id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
20134	Crash on Mac waking from sleep	bhogeba@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-26.3.1-arm64-arm-64bit
ChimeraX Version: 1.10rc202506100450 (2025-06-10 04:50:02 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault

Current thread 0x0000000206eff100 (most recent call first):
  File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 368 in event_loop
  File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1057 in init
  File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1220 in 
  File """", line 88 in _run_code
  File """", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, psutil._psutil_osx, psutil._psutil_posix, chimerax.surface._surface, chimerax.map._map, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.graphics._graphics, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 61)


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===== Log before crash start =====
UCSF ChimeraX version: 1.10rc202506100450 (2025-06-10)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open ""/Users/bhogeba/T4_dimeric
> tRNA/Ecoli_M1RNP/3'UAA_T4_tRNA/M1_Holo_T4dimer_ternary/Intermediates_and
> active conformer_publication.cxs""

Opened cryosparc_P23_J2582_006_volume_map.mrc as #2, grid size 456,456,456,
pixel 0.909, shown at level 0.103, step 2, values float32  
Opened cryosparc_P23_J2372_006_volume_map.mrc as #3, grid size 456,456,456,
pixel 0.909, shown at level 0.139, step 2, values float32  
Opened Productive_Ser_5mM_Ca_HoloM1_J1524_map_1.mrc as #6, grid size
384,384,384, pixel 0.999, shown at level 0.0712, step 2, values float32  

> view name session-start

opened ChimeraX session  

> show #!7 models

> select #1/A

8068 atoms, 9036 bonds, 375 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #5#!7 to #1 & sel

Using Nucleic matrix instead of BLOSUM-62 for matching  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
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 Int_2_5mM_Mg_3UAA_Ser_J2582-coot-1.pdb, chain A (#1) with
Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb, chain A (#5), sequence alignment score
= 1496  
RMSD between 156 pruned atom pairs is 1.086 angstroms; (across all 374 pairs:
3.812)  
  
Matchmaker Int_2_5mM_Mg_3UAA_Ser_J2582-coot-1.pdb, chain A (#1) with
Int_1_5mM_Mg_UAA_J2372_1-coot-1_real_space_refined_001.pdb, chain A (#7),
sequence alignment score = 1491.1  
RMSD between 208 pruned atom pairs is 0.979 angstroms; (across all 374 pairs:
3.576)  
  

> matchmaker #5#!7 to #1 & sel

Using Nucleic matrix instead of BLOSUM-62 for matching  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
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 Int_2_5mM_Mg_3UAA_Ser_J2582-coot-1.pdb, chain A (#1) with
Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb, chain A (#5), sequence alignment score
= 1496  
RMSD between 156 pruned atom pairs is 1.086 angstroms; (across all 374 pairs:
3.812)  
  
Matchmaker Int_2_5mM_Mg_3UAA_Ser_J2582-coot-1.pdb, chain A (#1) with
Int_1_5mM_Mg_UAA_J2372_1-coot-1_real_space_refined_001.pdb, chain A (#7),
sequence alignment score = 1491.1  
RMSD between 208 pruned atom pairs is 0.979 angstroms; (across all 374 pairs:
3.576)  
  

> select clear

Drag select of 394 atoms, 698 residues, 412 bonds  

> hide sel atoms

> select clear

Drag select of 238 atoms, 708 residues, 250 bonds  

> hide sel atoms

> select clear

> hide #!7 models

Drag select of 120 atoms, 200 residues, 125 bonds  

> hide sel atoms

> select clear

> select add #1/C:0

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

> select add #1/C:-1

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select add #1/C:-2

62 atoms, 66 bonds, 3 residues, 1 model selected  

> hide sel atoms

> select add #1/A:333

84 atoms, 90 bonds, 4 residues, 1 model selected  

> select add #1/C:76

104 atoms, 111 bonds, 5 residues, 1 model selected  

> select add #1/C:75

124 atoms, 132 bonds, 6 residues, 1 model selected  

> hide sel atoms

> select add #1/A:254

146 atoms, 156 bonds, 7 residues, 1 model selected  

> hide sel atoms

> select add #1/A:332

169 atoms, 181 bonds, 8 residues, 1 model selected  

> hide sel atoms

Drag select of 31 atoms, 150 residues, 28 bonds  

> ~label sel residues

> select clear

> select add #1/C:-1

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

> select add #1/C:-2

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select add #1/C:0

62 atoms, 66 bonds, 3 residues, 1 model selected  

> select add #1/C:75

82 atoms, 87 bonds, 4 residues, 1 model selected  

> select add #1/A:295

104 atoms, 111 bonds, 5 residues, 1 model selected  

> select add #1/C:76

124 atoms, 132 bonds, 6 residues, 1 model selected  

> select add #1/A:296

147 atoms, 157 bonds, 7 residues, 1 model selected  

> select add #1/A:332

170 atoms, 182 bonds, 8 residues, 1 model selected  

> ~label sel residues

> select add #1/C:77

193 atoms, 207 bonds, 9 residues, 1 model selected  

> select clear

> select #1/C:77

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #1/C:76

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

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> hide sel atoms

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> show sel atoms

> hide sel atoms

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> select clear

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 23 atom styles  

> select clear

> select add #1/A:68

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #1/A:67

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select add #1/A:69

65 atoms, 70 bonds, 3 residues, 1 model selected  

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> select add #1/C:77@O3'

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

> select up

88 atoms, 97 bonds, 4 residues, 1 model selected  

> select up

90 atoms, 99 bonds, 5 residues, 1 model selected  

> select up

108 atoms, 119 bonds, 5 residues, 1 model selected  

> select add #1/A:352

130 atoms, 143 bonds, 6 residues, 1 model selected  

> select add #1/A:351

152 atoms, 167 bonds, 7 residues, 1 model selected  

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> hide sel atoms

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> color sel byhetero

> show (sel-residues & sidechain) target ab

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> hide sel atoms

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 152 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 152 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 152 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 152 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 152 atom styles  

> nucleotides sel tube/slab shape box

> nucleotides sel ladder

> label sel text ""{0.name} {0.number}{0.insertion_code}""

> select Mg

26 atoms, 26 residues, 2 models selected  

> show (#!1 & sel) target ab

> select clear

> select add #1/D:14@MG

1 atom, 1 residue, 1 model selected  

> select add #1/C:77@OP2

2 atoms, 2 residues, 1 model selected  

> ui tool show Distances

> distance #1/D:14@MG #1/C:77@OP2

Distance between Int_2_5mM_Mg_3UAA_Ser_J2582-coot-1.pdb #1/D MG 14 MG and /C G
77 OP2: 11.76Å  

> select clear

> select #1/D:14@MG

1 atom, 1 residue, 1 model selected  

> color sel red

> color sel blue

> color sel cyan

> color sel orange

> color sel light sea green

> color sel forest green

> ui tool show ""Color Actions""

> color sel magenta

> select clear

> hide #!1 models

> show #!1 models

> show #!7 models

> hide #!1 models

> hide #!4 models

> hide #4.1 models

> show #!4 models

> show #4.1 models

> select add #7/A:248

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

> select clear

> select add #7/A:248

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

> select add #7/A:254

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

> select add #7/A:295

66 atoms, 72 bonds, 3 residues, 1 model selected  

> select add #7/C:76

86 atoms, 93 bonds, 4 residues, 1 model selected  
Drag select of 2 atoms, 5 residues, 2 bonds  

> select clear

Drag select of 115 atoms, 198 residues, 122 bonds  

> hide sel atoms

> ~label sel residues

> select #7/A:339

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

> select clear

> select add #7/A:248

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

> select add #7/C:165

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

> select add #7/C:166

66 atoms, 72 bonds, 3 residues, 1 model selected  

> select add #7/A:253

86 atoms, 93 bonds, 4 residues, 1 model selected  

> select subtract #7/A:253

66 atoms, 72 bonds, 3 residues, 1 model selected  

> select add #7/A:333

88 atoms, 96 bonds, 4 residues, 1 model selected  

> select add #7/A:332

111 atoms, 121 bonds, 5 residues, 1 model selected  

> hide sel atoms

> select add #7/B:17

122 atoms, 132 bonds, 6 residues, 1 model selected  

> select add #7/B:86

133 atoms, 142 bonds, 7 residues, 1 model selected  

> select add #7/B:26

144 atoms, 152 bonds, 8 residues, 1 model selected  

> select add #7/B:25

152 atoms, 159 bonds, 9 residues, 1 model selected  

> select add #7/B:13

163 atoms, 170 bonds, 10 residues, 1 model selected  

> hide sel atoms

> select clear

> show #!1 models

> hide #!1 models

> select clear

> select Mg

26 atoms, 26 residues, 2 models selected  

> show (#!7 & sel) target ab

> select clear

> select #7/D:14@MG

1 atom, 1 residue, 1 model selected  

> color sel magenta

> select clear

> select add #7/C:76

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

> select add #7/C:77

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

> select add #7/A:68

66 atoms, 71 bonds, 3 residues, 1 model selected  

> select add #7/A:67

88 atoms, 95 bonds, 4 residues, 1 model selected  

> select add #7/A:69

108 atoms, 116 bonds, 5 residues, 1 model selected  

> select add #7/A:352

130 atoms, 140 bonds, 6 residues, 1 model selected  

> select add #7/A:351

152 atoms, 164 bonds, 7 residues, 1 model selected  

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> show #!1 models

> hide #!1 models

> color sel byhetero

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> transparency #7/a 80 rings

> transparency #7/a 0 rings

> transparency #7/b 0 rings

> transparency #7/c 0 rings

> show #!1 models

> hide #!1 models

> label sel text ""{0.name} {0.number}{0.insertion_code}""

> show #!1 models

> hide #!1 models

> show #5 models

> hide #!7 models

> select add #7

12689 atoms, 14097 bonds, 670 residues, 2 models selected  

> transparency #7/c 80 ribbons

> transparency #5/c 80 ribbons

> transparency #5/a 80 ribbons

> transparency #5/b 80 ribbons

> hide #5 atoms

> select clear

> select Ca

5 atoms, 5 residues, 1 model selected  

> show sel target ab

> select clear

> select #5/F:5@CA

1 atom, 1 residue, 1 model selected  

> select add #5/A:68

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

> select add #5/A:67

46 atoms, 49 bonds, 3 residues, 1 model selected  

> select add #5/A:69

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

> select add #5/C:77

89 atoms, 95 bonds, 5 residues, 1 model selected  

> select add #5/C:76

109 atoms, 116 bonds, 6 residues, 1 model selected  

> select add #5/A:351

131 atoms, 140 bonds, 7 residues, 1 model selected  

> select add #5/A:352

153 atoms, 164 bonds, 8 residues, 1 model selected  

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> label sel text ""{0.name} {0.number}{0.insertion_code}""

> select #5/F:5@CA

1 atom, 1 residue, 1 model selected  

> ~label sel residues

> select clear

> select #5/F:5@CA

1 atom, 1 residue, 1 model selected  

> color sel magenta

> select clear

> show #!1 models

> show #!7 models

> hide #!1 models

> hide #!5 models

> hide #!7 models

> show #!5 models

> select clear

> select #5/C:77@OP1

1 atom, 1 residue, 1 model selected  

> select up

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #5/C:76@O3'

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

> select up

43 atoms, 47 bonds, 2 residues, 1 model selected  

> select add #5/A:67@P

44 atoms, 47 bonds, 3 residues, 1 model selected  

> select up

65 atoms, 71 bonds, 3 residues, 1 model selected  

> select add #5/A:68@OP1

66 atoms, 71 bonds, 4 residues, 1 model selected  

> select up

88 atoms, 97 bonds, 4 residues, 1 model selected  

> select add #5/A:351@O3'

89 atoms, 97 bonds, 5 residues, 1 model selected  

> select up

110 atoms, 121 bonds, 5 residues, 1 model selected  

> select add #5/A:352@C4'

111 atoms, 122 bonds, 6 residues, 1 model selected  

> select subtract #5/A:352@C4'

110 atoms, 121 bonds, 5 residues, 1 model selected  

> select add #5/A:352@C4'

111 atoms, 121 bonds, 6 residues, 1 model selected  

> select up

132 atoms, 146 bonds, 6 residues, 1 model selected  

> select add #5/A:69@O5'

133 atoms, 146 bonds, 7 residues, 1 model selected  

> select up

152 atoms, 168 bonds, 7 residues, 1 model selected  

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> color sel byhetero

> select clear

> select #5/F:5@CA

1 atom, 1 residue, 1 model selected  

> select add #5/C:77@OP1

2 atoms, 2 residues, 1 model selected  

> distance #5/F:5@CA #5/C:77@OP1

Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/F CA 5 CA and /C G
77 OP1: 2.14Å  

> select clear

> show #!1 models

> show #!7 models

> hide #!5 models

> hide #!1 models

> select add #7/C:77@OP1

1 atom, 1 residue, 1 model selected  

> select add #7/D:14@MG

2 atoms, 2 residues, 1 model selected  

> distance #7/C:77@OP1 #7/D:14@MG

Distance between Int_1_5mM_Mg_UAA_J2372_1-coot-1_real_space_refined_001.pdb
#7/C G 77 OP1 and /D MG 14 MG: 10.79Å  

> show #!1 models

> show #!5 models

> hide #!1 models

> hide #!7 models

> hide #!5 models

> show #!1 models

> show #!7 models

> hide #!4 models

> show #!4 models

> hide #!1 models

> show #!1 models

> show #!5 models

> hide #!1 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!7 models

> show #!1 models

> hide #!5 models

> hide #!1 models

> show #!5 models

> hide #!5 models

> show #!5 models

> show #!6 models

> hide #!6 models

> show #!7 models

> hide #!5 models

> show #!1 models

> hide #!1 models

> save /Users/bhogeba/Desktop/image4.png supersample 3

> hide #!7 models

> show #!1 models

> show #!5 models

> hide #!1 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!5 models

> hide #!7 models

> show #!5 models

> save /Users/bhogeba/Desktop/image5.png supersample 3

> show #!1 models

> hide #!5 models

> save /Users/bhogeba/Desktop/image6.png supersample 3

> hide #!1 models

> show #!6 models

> show #!7 models

> hide #!6 models

> save /Users/bhogeba/Desktop/image7.png supersample 3

> show #!5 models

> hide #!7 models

> select add #7

12689 atoms, 14097 bonds, 1 pseudobond, 670 residues, 3 models selected  

> select subtract #7

Nothing selected  

> select #5/C:161

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

> select add #5/C:162

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select add #5/C:163

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

> select add #5/C:164

83 atoms, 88 bonds, 4 residues, 1 model selected  

> select add #5/C:165

105 atoms, 112 bonds, 5 residues, 1 model selected  

> select subtract #5/C:161

85 atoms, 91 bonds, 4 residues, 1 model selected  

> select subtract #5/C:162

65 atoms, 70 bonds, 3 residues, 1 model selected  

> show sel atoms

> nucleotides sel ladder

> nucleotides sel atoms

> style nucleic & sel stick

Changed 65 atom styles  

> select add #5/A:294

85 atoms, 91 bonds, 4 residues, 1 model selected  

> select add #5/A:295

107 atoms, 115 bonds, 5 residues, 1 model selected  

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 107 atom styles  

> select add #5/A:293

130 atoms, 140 bonds, 6 residues, 1 model selected  

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 130 atom styles  

> select #5/A:50

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

> select clear

> select #5/A:296

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #5/A:297

46 atoms, 50 bonds, 2 residues, 1 model selected  

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 46 atom styles  

> hide sel atoms

> select clear

> select #5/A:295

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

> select add #5/A:294

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select add #5/A:293

65 atoms, 70 bonds, 3 residues, 1 model selected  

> select add #5/C:165

87 atoms, 94 bonds, 4 residues, 1 model selected  

> select add #5/C:164

107 atoms, 115 bonds, 5 residues, 1 model selected  

> select add #5/C:163

130 atoms, 140 bonds, 6 residues, 1 model selected  

> select subtract #5/C:164

110 atoms, 119 bonds, 5 residues, 1 model selected  

> select add #5/C:164

130 atoms, 140 bonds, 6 residues, 1 model selected  

> select subtract #5/C:163

107 atoms, 115 bonds, 5 residues, 1 model selected  

> select add #5/C:163

130 atoms, 140 bonds, 6 residues, 1 model selected  

> color sel byhetero

> select clear

> select add #5/C:164

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

> select add #5/C:165

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select subtract #5/C:165

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

> select add #5/A:293

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

> select add #5/A:294

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

> select add #5/A:295

85 atoms, 91 bonds, 4 residues, 1 model selected  

> label sel text ""{0.name} {0.number}{0.insertion_code}""

> select add #5/C:163

108 atoms, 116 bonds, 5 residues, 1 model selected  

> select add #5/C:165

130 atoms, 140 bonds, 6 residues, 1 model selected  

> label sel text ""{0.name} {0.number}{0.insertion_code}""

> select #5/C:164@O2

1 atom, 1 residue, 1 model selected  

> select add #5/A:295@N6

2 atoms, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 select true reveal true retainCurrent true

0 hydrogen bonds found  

> select clear

> select add #5/C:164@O4

1 atom, 1 residue, 1 model selected  

> select add #5/A:295@N6

2 atoms, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 select true reveal true retainCurrent true

0 hydrogen bonds found  

> select clear

> select #5/C:164@O2

1 atom, 1 residue, 1 model selected  

> select add #5/A:294@O2

2 atoms, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 select true reveal true retainCurrent true

0 hydrogen bonds found  

> select #5/A:295@N1

1 atom, 1 residue, 1 model selected  

> select add #5/C:164@N3

2 atoms, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 select true reveal true retainCurrent true

1 hydrogen bonds found  

> select clear

> select add #5/C:163@O2'

1 atom, 1 residue, 1 model selected  

> select clear

> select #5/C:163@O2'

1 atom, 1 residue, 1 model selected  

> select add #5/C:164@O2

2 atoms, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 select true reveal true retainCurrent true

1 hydrogen bonds found  

> select clear

> select add #5/C:165@O4'

1 atom, 1 residue, 1 model selected  

> select add #5/A:293@O6

2 atoms, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 select true reveal true retainCurrent true

1 hydrogen bonds found  

> hbonds sel dashes 6 select true reveal true retainCurrent true

1 hydrogen bonds found  

> select #5/A:295

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

> select #5/A:294

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

> save /Users/bhogeba/Desktop/image8.png supersample 3

> select clear

> select #5/A:294

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

> select add #5/C:164

40 atoms, 42 bonds, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 select true reveal true retainCurrent true

8 hydrogen bonds found  

> hbonds sel dashes 6 select true reveal true retainCurrent true

15 hydrogen bonds found  

> select clear

> select #5/A:295

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

> ui tool show H-Bonds

> select clear

> select add #5/A:294@O2'

1 atom, 1 pseudobond, 1 residue, 2 models selected  

> select add #5/A:295

23 atoms, 24 bonds, 1 pseudobond, 2 residues, 2 models selected  

> hbonds delete

> select clear

> select #5/C:164@N3

1 atom, 1 residue, 1 model selected  

> select add #5/A:294@O2

2 atoms, 2 residues, 1 model selected  

> hbonds select

Missing ""select"" keyword's argument  

> ui tool show H-Bonds

> hbonds sel restrict both select true reveal true

0 hydrogen bonds found  

> select #5/C:163@O2'

1 atom, 1 residue, 1 model selected  

> select add #5/C:164@N3

2 atoms, 2 residues, 1 model selected  

> hbonds sel restrict both select true reveal true

0 hydrogen bonds found  

> select #5/A:294@O2

1 atom, 1 residue, 1 model selected  

> select #5/A:294@N3

1 atom, 1 residue, 1 model selected  

> select #5/A:294

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

> select #5/C:164@N3

1 atom, 1 residue, 1 model selected  

> select add #5/A:294@O2

2 atoms, 2 residues, 1 model selected  

> hbonds sel restrict both select true reveal true

0 hydrogen bonds found  

> select add #5/C:164@N3

1 atom, 1 residue, 1 model selected  

> select #5/C:164@O4

1 atom, 1 residue, 1 model selected  

> select add #5/A:295@N1

2 atoms, 2 residues, 1 model selected  

> select clear

> select #5/A:295@N1

1 atom, 1 residue, 1 model selected  

> select add #5/C:164@N3

2 atoms, 2 residues, 1 model selected  

> hbonds sel restrict both select true reveal true

1 hydrogen bonds found  

> select clear

> select #5/C:163@O2'

1 atom, 1 residue, 1 model selected  

> select clear

> select #5/C:164@O2'

1 atom, 1 residue, 1 model selected  

> select add #5/A:293@N2

2 atoms, 2 residues, 1 model selected  

> hbonds sel restrict both select true reveal true

0 hydrogen bonds found  

> select #5/A:295@N1

1 atom, 1 residue, 1 model selected  

> select add #5/C:164@N3

2 atoms, 2 residues, 1 model selected  

> hbonds sel restrict both select true reveal true

1 hydrogen bonds found  

> select clear

> save /Users/bhogeba/Desktop/image9.png supersample 3

> save /Users/bhogeba/Desktop/image10.png supersample 3

> select add #5/C:0

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

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 22 atom styles  

> select clear

> select #5/C:158

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

> select add #5/C:159

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select add #5/C:157

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

> show sel atoms

> hide sel atoms

> select clear

> select #5/C:0

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

> color sel byhetero

> save /Users/bhogeba/Desktop/image11.png supersample 3

> ui tool show ""Model Panel""

> ui tool show ""Side View""

> select clear

> select #5/F:2@CA

1 atom, 1 residue, 1 model selected  

> color sel hot pink

> color sel orange

> color sel red

> color sel orange red

> color sel orange

> color sel yellow

> color sel orange

> color sel cornflower blue

> color sel light sea green

> color sel dodger blue

> color sel blue

> color sel pale violet red

> color sel deep pink

> color sel magenta

> color sel rebecca purple

> color sel dark slate blue

> color sel slate blue

> color sel medium slate blue

> color sel dim gray

> color sel pale green

> color sel light green

> color sel burly wood

> color sel light coral

> color sel burly wood

> color sel tan

> color sel burly wood

> color sel aquamarine

> color sel sky blue

> color sel light sky blue

> color sel light blue

> color sel light steel blue

> color sel silver

> color sel thistle

> color sel rosy brown

> ui tool show Distances

> select #5/F:5@CA

1 atom, 1 residue, 1 model selected  

> select add #5/A:67@OP1

2 atoms, 2 residues, 1 model selected  

> distance #5/F:5@CA #5/A:67@OP1

Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/F CA 5 CA and /A A
67 OP1: 1.88Å  

> select clear

> select #5/A:67@OP2

1 atom, 1 residue, 1 model selected  

> select add #5/F:2@CA

2 atoms, 2 residues, 1 model selected  

> distance #5/A:67@OP2 #5/F:2@CA

Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/A A 67 OP2 and /F
CA 2 CA: 2.12Å  

> select #5/F:5@CA

1 atom, 1 residue, 1 model selected  

> select add #5/A:352@OP2

2 atoms, 2 residues, 1 model selected  

> distance #5/F:5@CA #5/A:352@OP2

Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/F CA 5 CA and /A A
352 OP2: 1.95Å  

> select #5/F:5@CA

1 atom, 1 residue, 1 model selected  

> select add #5/A:351@OP1

2 atoms, 2 residues, 1 model selected  

> distance #5/F:5@CA #5/A:351@OP1

Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/F CA 5 CA and /A A
351 OP1: 1.91Å  

> distance style symbol false

> distance style symbol true

> label size 2

> label size 1

> label size 150

> label height 1.5

> label height 1

> label height 0.5

> select #5/F:5@CA

1 atom, 1 residue, 1 model selected  

> select add #5/C:76@O3'

2 atoms, 2 residues, 1 model selected  

> distance #5/F:5@CA #5/C:76@O3'

Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/F CA 5 CA and /C U
76 O3': 2.21Å  

> label height 0.5

> select #5/F:2@CA

1 atom, 1 residue, 1 model selected  

> select add #5/C:77@OP1

2 atoms, 2 residues, 1 model selected  

> distance #5/F:2@CA #5/C:77@OP1

Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/F CA 2 CA and /C G
77 OP1: 2.71Å  

> label height 0.5

> select #5/A:68@OP2

1 atom, 1 residue, 1 model selected  

> select add #5/F:2@CA

2 atoms, 2 residues, 1 model selected  

> distance #5/A:68@OP2 #5/F:2@CA

Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/A G 68 OP2 and /F
CA 2 CA: 2.89Å  

> label height 0.5

> select add #5/F:2@CA

21 atoms, 2 residues, 1 model selected  
Exactly two atoms must be selected!  

> select clear

> nucleotides sel atoms

> style nucleic & sel stick

Changed 20 atom styles  

> show sel atoms

> select clear

> select #5/A:69@O4

1 atom, 1 residue, 1 model selected  

> select add #5/F:2@CA

2 atoms, 2 residues, 1 model selected  

> distance #5/A:69@O4 #5/F:2@CA

Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/A U 69 O4 and /F CA
2 CA: 1.91Å  

> label height 0.5

> select clear

> select #5/F:2@CA

1 atom, 1 residue, 1 model selected  

> ui tool show ""Selection Inspector""

> style sel ball

Changed 1 atom style  

> style sel stick

Changed 1 atom style  

> style sel ball

Changed 1 atom style  

> style sel sphere

Changed 1 atom style  

> select down

1 atom, 1 residue, 1 model selected  


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.10rc202506100450 (2025-06-10)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open ""/Users/bhogeba/T4_dimeric tRNA/Gst_RNP/J1387_GstRNR.pdb""

Chain information for J1387_GstRNR.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac15,6
      Model Number: Z1AU00299LL/A
      Chip: Apple M3 Pro
      Total Number of Cores: 11 (5 Performance and 6 Efficiency)
      Memory: 18 GB
      System Firmware Version: 13822.81.10
      OS Loader Version: 13822.81.10

Software:

    System Software Overview:

      System Version: macOS 26.3.1 (25D2128)
      Kernel Version: Darwin 25.3.0
      Time since boot: 9 days, 19 hours, 58 minutes

Graphics/Displays:

    Apple M3 Pro:

      Chipset Model: Apple M3 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 14
      Vendor: Apple (0x106b)
      Metal Support: Metal 4
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL P2715Q:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 30.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported
        DELL P2715Q:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.3.4
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.18
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10rc202506100450
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.2.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.3
    ChimeraX-ProfileGrids: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-QScore: 1.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.8.2
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.58.2
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.0
    pytest-cov: 6.1.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 26.4.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.0
    tzdata: 2025.2
    urllib3: 2.4.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
}}}
"	defect	closed	normal		Window Toolkit		duplicate						all	ChimeraX