Pseudobond drawing: Cylinder end point, radii or rotation array not contiguous

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-12.5-arm64-arm-64bit
ChimeraX Version: 1.5.dev202208030611 (2022-08-03 06:11:58 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5.dev202208030611 (2022-08-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/wangzhiming/Desktop/ChimeraX/nacht_dimer_J24-coot-36_16_real_space_refined_013.pdb

Chain information for nacht_dimer_J24-coot-36_16_real_space_refined_013.pdb #1  
---  
Chain | Description  
A B | No description available  
  

> hide #!1 models

> open
> /Users/wangzhiming/Desktop/ChimeraX/cryosparc_P92_J24_006_volume_map_sharp_zflip.mrc

Opened cryosparc_P92_J24_006_volume_map_sharp_zflip.mrc as #2, grid size
360,360,360, pixel 0.84, shown at level 0.0814, step 2, values float32  

> surface dust #2

> volume #2 level 0.2096

> volume #2 step 1

> show #!1 models

> hide #!1 models

> color sel salmon

> select add #2

2 models selected  

> color sel salmon

> color sel green

> color sel blue

> color sel purple

> color sel orange

> color sel green

> color sel salmon

> volume #2 subdivideSurface true

> volume #2 subdivideSurface true subdivisionLevels 2

> color zone #2 near #1 distance 8

[Repeated 2 time(s)]

> select subtract #2

Nothing selected  

> show #!1 models

> hide #!2 models

> select add #1

9726 atoms, 9922 bonds, 2 pseudobonds, 1190 residues, 2 models selected  

> color bychain

> select subtract #1

Nothing selected  

> show #!2 models

> color zone #2 near #1 distance 8

> select add #1

9726 atoms, 9922 bonds, 2 pseudobonds, 1190 residues, 2 models selected  

> select add #2

9726 atoms, 9922 bonds, 2 pseudobonds, 1190 residues, 4 models selected  

> select subtract #2

9726 atoms, 9922 bonds, 2 pseudobonds, 1190 residues, 2 models selected  

> select subtract #1

Nothing selected  

> volume #2 level 0.3063

> volume #2 level 0.3661

> volume #2 level 0.2603

> select add #1

9726 atoms, 9922 bonds, 2 pseudobonds, 1190 residues, 2 models selected  

> select add #2

9726 atoms, 9922 bonds, 2 pseudobonds, 1190 residues, 4 models selected  

> volume #2 level 0.2142

> volume #2 level 0.1498

> select subtract #1

2 models selected  

> select add #1

9726 atoms, 9922 bonds, 2 pseudobonds, 1190 residues, 4 models selected  

> volume #2 level 0.113

> volume #2 level 0.2096

> select subtract #1

2 models selected  

> select add #1

9726 atoms, 9922 bonds, 2 pseudobonds, 1190 residues, 4 models selected  

> select subtract #2

9726 atoms, 9922 bonds, 2 pseudobonds, 1190 residues, 2 models selected  

> select subtract #1

Nothing selected  

> color zone #2 near #1 distance 5

> select add #2

2 models selected  

> select add #1

9726 atoms, 9922 bonds, 2 pseudobonds, 1190 residues, 4 models selected  

> color zone #2 near #1 distance 5

> volume #2 style image

> volume #2 style surface

> volume #2 level 0.15

> volume #2 change image level -0.02646,0 level 0.08121,0.8 level 1.623,1

> volume #2 level 0.3

> select add #2

9726 atoms, 9922 bonds, 2 pseudobonds, 1190 residues, 5 models selected  

> select add #2

9726 atoms, 9922 bonds, 2 pseudobonds, 1190 residues, 5 models selected  

> select subtract #1

3 models selected  

> select add #2

3 models selected  

> hide #!1 models

> show #!1 models

> hide #!2 models

> select add #2

3 models selected  

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> volume #2 level 0.35

> select add #2

3 models selected  

> select add #2

3 models selected  

> select add #1

9726 atoms, 9922 bonds, 2 pseudobonds, 1190 residues, 5 models selected  

> select subtract #1

3 models selected  

> select add #1

9726 atoms, 9922 bonds, 2 pseudobonds, 1190 residues, 5 models selected  

> select subtract #1

3 models selected  

> select add #2

3 models selected  

> select add #2.2

3 models selected  

> select subtract #2.1

2 models selected  

> color zone #2 near #1 distance 8

> select add #1

9726 atoms, 9922 bonds, 2 pseudobonds, 1190 residues, 4 models selected  

> select add #2.1

9726 atoms, 9922 bonds, 2 pseudobonds, 1190 residues, 5 models selected  

> show #2.2 models

> color zone #2 near #1 distance 8

> select subtract #1

3 models selected  

> select subtract #2.1

2 models selected  

> volume #2 change surface level 0.3

> volume #2 change surface level 0.25

> volume #2 change surface level 0.2

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> volume #2 change surface level 0.3

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> volume #2 change surface level 0.25

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!2 target m

> view #2 clip false

[Repeated 1 time(s)]

> volume #2 change surface level 0.3

> volume #2 change surface level 0.25

> volume #2 change surface level 0.27

> volume #2 change surface level 0.28

> volume #2 change surface level 0.27

> volume #2 change surface level 0.26

> volume #2 change surface level 0.25

> volume #2 change surface level 0.23

> volume #2 change surface level 0.25

> open
> /Users/wangzhiming/Desktop/桌面/longfei_data/NACHT/dimer_inhibition_state/phenix/RealSpaceRefine_13/nacht_dimer_J24-coot-36_16_real_space_refined_013.pdb

Chain information for nacht_dimer_J24-coot-36_16_real_space_refined_013.pdb #3  
---  
Chain | Description  
A B | No description available  
  

> open
> /Users/wangzhiming/Desktop/桌面/longfei_data/NACHT/dimer_inhibition_state/phenix/RealSpaceRefine_13/nacht_dimer_J24-coot-36_16_real_space_refined_013.pdb

Chain information for nacht_dimer_J24-coot-36_16_real_space_refined_013.pdb #4  
---  
Chain | Description  
A B | No description available  
  

> close #3

> close #4

> surface zone #2 nearAtoms #1/A:60-656

> surface zone #2 nearAtoms #1/A:60-656 B:60-656

Expected a keyword  

> surface zone #2 nearAtoms #1/A:60-656 #1/B:60-656

> show #!1 models

> hide #!1 models

> show #!1 models

> surface zone #2 nearAtoms #1/A:50-656 #1/B:50-656

> volume #2 change surface level 0.2

> hide #!1 models

> volume #2 change surface level 0.25

> volume #2 change surface level 0.3

> volume #2 change surface level 0.25

> surface zone #2 nearAtoms #1/A:50-656 #1/B:50-656 distance 2

[Repeated 1 time(s)]

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> volume #2 change surface level 0.3

> volume #2 change surface level 0.25

> show target m

> view clip false

> hide #!1 models

> volume #2 change surface level 0.2

> volume #2 change surface level 0.15

> volume #2 change surface level 0.2

> toolshed show

> volume #2 change surface level 0.15

> volume #2 change surface level 0.2

> surface zone #2 nearAtoms #1/A:50-656 #1/B:50-656

> volume #2 change surface level 0.25

> select add #2.1

3 models selected  

> select subtract #2.1

2 models selected  

> hide #2.2 models

> show #2.2 models

> hide #2.2 models

> show #2.2 models

> hide #2.2 models

> select add #2.2

2 models selected  

> select add #2.2

2 models selected  

> hide #2.1 models

> show #2.1 models

> hide #!2 models

> show #!2 models

> select add #2

3 models selected  

> select add #2

3 models selected  

> select subtract #2.1

2 models selected  

> surface zone #2 nearAtoms #1/A:50-656 #1/B:50-656

> volume sel step 1

> save /Users/wangzhiming/Desktop/image1.png supersample 3

> save /Users/wangzhiming/Desktop/ChimeraX/Nacht_dimer_map_surface.gif width
> 817 height 597 supersample 3

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> preset "overall look" "publication 2 (depth-cued)"

Using preset: Overall Look / Publication 2 (Depth-Cued)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes f
    lighting depthCue t

  

> preset "overall look" interactive

Using preset: Overall Look / Interactive  
Preset expands to these ChimeraX commands:

    
    
    ~set bg
    graphics silhouettes f
    lighting depthCue t

  

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> preset "overall look" interactive

Using preset: Overall Look / Interactive  
Preset expands to these ChimeraX commands:

    
    
    ~set bg
    graphics silhouettes f
    lighting depthCue t

  

> volume #2 level 0.1

> volume #2 level 0.2

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> save /Users/wangzhiming/Desktop/ChimeraX/Nacht_dimer_map_surface_2.gif width
> 817 height 597 supersample 4

> preset "overall look" interactive

Using preset: Overall Look / Interactive  
Preset expands to these ChimeraX commands:

    
    
    ~set bg
    graphics silhouettes f
    lighting depthCue t

  

> help help:quickstart

> hide #!2 models

> show #!1 models

> help help:quickstart

> show #!2 models

> save /Users/wangzhiming/Desktop/ChimeraX/nacht_dimer_refine13.cxs

> sequence chain #1/A#1/B

Alignment identifier is 1  

> help help:quickstart

[Repeated 1 time(s)]

> help help:user

> help help:quickstart

> help help:user

> close session

> open
> /Users/wangzhiming/Desktop/ChimeraX/cryosparc_P92_J24_006_volume_map_sharp_zflip.mrc

Opened cryosparc_P92_J24_006_volume_map_sharp_zflip.mrc as #1, grid size
360,360,360, pixel 0.84, shown at level 0.0814, step 2, values float32  

> help help:quickstart

> close

> close session

> open
> /Users/wangzhiming/Desktop/ChimeraX/cryosparc_p92_J24_006_volume_map_sharp_zflip.mrc

Opened cryosparc_p92_J24_006_volume_map_sharp_zflip.mrc as #1, grid size
360,360,360, pixel 0.84, shown at level 0.0814, step 2, values float32  

> close

> open ~./cryosparc_p92_J24_006_volume_map_sharp_zflip.mrc

No such file/path: ~./cryosparc_p92_J24_006_volume_map_sharp_zflip.mrc  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)  

> open ~./cryosparc_p92_J24_006_volume_map_sharp_zflip.mrc

No such file/path: ~./cryosparc_p92_J24_006_volume_map_sharp_zflip.mrc  

> open
> /Users/wangzhiming/Desktop/ChimeraX/cryosparc_p92_J24_006_volume_map_sharp_zflip.mrc

Opened cryosparc_p92_J24_006_volume_map_sharp_zflip.mrc as #1, grid size
360,360,360, pixel 0.84, shown at level 0.0814, step 2, values float32  

> lighting full

> volume #1 level 0.9

> volume #1 level 0.3

> volume #1 step 1

> volume #1 step 1 level 0.5

> volume #1 step 1 level 0.3

> volume #1 step 1 level 0.2

> volume #1 step 1 level 0.2.5

Invalid "level" argument: Expected a number  

> volume #1 step 1 level 0.25

> volume #1 step 1 level 0.2

> volume #1 step 1 level 0.3

> volume #1 step 1 level 0.2.5

Invalid "level" argument: Expected a number  

> volume #1 step 1 level 0.25

> open
> /Users/wangzhiming/Desktop/ChimeraX/nacht_dimer_J24-coot-36_16_real_space_refined_013.pdb

Chain information for nacht_dimer_J24-coot-36_16_real_space_refined_013.pdb #2  
---  
Chain | Description  
A B | No description available  
  

> lighting full

> lighting default

> volume #1 level 0.3

> volume #1 level 0.2

> volume #1 level 0.25

> color #2 bychain

> surface dust #1

> volume #1 subdivideSurface true

> surface dust #1

> color zone #1 near #2 distance 8

> color zone #1 near #2 distance 6

> color zone #1 near #2 distance 8

[Repeated 1 time(s)]

> color zone #1 near #2 distance 10

> color zone #1 near #2 distance 8

> surface zone #1 nearAtoms #2/A:50-652 #2/B:50-652 distance 8

> surface zone #1 nearAtoms #2/A:50-652 #2/B:50-652 distance 2

> surface zone #1 nearAtoms #2/A:50-652 #2/B:50-652 distance 1

> surface zone #1 nearAtoms #2/A:50-652 #2/B:50-652 distance 2

> surface zone #1 nearAtoms #2/A:50-652 #2/B:50-652 distance 3

> surface zone #1 nearAtoms #2/A:50-652 #2/B:50-652 distance 4

> surface zone #1 nearAtoms #2/A:50-652 #2/B:50-652 distance 2

> surface zone #1 nearAtoms #2/A:50-652 #2/B:50-652 distance 3

> surface zone #1 nearAtoms #2/A:50-652 #2/B:50-652 distance 4

> surface zone #1 nearAtoms #2/A:50-652 #2/B:50-652 distance 2

> surface zone #1 nearAtoms #2/A:50-652 #2/B:50-652 distance 4

> surface zone #1 nearAtoms #2/A:50-652 #2/B:50-652 distance 2

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> help help:quickstart

> set bg.white

Expected a keyword  

> set bgColor gray

> set bgColor #80808000

> set silhouettes true

> set bg.black

Expected a keyword  

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> set silhouettes true

> hide #!2 models

> save /Users/wangzhiming/Desktop/image1.png supersample 3

[Repeated 1 time(s)]

> help help:user

> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html

Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html  

> save /Users/wangzhiming/Desktop/image1.png supersample 3

[Repeated 1 time(s)]

> hide #!1 models

> show #!2 models

> set #2 cartoon

Expected a keyword  

> set #2 Cartoons

Expected a keyword  

> set #2 Cartoon

Expected a keyword  

> help help:quickstart

> ribbon

> hide cartoons

Traceback (most recent call last):  
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 1766, in
_update_graphics_if_needed  
s[i].update_graphics_if_needed()  
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 358, in update_graphics_if_needed  
self._update_graphics(gc)  
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 376, in _update_graphics  
pbg._update_graphics(changes)  
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/pbgroup.py", line 221, in _update_graphics  
d.positions = self._update_positions(pbonds, bond_atoms)  
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/pbgroup.py", line 238, in _update_positions  
return s._halfbond_cylinder_placements(axyz0, axyz1, pbonds.radii)  
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 2284, in
_halfbond_cylinder_placements  
half_cylinder_rotations(axyz0, axyz1, radii, p)  
ValueError: Cylinder end point, radii or rotation array not contiguous.  
  
Error processing trigger "graphics update":  
ValueError: Cylinder end point, radii or rotation array not contiguous.  
  
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 2284, in
_halfbond_cylinder_placements  
half_cylinder_rotations(axyz0, axyz1, radii, p)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.1
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac mini
      Model Identifier: Macmini9,1
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 7459.141.1
      OS Loader Version: 7459.141.1

Software:

    System Software Overview:

      System Version: macOS 12.5 (21G72)
      Kernel Version: Darwin 21.6.0
      Time since boot: 1 day 1:43

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        U28G2G6B:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.0.5
    Babel: 2.10.3
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.7.0
    certifi: 2021.10.8
    cftime: 1.6.1
    charset-normalizer: 2.1.0
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.5.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.7
    ChimeraX-AtomicLibrary: 7.0.2
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1.1
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChangeChains: 1.0
    ChimeraX-CheckWaters: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.1
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5.dev202208030611
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.6
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.2.1
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.5
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.7
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.21.4
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.2
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 0.9.1
    filelock: 3.4.2
    fonttools: 4.34.4
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.33
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 4.12.0
    ipykernel: 6.15.1
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 4.11.1
    kiwisolver: 1.4.4
    line-profiler: 3.4.0
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.3
    msgpack: 1.0.4
    nest-asyncio: 1.5.5
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.3
    numpy: 1.23.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.12.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.30
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.1
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.1
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.2.0
    qtconsole: 5.3.1
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 62.6.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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
    stack-data: 0.3.0
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.11
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.3.0
    zipp: 3.8.1