Chain | Description  
A | No description available  
  

> select #8

1358 atoms, 1397 bonds, 171 residues, 1 model selected  

> view matrix models #8,1,0,0,67.925,0,1,0,74.37,0,0,1,5.2115

> preset cartoons/nucleotides cylinders/stubs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> view matrix models #8,1,0,0,160.54,0,1,0,175.99,0,0,1,-5.1188

> view matrix models #8,1,0,0,167.48,0,1,0,165.05,0,0,1,-14.47

> view matrix models #8,1,0,0,166.53,0,1,0,181.45,0,0,1,53.769

> ~select #8

Nothing selected  

> select #8

1358 atoms, 1397 bonds, 171 residues, 1 model selected  

> show sel surfaces

> color (#!8 & sel) #ff9e18ff

> ~select #8

1 model selected  

> select #8

1358 atoms, 1397 bonds, 171 residues, 1 model selected  

> hide sel surfaces

> ~select #8

1 model selected  

> select #8

1358 atoms, 1397 bonds, 171 residues, 1 model selected  

> view matrix models #8,1,0,0,102.53,0,1,0,89.346,0,0,1,211.52

> open /Users/basem/Downloads/7n6i.pdb

7n6i.pdb title:  
ATP-bound TNSC-tniq complex from shcast system [more info...]  
  
Chain information for 7n6i.pdb #16  
---  
Chain | Description  
A B | tniq (homology model)  
C D E F G H I J | TNSC  
K | DNA (5'- D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')  
L | DNA (5'- D(P*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*A)-3')  
  
Non-standard residues in 7n6i.pdb #16  
---  
ATP — adenosine-5'-triphosphate  
MG — magnesium ion  
  

> preset cartoons/nucleotides cylinders/stubs

Changed 18715 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> select #16

18939 atoms, 19275 bonds, 22 pseudobonds, 2406 residues, 2 models selected  

> mmaker #16 to #9

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 tnsC_1e5a1_unrelaxed_rank_1_model_3.pdb, chain A (#9) with
7n6i.pdb, chain J (#16), sequence alignment score = 1045.7  
RMSD between 248 pruned atom pairs is 1.044 angstroms; (across all 257 pairs:
1.179)  
  

> ~select #16

Nothing selected  

> select #16

18939 atoms, 19275 bonds, 22 pseudobonds, 2406 residues, 2 models selected  

> view matrix models
> #16,-0.87697,-0.44629,-0.17816,419.28,-0.43786,0.89488,-0.086354,0.57744,0.19797,0.0022801,-0.9802,443.37

> view matrix models
> #16,-0.87697,-0.44629,-0.17816,428.84,-0.43786,0.89488,-0.086354,5.9908,0.19797,0.0022801,-0.9802,465.48

> view matrix models
> #16,-0.87697,-0.44629,-0.17816,415.53,-0.43786,0.89488,-0.086354,-0.45018,0.19797,0.0022801,-0.9802,505.21

> mmaker #8 to #16

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 7n6i.pdb, chain A (#16) with
tniQ_6ef23_unrelaxed_rank_1_model_5.pdb, chain A (#8), sequence alignment
score = 560  
RMSD between 65 pruned atom pairs is 1.120 angstroms; (across all 151 pairs:
4.919)  
  

> ~select #16

Nothing selected  

> select #8

1358 atoms, 1397 bonds, 171 residues, 1 model selected  

> view matrix models
> #8,-0.87305,-0.28058,0.39882,151.47,0.43212,-0.066183,0.89938,-28.788,-0.22596,0.95755,0.17903,334.31

> view matrix models
> #8,-0.87305,-0.28058,0.39882,149.48,0.43212,-0.066183,0.89938,6.2246,-0.22596,0.95755,0.17903,326.18

> view matrix models
> #8,-0.87305,-0.28058,0.39882,122.04,0.43212,-0.066183,0.89938,-16.583,-0.22596,0.95755,0.17903,315.78

> view matrix models
> #8,-0.87305,-0.28058,0.39882,123.81,0.43212,-0.066183,0.89938,3.6825,-0.22596,0.95755,0.17903,317.68

> view matrix models
> #8,-0.87305,-0.28058,0.39882,120.92,0.43212,-0.066183,0.89938,-0.29009,-0.22596,0.95755,0.17903,317.12

> view matrix models
> #8,-0.87305,-0.28058,0.39882,119.89,0.43212,-0.066183,0.89938,6.9222,-0.22596,0.95755,0.17903,317.48

> view matrix models
> #8,-0.87305,-0.28058,0.39882,117.87,0.43212,-0.066183,0.89938,7.0309,-0.22596,0.95755,0.17903,317.34

> hide #!16 models

> select #5

15475 atoms, 16088 bonds, 10 pseudobonds, 1750 residues, 2 models selected  

> ~select #5

7 models selected  

> select #3

8295 atoms, 8922 bonds, 7 pseudobonds, 676 residues, 2 models selected  

> ~select #3

2 models selected  

> open /Users/basem/Downloads/7pla.cif.gz

File reader requires uncompressed file; '/Users/basem/Downloads/7pla.cif.gz'
is compressed  

> open /Users/basem/Downloads/7pla.cif

Summary of feedback from opening /Users/basem/Downloads/7pla.cif  
---  
warning | Atom OP1 has no neighbors to form bonds with according to residue
template for DT /D:11  
  
7pla.cif title:  
Cryo-EM structure of ShCas12k in complex with a sgRNA and a dsDNA target [more
info...]  
  
Chain information for 7pla.cif #17  
---  
Chain | Description  
A | ShCas12k  
B | sgRNA  
C | DNA target strand  
D | DNA non-target strand  
  

> lighting flat

> lighting soft

> select #17

8701 atoms, 9374 bonds, 257 pseudobonds, 681 residues, 3 models selected  

> mmaker #17 to #1

No chains in reference structure example1 (27).pdb #1 compatible with
BLOSUM-62 similarity matrix  

> mmaker #17 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker test_8289a_unrelaxed_rank_1_model_5.pdb, chain A (#2) with
7pla.cif, chain A (#17), sequence alignment score = 2007.2  
RMSD between 239 pruned atom pairs is 1.083 angstroms; (across all 436 pairs:
3.051)  
  

> view matrix models
> #17,-0.72022,0.69238,-0.04341,163.24,-0.65556,-0.69973,-0.28394,317.13,-0.22697,-0.17604,0.95786,-23.49

> preset cartoons/nucleotides cylinders/stubs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> mmaker #1 to #17

No chains in match structure example1 (27).pdb #1 compatible with BLOSUM-62
similarity matrix  

> save /Users/basem/Downloads/cas12k_new_docked.cxs

Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 695, in take_snapshot  
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 96, in take_snapshot  
data['shown'] = self.tool_window.shown  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1983, in shown  
return self.__toolkit.shown  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2267, in shown  
return not self.dock_widget.isHidden()  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fd1902f1bb0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fd18183d2b0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save  
mgr.discovery(self._state_containers)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fd1902f1bb0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7fd18183d2b0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fd1902f1bb0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fd18183d2b0>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 695, in take_snapshot  
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 96, in take_snapshot  
data['shown'] = self.tool_window.shown  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1983, in shown  
return self.__toolkit.shown  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2267, in shown  
return not self.dock_widget.isHidden()  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fd1902f1bb0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fd18183d2b0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save  
mgr.discovery(self._state_containers)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fd1902f1bb0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7fd18183d2b0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fd1902f1bb0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fd18183d2b0>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save /Users/basem/Downloads/cas12k_new.cxs

Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 695, in take_snapshot  
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 96, in take_snapshot  
data['shown'] = self.tool_window.shown  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1983, in shown  
return self.__toolkit.shown  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2267, in shown  
return not self.dock_widget.isHidden()  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fd1902f1bb0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fd18183d2b0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save  
mgr.discovery(self._state_containers)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fd1902f1bb0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7fd18183d2b0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fd1902f1bb0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fd18183d2b0>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 695, in take_snapshot  
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 96, in take_snapshot  
data['shown'] = self.tool_window.shown  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1983, in shown  
return self.__toolkit.shown  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2267, in shown  
return not self.dock_widget.isHidden()  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fd1902f1bb0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fd18183d2b0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save  
mgr.discovery(self._state_containers)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fd1902f1bb0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7fd18183d2b0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fd1902f1bb0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fd18183d2b0>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> select #1

6886 atoms, 7425 bonds, 215 residues, 1 model selected  

> ~select #1

1 model selected  

> mmaker #1 to #18

No 'to' model specified  

> mmaker #1 to #17

No chains in match structure example1 (27).pdb #1 compatible with BLOSUM-62
similarity matrix  

> select #1

6886 atoms, 7425 bonds, 215 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.97989,0.044394,-0.19456,14.792,0.037493,0.91663,0.39798,-1.6687,0.19601,-0.39727,0.89652,38.258

> view matrix models
> #1,0.69616,0.66027,-0.28178,29.171,0.1466,0.25349,0.95617,-2.712,0.70276,-0.70695,0.079675,4.2805

> view matrix models
> #1,0.41593,0.90111,0.12248,48.389,0.46725,-0.32731,0.82131,-22.919,0.78018,-0.28438,-0.55718,-3.8704

> view matrix models
> #1,-0.44932,0.89158,-0.05653,44.01,0.6439,0.36707,0.67131,-8.9728,0.61927,0.26523,-0.73902,5.6857

> view matrix models
> #1,-0.53572,0.83352,0.13509,48.432,0.52764,0.20554,0.82422,-8.4581,0.65924,0.51283,-0.54991,18.028

> view matrix models
> #1,-0.4647,0.8853,-0.017331,45.046,0.62163,0.34011,0.70563,-8.6411,0.63059,0.31713,-0.70837,8.0193

Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2149, in <lambda>  
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 626, in close_request  
tool_instance.delete()  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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.  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2149, in <lambda>  
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 626, in close_request  
tool_instance.delete()  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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.  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2149, in <lambda>  
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 626, in close_request  
tool_instance.delete()  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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.  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2149, in <lambda>  
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 626, in close_request  
tool_instance.delete()  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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.  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2149, in <lambda>  
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 626, in close_request  
tool_instance.delete()  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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.  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2149, in <lambda>  
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 626, in close_request  
tool_instance.delete()  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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.  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2149, in <lambda>  
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 626, in close_request  
tool_instance.delete()  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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.  
  

> save /Users/basem/Downloads/cas12k.cxs

Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 695, in take_snapshot  
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 96, in take_snapshot  
data['shown'] = self.tool_window.shown  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1983, in shown  
return self.__toolkit.shown  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2267, in shown  
return not self.dock_widget.isHidden()  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fd1902f1bb0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fd1a7938f70>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save  
mgr.discovery(self._state_containers)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fd1902f1bb0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7fd1a7938f70>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fd1902f1bb0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fd1a7938f70>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 695, in take_snapshot  
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 96, in take_snapshot  
data['shown'] = self.tool_window.shown  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1983, in shown  
return self.__toolkit.shown  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2267, in shown  
return not self.dock_widget.isHidden()  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fd1902f1bb0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fd1a7938f70>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save  
mgr.discovery(self._state_containers)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fd1902f1bb0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7fd1a7938f70>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fd1902f1bb0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fd1a7938f70>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #3/B

Alignment identifier is 3/B  

> select #1/A:1

31 atoms, 33 bonds, 1 residue, 1 model selected  

> select #1/A:1-215

6886 atoms, 7425 bonds, 215 residues, 1 model selected  

> select #1/A:1

31 atoms, 33 bonds, 1 residue, 1 model selected  

> select #1/A:1-35

1105 atoms, 1188 bonds, 35 residues, 1 model selected  

> select #1/A:1

31 atoms, 33 bonds, 1 residue, 1 model selected  

> select #1/A:1-215

6886 atoms, 7425 bonds, 215 residues, 1 model selected  

> select #3/B:9-238

4734 atoms, 5289 bonds, 4 pseudobonds, 222 residues, 2 models selected  

> select #3/B:9-238

4734 atoms, 5289 bonds, 4 pseudobonds, 222 residues, 2 models selected  

> select #3/B:9-238

4734 atoms, 5289 bonds, 4 pseudobonds, 222 residues, 2 models selected  

> save /Users/basem/Downloads/cas12k_new.cxs

Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 695, in take_snapshot  
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 96, in take_snapshot  
data['shown'] = self.tool_window.shown  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1983, in shown  
return self.__toolkit.shown  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2267, in shown  
return not self.dock_widget.isHidden()  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fd1902f1bb0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fd1a7938f70>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save  
mgr.discovery(self._state_containers)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fd1902f1bb0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7fd1a7938f70>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fd1902f1bb0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fd1a7938f70>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 695, in take_snapshot  
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 96, in take_snapshot  
data['shown'] = self.tool_window.shown  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1983, in shown  
return self.__toolkit.shown  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2267, in shown  
return not self.dock_widget.isHidden()  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fd1902f1bb0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fd1a7938f70>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save  
mgr.discovery(self._state_containers)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fd1902f1bb0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7fd1a7938f70>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fd1902f1bb0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fd1a7938f70>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2149, in <lambda>  
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 626, in close_request  
tool_instance.delete()  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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.  
  
Traceback (most recent call last):  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2149, in <lambda>  
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 626, in close_request  
tool_instance.delete()  
File
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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
"/private/var/folders/b0/__qqps0906l6tk06_5dwljh00000gn/T/AppTranslocation/F295A98C-FF4B-47AF-
BA8D-78A5E8A64E83/d/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.  
  




OpenGL version: 4.1 ATI-3.5.5
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 64 GB
      Boot ROM Version: 1037.80.53.0.0 (iBridge: 17.16.13050.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.3 (19D76)
      Kernel Version: Darwin 19.3.0
      Time since boot: 4 days 14:41

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-019
      Option ROM Version: 113-D32206U1-019
      EFI Driver Version: 01.01.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        LG HDR WQHD:
          Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
          UI Looks like: 3440 x 1440 @ 60 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: DisplayPort

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-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-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

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component:	Unassigned → UI
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Save dead dock widget shown state in session

comment:2 by Eric Pettersen, 3 years ago

Resolution:	→ can't reproduce
Status:	accepted → closed

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