id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
17128	Crash on Mac waking from sleep	chimerax-bug-report@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-15.3.2-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 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 0x00000001f2e30840 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 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.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.alignment_algs._sw, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.mmcif.mmcif_write, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 60)


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===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/closed_conformer_beforeMD.pdb

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

> open
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/trueB_ETasq_Bfox_Hie290_aligned.pdb

Chain information for trueB_ETasq_Bfox_Hie290_aligned.pdb #2  
---  
Chain | Description  
? | No description available  
  
Computing secondary structure  

> open
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/trueB_EThq_Bfox_Hip290_aligned.pdb

Chain information for trueB_EThq_Bfox_Hip290_aligned.pdb #3  
---  
Chain | Description  
? | No description available  
  
Computing secondary structure  

> open
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/trueB_ETox_Bfox_Hip290_aligned.pdb

Chain information for trueB_ETox_Bfox_Hip290_aligned.pdb #4  
---  
Chain | Description  
? | No description available  
  
Computing secondary structure  

> open
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/trueB_withNAD_BFahq_HID290_aligned.pdb

Chain information for trueB_withNAD_BFahq_HID290_aligned.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  

> open
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/open_conformer_beforeMD_renum.pdb

Chain information for open_conformer_beforeMD_renum.pdb #6  
---  
Chain | Description  
? | No description available  
  
Computing secondary structure  
Drag select of 55 residues  

> cartoon style width 1.5

> cartoon style thickness 0.2

> hide @H*

> hide protein

> select clear

> hide #2 models

> hide #3 models

> hide #4 models

> hide #5 models

> hide #6 models

> ui tool show ""Color Actions""

> undo

> hide #6 models

> select :347

38 atoms, 36 bonds, 2 residues, 1 model selected  

> show sel

> show #2 models

> hide #2 models

> hide #1 models

> show #2 models

> hide #2 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> show #4 models

> hide #4 models

> show #5 models

> hide #5 models

> show #6 models

> hide #6 models

> show #5 models

> open /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/4KPU.cif

4KPU.cif title:  
Electron transferring flavoprotein of Acidaminococcus fermentans: Towards a
mechanism of flavin-based electron bifurcation [more info...]  
  
Chain information for 4KPU.cif #7  
---  
Chain | Description | UniProt  
A | Electron transfer flavoprotein alpha subunit | D2RIQ3_ACIFV 1-340  
B | Electron transfer flavoprotein alpha/beta-subunit | D2RIQ2_ACIFV 1-263  
  
Non-standard residues in 4KPU.cif #7  
---  
CL — chloride ion  
FAD — flavin-adenine dinucleotide  
  
115 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> cartoon style width 1.5

> cartoon style width 1.2

> cartoon style thickness 0.2

> hide #5 models

> show #4 models

> hide #4 models

> show #3 models

> hide #3 models

> show #2 models

> hide #2 models

> show #1 models

> help mm

> hide #7 models

> show #2 models

> hide #1 models

> hide #2 models

> show #1 models

> show #2 models

> show #3 models

> hide #1 models

> hide #2 models

> show #4 models

> hide #3 models

> show #5 models

> hide #4 models

> show #4 models

> close #5

> undo

> show #1 models

> show #2 models

> show #3 models

> show #4 models

> show #6 models

> show #7 models

> hide #7 models

> hide #4 models

> hide #3 models

> hide #2 models

> hide #1 models

> hide #6 models

> show #4 models

> show #3 models

> hide #4 models

> show #2 models

> show #1 models

> hide #1 models

> hide #2 models

> hide #3 models

> show #2 models

> hide #2 models

> show #4 models

> show #2 models

> show #3 models

> show #6 models

> show #1 models

> hide #1 models

> hide #2 models

> hide #3 models

> hide #4 models

> show #7 models

> hide #6 models

> select #7(/A:13-207 & /B:1-11,32-227)

Expected an objects specifier or a keyword  

> select #7/A:13-207 & #7/B:1-11,32-227

Nothing selected  

> select #7/A:13-207

1530 atoms, 1559 bonds, 195 residues, 1 model selected  

> select #7/A:13-207 and #7/B:1-11,32-227

Expected a keyword  

> select #7/A:13-207 && #7/B:1-11

Expected a keyword  

> select #7/A:13-207 & #7/B:1-11

Nothing selected  

> select #7/A:13-207/B:1-11

1613 atoms, 1642 bonds, 206 residues, 1 model selected  

> select #7/A:13-207/B:1-11,32-227

3078 atoms, 3128 bonds, 402 residues, 1 model selected  

> select #1:13-207,348-358,379-574

6173 atoms, 6223 bonds, 402 residues, 1 model selected  

> show #1 models

> mmaker #7/A:13-207/B:1-11,32-227 to #1:13-207,348-358,379-574

Computing secondary structure  
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 closed_conformer_beforeMD.pdb, chain (blank) (#1) with 4KPU.cif,
chain B (#7), sequence alignment score = 1029.8  
RMSD between 207 pruned atom pairs is 0.102 angstroms; (across all 207 pairs:
0.102)  
  

> hide #7 models

> show #7 models

> hide #1 models

> open
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/trueB_withNAD_BFahq_HID290_aligned.pdb

Chain information for trueB_withNAD_BFahq_HID290_aligned.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  

> hide #7 models

> select :5:350

251 atoms, 237 bonds, 14 residues, 7 models selected  

> close #5

> show #7 models

> show #1 models

> close #7

> open /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/4KPU.cif

4KPU.cif title:  
Electron transferring flavoprotein of Acidaminococcus fermentans: Towards a
mechanism of flavin-based electron bifurcation [more info...]  
  
Chain information for 4KPU.cif #5  
---  
Chain | Description | UniProt  
A | Electron transfer flavoprotein alpha subunit | D2RIQ3_ACIFV 1-340  
B | Electron transfer flavoprotein alpha/beta-subunit | D2RIQ2_ACIFV 1-263  
  
Non-standard residues in 4KPU.cif #5  
---  
CL — chloride ion  
FAD — flavin-adenine dinucleotide  
  
115 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> mmaker #5/A:13-207/B:1-11,32-227 to #1:13-207,348-358,379-574 reportMatrix
> true

Computing secondary structure  
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 closed_conformer_beforeMD.pdb, chain (blank) (#1) with 4KPU.cif,
chain B (#5), sequence alignment score = 1029.8  
Alignment matrix in structure 4KPU.cif coordinates  
Matrix rotation and translation  
0.99998158 0.00507753 0.00332539 -0.54964193  
-0.00506508 0.99998018 -0.00373975 30.50034703  
-0.00334431 0.00372283 0.99998748 26.20970306  
Axis 0.52370927 0.46806599 -0.71178847  
Axis point 6454.37435968 -349.74733187 0.00000000  
Rotation angle (degrees) 0.40822084  
Shift along axis -4.66744209  
  
RMSD between 207 pruned atom pairs is 0.102 angstroms; (across all 207 pairs:
0.102)  
  
Downloading file 1471-2105-7-339.pdf  

> save
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/4KPUonClosedBeforeMD.cif
> models #5 relModel #1

> open
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/4KPUonClosedBeforeMD.cif

Chain information for 4KPUonClosedBeforeMD.cif #7  
---  
Chain | Description  
A | Electron transfer flavoprotein alpha subunit  
B | Electron transfer flavoprotein alpha/beta-subunit  
  
115 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide #5 models

> cartoon style width 1.2

> cartoon style thickness 0.2

> select clear

> select #1:221-338,584-605

2107 atoms, 2124 bonds, 140 residues, 1 model selected  

> select #7:/A:221-338/B:237-258

Expected an objects specifier or a keyword  

> select #7/A:221-338/B:237-258

1045 atoms, 1062 bonds, 140 residues, 1 model selected  

> help measure rotation

> select #7/A:221-338/B:237-258@CA

893 atoms, 887 bonds, 140 residues, 1 model selected  

> select #1:221-338,584-605@CA

140 atoms, 140 residues, 1 model selected  

> hide #1 models

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> cartoon hide sel

> select clear

> select #7/A:221-338/B:237-258@CA

893 atoms, 887 bonds, 140 residues, 1 model selected  

> hide cartoons

> hide sel

> hide #7

> select #7/A:221-338/B:237-258@CA

893 atoms, 887 bonds, 140 residues, 1 model selected  

> show sel

> select #7/A:221-338/B:237-258@C*

981 atoms, 976 bonds, 21 pseudobonds, 140 residues, 2 models selected  

> select #7/A:221-338/B:237-258@C*

981 atoms, 976 bonds, 21 pseudobonds, 140 residues, 2 models selected  

> hide sel

> select #7/A:221-338/B:237-258@CA

893 atoms, 887 bonds, 140 residues, 1 model selected  

> select #7/A:221-338/B:237-258@CA

893 atoms, 887 bonds, 140 residues, 1 model selected  

> select #7/A:221-338/B:237-258@CB

893 atoms, 887 bonds, 140 residues, 1 model selected  

> select #7/A:221-338/B:237-258@C

893 atoms, 887 bonds, 140 residues, 1 model selected  

> select #7/A:221-338/B:237-258@CA!

Expected an objects specifier or a keyword  

> select #7/A:221-338/B:237-258@N

893 atoms, 887 bonds, 140 residues, 1 model selected  

> select #7/A:221-338@CA/B:237-258@CA

140 atoms, 140 residues, 1 model selected  

> select #7/A:221-338@CA/B:237-258@CA

140 atoms, 140 residues, 1 model selected  

> select #1:221-338,584-605@CA

140 atoms, 140 residues, 1 model selected  

> show sel

> show sel ribbons

> show sel cartoons

> show #1 models

> select #7/A:221-338@CA/B:237-258@CA

140 atoms, 140 residues, 1 model selected  

> show sel cartoons

> show :FAD

> hide @H

> select add #7

5265 atoms, 4751 bonds, 1201 residues, 1 model selected  

> select subtract #7

Nothing selected  

> select add #7

5265 atoms, 4751 bonds, 1201 residues, 1 model selected  

> select add #1

14728 atoms, 14303 bonds, 1812 residues, 2 models selected  

> select subtract #1

5265 atoms, 4751 bonds, 1201 residues, 1 model selected  

> select subtract #7

Nothing selected  

> hide @H

> select @H*

23608 atoms, 3055 residues, 5 models selected  

> hide sel

> align sel #7/A:221-338@CA/B:237-258@CA toAtoms #1:221-338,584-605@CA
> reportMatrix true

Expected a keyword  

> align #7/A:221-338@CA/B:237-258@CA toAtoms #1:221-338,584-605@CA
> reportMatrix true

Alignment matrix in structure 4KPUonClosedBeforeMD.cif coordinates  
Matrix rotation and translation  
0.99999350 0.00110659 0.00343249 -0.11580679  
-0.00108237 0.99997455 -0.00705109 0.33018451  
-0.00344021 0.00704733 0.99996925 -0.16493655  
Axis 0.89025523 0.43398140 -0.13822361  
Axis point 0.00000000 22.35562099 42.86955782  
Rotation angle (degrees) 0.45368377  
Shift along axis 0.06299446  
  
RMSD between 140 atom pairs is 0.119 angstroms  

> hide #7 models

> show #2 models

> select #2:221-338,584-605@CA

140 atoms, 140 residues, 1 model selected  

> show sel cartoons

> align #2:221-338,584-605@CA toAtoms #1:221-338,584-605@CA reportMatrix true

Alignment matrix in structure trueB_ETasq_Bfox_Hie290_aligned.pdb coordinates  
Matrix rotation and translation  
0.99339521 -0.09046281 0.07058633 6.24976923  
0.10022218 0.98361014 -0.14988868 -3.68156891  
-0.05587008 0.15597301 0.98617998 -7.67453128  
Axis 0.80074167 0.33106115 0.49921067  
Axis point 0.00000000 46.44098124 -29.53952257  
Rotation angle (degrees) 11.01036041  
Shift along axis -0.04558171  
  
RMSD between 140 atom pairs is 0.629 angstroms  

> close #2

> open
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/trueB_ETasq_Bfox_Hie290_aligned.pdb

Chain information for trueB_ETasq_Bfox_Hie290_aligned.pdb #2  
---  
Chain | Description  
? | No description available  
  
Computing secondary structure  

> select #2:221-338,584-605@CA

140 atoms, 140 residues, 1 model selected  

> hide #2

> hide #2 ribbons

> select #2:221-338,584-605@CA

140 atoms, 140 residues, 1 model selected  

> show sel ribbons

> show #2:FAD

> hide @H*

> align #2:221-338,584-605@CA toAtoms #1:221-338,584-605@CA reportMatrix true
> move nothing

Alignment matrix in structure trueB_ETasq_Bfox_Hie290_aligned.pdb coordinates  
Matrix rotation and translation  
0.99339521 -0.09046281 0.07058633 6.24976923  
0.10022218 0.98361014 -0.14988868 -3.68156891  
-0.05587008 0.15597301 0.98617998 -7.67453128  
Axis 0.80074167 0.33106115 0.49921067  
Axis point 0.00000000 46.44098124 -29.53952257  
Rotation angle (degrees) 11.01036041  
Shift along axis -0.04558171  
  
RMSD between 140 atom pairs is 0.629 angstroms  

> align #2:13-207,348-358,379-574@CA toAtoms #1:13-207,348-358,379-574@CA
> reportMatrix true move nothing

Alignment matrix in structure trueB_ETasq_Bfox_Hie290_aligned.pdb coordinates  
Matrix rotation and translation  
0.99999478 -0.00256142 -0.00196974 0.27675587  
0.00255477 0.99999104 -0.00337442 -0.09504772  
0.00197837 0.00336937 0.99999237 -0.45066051  
Axis 0.72200816 -0.42269479 0.54775299  
Axis point 0.00000000 132.57120457 -29.37762169  
Rotation angle (degrees) 0.26758169  
Shift along axis -0.00685447  
  
RMSD between 402 atom pairs is 1.290 angstroms  

> align #3:221-338,584-605@CA toAtoms #1:221-338,584-605@CA reportMatrix true
> move nothing

Alignment matrix in structure trueB_EThq_Bfox_Hip290_aligned.pdb coordinates  
Matrix rotation and translation  
0.97255225 -0.14092020 -0.18515837 20.55175664  
0.12376651 0.98713738 -0.10120097 -6.47801378  
0.19703801 0.07550683 0.97748388 -18.84704686  
Axis 0.35529743 -0.76846290 0.53219217  
Axis point 112.02142686 0.00000000 90.07237907  
Rotation angle (degrees) 14.39917143  
Shift along axis 2.24984877  
  
RMSD between 140 atom pairs is 0.926 angstroms  

> hide #2 models

> show #3 models

> align #3:221-338,584-605@CA toAtoms #1:221-338,584-605@CA reportMatrix true
> move nothing

Alignment matrix in structure trueB_EThq_Bfox_Hip290_aligned.pdb coordinates  
Matrix rotation and translation  
0.97255225 -0.14092020 -0.18515837 20.55175664  
0.12376651 0.98713738 -0.10120097 -6.47801378  
0.19703801 0.07550683 0.97748388 -18.84704686  
Axis 0.35529743 -0.76846290 0.53219217  
Axis point 112.02142686 0.00000000 90.07237907  
Rotation angle (degrees) 14.39917143  
Shift along axis 2.24984877  
  
RMSD between 140 atom pairs is 0.926 angstroms  

> show #3:221-338,584-605 ribbons

> show #3:FAD

> align #3:13-207,348-358,379-574@CA toAtoms #1:13-207,348-358,379-574@CA
> reportMatrix true move nothing

Alignment matrix in structure trueB_EThq_Bfox_Hip290_aligned.pdb coordinates  
Matrix rotation and translation  
0.99999950 -0.00018786 0.00098471 -0.03403364  
0.00018573 0.99999764 0.00216596 -0.10256011  
-0.00098511 -0.00216578 0.99999717 0.17442726  
Axis -0.90750661 0.41268129 0.07826816  
Axis point 0.00000000 80.39550076 47.86029184  
Rotation angle (degrees) 0.13674298  
Shift along axis 0.00221322  
  
RMSD between 402 atom pairs is 1.837 angstroms  

> show #4:221-338,584-605 ribbons

> show #4 models

> hide #3 models

> align #4:221-338,584-605@CA toAtoms #1:221-338,584-605@CA reportMatrix true
> move nothing

Alignment matrix in structure trueB_ETox_Bfox_Hip290_aligned.pdb coordinates  
Matrix rotation and translation  
0.99700573 -0.03057031 -0.07102834 6.46763417  
0.02004192 0.98930614 -0.14447034 1.00651003  
0.07468528 0.14261422 0.98695658 -14.57981578  
Axis 0.88089442 -0.44710977 0.15529929  
Axis point 0.00000000 106.24321778 8.33464960  
Rotation angle (degrees) 9.37820164  
Shift along axis 2.98304730  
  
RMSD between 140 atom pairs is 1.014 angstroms  

> align #4:13-207,348-358,379-574@CA toAtoms #1:13-207,348-358,379-574@CA
> reportMatrix true move nothing

Alignment matrix in structure trueB_ETox_Bfox_Hip290_aligned.pdb coordinates  
Matrix rotation and translation  
0.99999882 -0.00056880 0.00142766 -0.10337220  
0.00056511 0.99999650 0.00258477 -0.17347437  
-0.00142913 -0.00258396 0.99999564 0.20941812  
Axis -0.85951457 0.47505836 0.18855837  
Axis point 0.00000000 77.56634079 75.66006090  
Rotation angle (degrees) 0.17227567  
Shift along axis 0.04592700  
  
RMSD between 402 atom pairs is 1.854 angstroms  

> show #6:221-338,584-605 ribbons

> show #6 models

> hide #4 models

> align #6:221-338,584-605@CA toAtoms #1:221-338,584-605@CA reportMatrix true
> move nothing

Alignment matrix in structure open_conformer_beforeMD_renum.pdb coordinates  
Matrix rotation and translation  
0.27568379 -0.75863596 0.59031342 74.16162513  
0.43350953 0.64623661 0.62805074 -26.76640737  
-0.85794402 0.08276309 0.50703287 56.92569079  
Axis -0.27913965 0.74138132 0.61027436  
Axis point 82.74941003 0.00000000 -21.35205297  
Rotation angle (degrees) 77.61517553  
Shift along axis -5.80527463  
  
RMSD between 140 atom pairs is 1.252 angstroms  

> align #6:13-207,348-358,379-574@CA toAtoms #1:13-207,348-358,379-574@CA
> reportMatrix true move nothing

Alignment matrix in structure open_conformer_beforeMD_renum.pdb coordinates  
Matrix rotation and translation  
0.99998133 0.00536441 0.00292695 -0.61534261  
-0.00536948 0.99998410 0.00172505 0.42158678  
-0.00291765 -0.00174074 0.99999423 0.38909374  
Axis -0.27281435 0.46006521 -0.84493333  
Axis point 75.34609027 113.28854301 0.00000000  
Rotation angle (degrees) 0.36394042  
Shift along axis 0.03307344  
  
RMSD between 402 atom pairs is 1.516 angstroms  

> align #7/A:221-338@CA/B:237-258@CA toAtoms #1:221-338,584-605@CA
> reportMatrix true move nothing

Alignment matrix in structure 4KPUonClosedBeforeMD.cif coordinates  
Matrix rotation and translation  
1.00000000 -0.00000000 0.00000000 0.00000000  
0.00000000 1.00000000 0.00000000 -0.00000000  
-0.00000000 -0.00000000 1.00000000 0.00000000  
Axis -0.34927381 0.19934968 0.91556950  
Axis point 151.54834895 118.33100974 0.00000000  
Rotation angle (degrees) 0.00000000  
Shift along axis 0.00000000  
  
RMSD between 140 atom pairs is 0.119 angstroms  

> align #7/a:13-207@CA/B:1-11,32-227@CA toAtoms #1:13-207,348-358,379-574@CA
> reportMatrix true move nothing

Alignment matrix in structure 4KPUonClosedBeforeMD.cif coordinates  
Matrix rotation and translation  
0.99999086 -0.00156786 -0.00397823 0.18454925  
0.00159649 0.99997278 0.00720353 -0.39029404  
0.00396682 -0.00720982 0.99996614 0.14218805  
Axis -0.86000954 -0.47406186 0.18880929  
Axis point 0.00000000 18.09107827 50.75113083  
Rotation angle (degrees) 0.48013050  
Shift along axis 0.05315582  
  
RMSD between 402 atom pairs is 0.109 angstroms  

> define axis fromPoint (0,0,0) topoint (10.9, 28.9, 23.3) id 8 color yellow
> radius 0.3

Invalid ""fromPoint"" argument: Expected a number  

> define axis fromPoint 0,0,0 toPoint 10.9, 28.9, 23.3 id 8 color yellow
> radius 0.3

Axis 'axis' centered at [ 5.45 14.45 11.65] with direction [10.9 28.9 23.3],
radius 0.3, and length 38.6899  

> define axis fromPoint 0,0,0 toPoint 8.3, -4.2, 1.5 id 9 color springgreen
> radius 0.3

Axis 'axis' centered at [ 4.15 -2.1 0.75] with direction [ 8.3 -4.2 1.5],
radius 0.3, and length 9.42231  

> define axis fromPoint 0,0,0 toPoint 8.8, 3.6, 5.5 id 10 color dodgerblue
> radius 0.3

Axis 'axis' centered at [4.4 1.8 2.75] with direction [8.8 3.6 5.5], radius
0.3, and length 10.9841  

> define axis fromPoint 0,0,0 toPoint 5.2, -11.1, 7.6 id 11 color orchid
> radius 0.3

Axis 'axis' centered at [ 2.6 -5.55 3.8 ] with direction [ 5.2 -11.1 7.6],
radius 0.3, and length 14.4226  

> save
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/DomainReorientations.cxs

> define axis fromPoint 0,0,0 toPoint 5.2, -11.1, 7.6 id 11 color orchid
> radius 0.3

Axis 'axis' centered at [ 2.6 -5.55 3.8 ] with direction [ 5.2 -11.1 7.6],
radius 0.3, and length 14.4226  

> hide cartoons

> hide protein

> show #2 models

> show #3 models

> show #4 models

> hide @H*

> name flavinatoms
> @N1,C2,O2,N3,C4,C4X,O4,C5X,N5,C6,C7,C7M,C8,C8M,C9,C9A,C10,N10

> hide :FAD

> hide :FDM

> show flavinatoms

> ui tool show ""Side View""

> hide #11.1 models

> save
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/AxesRotationHead_FirstTry.png
> width 461 height 831 supersample 3

> open
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/trueB_withNAD+_BFahq_Hid290_aligned.pdb

Chain information for trueB_withNAD+_BFahq_Hid290_aligned.pdb #12  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  

> close 11.1

Expected a models specifier or a keyword  

> close #11.1

> color #12 #7f6919ff

> color #12 #7f5b14ff

> color #12 #7f6a25ff

> color #12 #7f6e39ff

> color #12 #e6c868ff

> color #12 #e69384ff

> color #12 #e6893aff

> color #12 #e6b02eff

> color #12 #e6a034ff

> color #12 #e68f0bff

> color #12 #ff9f0cff

> color #12 #ffad4eff

> hide protein

> select #12:347

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #12:13-207,348-358,379-574

6166 atoms, 6216 bonds, 402 residues, 1 model selected  

> select #12:221-338,584-605

2114 atoms, 2131 bonds, 140 residues, 1 model selected  

> close #12

> select #1:221-338,584-605

2107 atoms, 2124 bonds, 140 residues, 1 model selected  

> show cartoons sel

Expected ',' or a keyword  

> show sel cartoons

> measure center #1:221-338,584-605

Center of mass of 2107 atoms = (58.82, 66.36, 37.16)  

> measure center #1:221-338,584-605@C*

Center of mass of 666 atoms = (58.52, 66.30, 36.92)  

> open
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/trueB_withNAD__BFahq_Hid290_aligned_renum.pdb

Chain information for trueB_withNAD__BFahq_Hid290_aligned_renum.pdb #12  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  

> color #12 #a97817ff

> color #12 #ffb624ff

> color #12 #ffa724ff

> color #12 #ff9727ff

> color #12 #ff8722ff

> color #12 #ffad66ff

> color #12 #ffa442ff

> select #12:13-207,348-358,379-574

6173 atoms, 6223 bonds, 402 residues, 1 model selected  

> align #12:221-338,584-605@CA toAtoms #1:221-338,584-605@CA reportMatrix true
> move nothing

Alignment matrix in structure trueB_withNAD__BFahq_Hid290_aligned_renum.pdb
coordinates  
Matrix rotation and translation  
0.96342787 -0.18037943 0.19816658 13.39127429  
0.23666858 0.91960542 -0.31355039 -3.05142166  
-0.12567702 0.34898299 0.92866364 -17.23809046  
Axis 0.78202365 0.38224996 0.49226413  
Axis point 0.00000000 45.95014549 -22.51339336  
Rotation angle (degrees) 25.06219877  
Shift along axis 0.82019388  
  
RMSD between 140 atom pairs is 1.212 angstroms  

> align #12:13-207,348-358,379-574@CA toAtoms #1:13-207,348-358,379-574@CA
> reportMatrix true move nothing

Alignment matrix in structure trueB_withNAD__BFahq_Hid290_aligned_renum.pdb
coordinates  
Matrix rotation and translation  
0.99999480 0.00272965 0.00171683 -0.22484504  
-0.00272426 0.99999138 -0.00313200 0.27460455  
-0.00172537 0.00312730 0.99999362 -0.16213848  
Axis 0.69645600 0.38300456 -0.60684145  
Axis point 0.00000000 42.89811732 81.81495091  
Rotation angle (degrees) 0.25746986  
Shift along axis 0.04697247  
  
RMSD between 402 atom pairs is 1.594 angstroms  

> define axis fromPoint 0,0,0 toPoint 19.5, 9.5, 12.3 id 13 color orange
> radius 0.3

Axis 'axis' centered at [9.75 4.75 6.15] with direction [19.5 9.5 12.3],
radius 0.3, and length 24.9357  

> hide #12 cartoons

> hide #12 protein

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide protein

> name flavinatoms
> @N1,C2,O2,N3,C4,C4X,O4,C5X,N5,C6,C7,C7M,C8,C8M,C9,C9A,C10,N10

> hide

> show flavinAtoms

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show flavinAtom

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> select @N1,C2,O2,N3,C4,C4X,O4,C5X,N5,C6,C7,C7M,C8,C8M,C9,C9A,C10,N10

300 atoms, 328 bonds, 17 residues, 8 models selected  

> show sel

> name flavinAtons sel

> select clear

> select flavinAtoms

Expected an objects specifier or a keyword  

> close #8

> define axis fromPoint 0,0,0 toPoint 21.8, 57.7, 46.6 id 8 color yellow
> radius 0.3

Axis 'axis' centered at [10.9 28.85 23.3 ] with direction [21.8 57.7 46.6],
radius 0.3, and length 77.3052  

> hide :NDP

> help name

> name flavinatoms
> @N1,C2,O2,N3,C4,C4X,O4,C5X,N5,C6,C7,C7M,C8,C8M,C9,C9A,C10,N10

> hide flavinAtoms

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> save
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/DomainReorientations.cxs

> name frozen flavinatoms
> @N1,C2,O2,N3,C4,C4X,O4,C5X,N5,C6,C7,C7M,C8,C8M,C9,C9A,C10,N10

> select flavinatoms

300 atoms, 328 bonds, 17 residues, 8 models selected  

> name delete flavinatons

deregistering unregistered selector ""flavinatons""  

> select clear

> save
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/DomainReorientations.cxs

> color flavinatoms byhetero

> save
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/DomainReorientations.cxs

> close #8

> close #9

> close #10

> close #11

> close #13

> define axis fromPoint 58.2,66.3,36.9 toPoint 67.3, 69.9, 42.4 id 8 color
> dodgerblue radius 0.3

Axis 'axis' centered at [62.75 68.1 39.65] with direction [9.1 3.6 5.5],
radius 0.3, and length 11.2259  

> define axis fromPoint 58.2,66.3,36.9 toPoint 63.7, 55.2, 44.6 id 9 color
> orchid radius 0.3

Axis 'axis' centered at [60.95 60.75 40.75] with direction [ 5.5 -11.1 7.7],
radius 0.3, and length 14.586  

> define axis fromPoint 58.2,66.3,36.9 toPoint 66.8, -62.1, 38.4 id 10 color
> springgreen radius 0.3

Axis 'axis' centered at [62.5 2.1 37.65] with direction [ 8.6 -128.4 1.5],
radius 0.3, and length 128.696  

> close #10

> define axis fromPoint 58.2,66.3,36.9 toPoint 66.8, 62.1, 38.4 id 10 color
> springgreen radius 0.3

Axis 'axis' centered at [62.5 64.2 37.65] with direction [ 8.6 -4.2 1.5],
radius 0.3, and length 9.68762  

> define axis fromPoint 58.2, 66.3, 36.9 toPoint 78.1, 75.8, 49.2 id 11 color
> orange radius 0.3

Axis 'axis' centered at [68.15 71.05 43.05] with direction [19.9 9.5 12.3],
radius 0.3, and length 25.2498  

> define axis fromPoint 58.2, 66.3, 36.9 toPoint 36.8, 123.7, 84.3 id 12 color
> yellow radius 0.3

Axis 'axis' centered at [47.5 95. 60.6] with direction [-21.4 57.4 47.4],
radius 0.3, and length 77.4563  
Drag select of 3 residues  

> select clear

> show #3:221-338,584-605 ribbons

> align #3:221-338,584-605@CA toAtoms #1:221-338,584-605@CA reportMatrix true
> move nothing

Alignment matrix in structure trueB_EThq_Bfox_Hip290_aligned.pdb coordinates  
Matrix rotation and translation  
0.97255225 -0.14092020 -0.18515837 20.55175664  
0.12376651 0.98713738 -0.10120097 -6.47801378  
0.19703801 0.07550683 0.97748388 -18.84704686  
Axis 0.35529743 -0.76846290 0.53219217  
Axis point 112.02142686 0.00000000 90.07237907  
Rotation angle (degrees) 14.39917143  
Shift along axis 2.24984877  
  
RMSD between 140 atom pairs is 0.926 angstroms  

> show #3 ribbons

> show #1 ribbons

> hide #1 ribbons

> show #1:221-338,584-605 ribbons

> hide #3 ribbons

> show #3:221-338,584-605 ribbons

> define axis fromPoint 65.0, 67.3, 22.3 toPoint 73.24, 63.1, 23.8 id 10 color
> springgreen radius 0.3

Axis 'axis' centered at [69.12 65.2 23.05] with direction [ 8.24 -4.2 1.5 ],
radius 0.3, and length 9.3695  

> close #10.1


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

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/closed_conformer_beforeMD.pdb

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




OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M3
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: Mac15,13
      Model Number: Z1BV0006PLL/A
      Chip: Apple M3
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.81.4
      OS Loader Version: 11881.81.4

Software:

    System Software Overview:

      System Version: macOS 15.3.2 (24D81)
      Kernel Version: Darwin 24.3.0
      Time since boot: 2 hours, 5 minutes

Graphics/Displays:

    Apple M3:

      Chipset Model: Apple M3
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2880 x 1864 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    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: 1.2.1
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-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
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    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: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    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: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    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: 1.18.1
    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
    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: 1.41
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    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: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
}}}
"	defect	closed	normal		Window Toolkit		duplicate						all	ChimeraX