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Opened 3 years ago
Closed 3 years ago
#7355 closed defect (can't reproduce)
Save dead dock widget shown state in session
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| 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 , 3 years ago
| Component: | Unassigned → UI |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Save dead dock widget shown state in session |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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