Segger: bounding_grid() missing 1 required positional argument: 'cube'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-15.1-x86_64-i386-64bit
ChimeraX Version: 1.9.dev202409210117 (2024-09-21 01:17:36 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.9.dev202409210117 (2024-09-21)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/yuliiamironova/Downloads/7fj1.cif

7fj1.cif title:  
Cryo-EM structure of pseudorabies virus C-capsid [more info...]  
  
Chain information for 7fj1.cif #1  
---  
Chain | Description | UniProt  
0 A S U a e f g l m n p q u w y | Major capsid protein | G3G8T2_9ALPH 1-1330  
1 2 3 j k o s v x z | Triplex capsid protein 2 | G3G8T3_9ALPH 1-296  
B | Capsid vertex component 1 | G3G8T5_9ALPH 1-597  
E F G H I J K L M N O P Q R V | Small capsomere-interacting protein | G3G8R4_9ALPH 1-103  
T h i r t | Triplex capsid protein 1 | Q85211_9ALPH 1-368  
X c | DNA packaging tegument protein UL25 | G3G971_9ALPH -11-522 1-534  
Y Z | VP1/2 | G3G8Y0_9ALPH 3077-3138  
  
7fj1.cif mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
  

> select /X:1-73

552 atoms, 565 bonds, 73 residues, 1 model selected  

> select /c:10-84

558 atoms, 571 bonds, 75 residues, 1 model selected  

> select /Y

353 atoms, 354 bonds, 45 residues, 1 model selected  

> select /Y/Z

641 atoms, 643 bonds, 80 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /E

722 atoms, 736 bonds, 1 pseudobond, 91 residues, 2 models selected  

> select /E/F/G/H/I/J/K/L/M/N/O/P/Q/R/V

10830 atoms, 11040 bonds, 15 pseudobonds, 1365 residues, 2 models selected  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> select /B

4023 atoms, 4120 bonds, 1 pseudobond, 524 residues, 2 models selected  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> select /X/c

1110 atoms, 1136 bonds, 148 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> save /Users/yuliiamironova/Documents/writing/mcp_triplex.pdb displayedOnly
> true relModel #1

> select /e

8722 atoms, 8938 bonds, 11 pseudobonds, 1126 residues, 2 models selected  

> save /Users/yuliiamironova/Documents/writing/penton.pdb selectedOnly true
> relModel #1

> close

> open /Users/yuliiamironova/Documents/writing/penton.pdb format pdb

Summary of feedback from opening
/Users/yuliiamironova/Documents/writing/penton.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ASN 0 36 GLY 0 40 1 5  
Start residue of secondary structure not found: HELIX 2 2 GLY 0 63 VAL 0 66 1
4  
Start residue of secondary structure not found: HELIX 3 3 GLU 0 75 VAL 0 79 1
5  
Start residue of secondary structure not found: HELIX 4 4 ALA 0 125 GLY 0 134
1 10  
Start residue of secondary structure not found: HELIX 5 5 SER 0 143 ALA 0 181
1 39  
1664 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (44 )  
Cannot find LINK/SSBOND residue CYS (44 )  
Cannot find LINK/SSBOND residue CYS (44 )  
Cannot find LINK/SSBOND residue CYS (44 )  
Cannot find LINK/SSBOND residue CYS (44 )  
  
Chain information for penton.pdb #1  
---  
Chain | Description  
e | No description available  
  

> open
> /Users/yuliiamironova/Documents/writing/run2_fromIter9_symm_c5_AvgVol_0P1440.mrc

Summary of feedback from opening
/Users/yuliiamironova/Documents/writing/run2_fromIter9_symm_c5_AvgVol_0P1440.mrc  
---  
note | /Users/yuliiamironova/Documents/writing/run2_fromIter9_symm_c5_AvgVol_0P1440.mrc: invalid cell angles 0,0,0 must be between 0 and 180.  
  
Opened run2_fromIter9_symm_c5_AvgVol_0P1440.mrc as #2, grid size 48,48,48,
pixel 17.2, shown at level 2, step 1, values float32  

> vop scale #2 factor -1

Opened run2_fromIter9_symm_c5_AvgVol_0P1440.mrc scaled as #3, grid size
48,48,48, pixel 17.2, shown at step 1, values float32  

> close #2

> volume #3 level 0.04663

> volume #3 level -0.1695

> select add #1

8722 atoms, 8938 bonds, 11 pseudobonds, 1126 residues, 3 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.77992,-0.38576,0.49286,-150.23,-0.5531,-0.79337,0.25426,650.51,0.29294,-0.47091,-0.83213,1428.3

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.77992,-0.38576,0.49286,-67.131,-0.5531,-0.79337,0.25426,598.62,0.29294,-0.47091,-0.83213,1135.2

> view matrix models
> #1,0.77992,-0.38576,0.49286,-14.978,-0.5531,-0.79337,0.25426,594.33,0.29294,-0.47091,-0.83213,1147

> ui tool show "Fit in Map"

> fitmap #1 inMap #3

Fit molecule penton.pdb (#1) to map run2_fromIter9_symm_c5_AvgVol_0P1440.mrc
scaled (#3) using 8722 atoms  
average map value = -0.1581, steps = 104  
shifted from previous position = 37.7  
rotated from previous position = 61.1 degrees  
atoms outside contour = 4151, contour level = -0.16951  
  
Position of penton.pdb (#1) relative to
run2_fromIter9_symm_c5_AvgVol_0P1440.mrc scaled (#3) coordinates:  
Matrix rotation and translation  
0.11521754 0.21102294 0.97066690 -432.81410124  
-0.48918731 -0.83841158 0.24033686 641.09159328  
0.86453496 -0.50252895 0.00663003 400.20514692  
Axis -0.72378914 0.10340649 -0.68222897  
Axis point 0.00000000 379.84062564 283.88262521  
Rotation angle (degrees) 149.12423024  
Shift along axis 106.52763426  
  
Opened penton.pdb map 25 as #2, grid size 36,31,30, pixel 8.33, shown at level
0.0258, step 1, values float32  

> fitmap #1 inMap #3 resolution 25 metric correlation

Fit map penton.pdb map 25 in map run2_fromIter9_symm_c5_AvgVol_0P1440.mrc
scaled using 686 points  
correlation = -0.347, correlation about mean = 0.2402, overlap = -18.05  
steps = 80, shift = 1.74, angle = 1.55 degrees  
  
Position of penton.pdb map 25 (#2) relative to
run2_fromIter9_symm_c5_AvgVol_0P1440.mrc scaled (#3) coordinates:  
Matrix rotation and translation  
0.10532815 0.23143672 0.96713134 -436.76775032  
-0.50002121 -0.82833130 0.25267777 631.13712109  
0.85958407 -0.51020026 0.02847667 387.29450578  
Axis -0.71810662 0.10123559 -0.68853049  
Axis point -0.00000000 377.60678275 278.92323861  
Rotation angle (degrees) 147.91524036  
Shift along axis 110.87527532  
  
Average map value = -0.16 for 8722 atoms, 4129 outside contour  

> show #!2 models

Opened penton.pdb map 16 as #2, grid size 46,38,37, pixel 5.33, shown at level
0.0425, step 1, values float32  

> fitmap #1 inMap #3 resolution 16 metric correlation

Fit map penton.pdb map 16 in map run2_fromIter9_symm_c5_AvgVol_0P1440.mrc
scaled using 1924 points  
correlation = -0.3817, correlation about mean = 0.1743, overlap = -62.76  
steps = 80, shift = 1.52, angle = 4.11 degrees  
  
Position of penton.pdb map 16 (#2) relative to
run2_fromIter9_symm_c5_AvgVol_0P1440.mrc scaled (#3) coordinates:  
Matrix rotation and translation  
0.08303306 0.28273216 0.95559826 -441.74765707  
-0.45888564 -0.84034981 0.28850680 599.40821447  
0.88460696 -0.46246592 0.05996491 338.59141306  
Axis -0.70992055 0.06711053 -0.70107702  
Axis point 0.00000000 363.50332010 268.20968883  
Rotation angle (degrees) 148.06794543  
Shift along axis 116.45368701  
  
Average map value = -0.1663 for 8722 atoms, 4191 outside contour  

> show #!2 models

> view matrix models
> #1,0.083033,0.28273,0.9556,-435.07,-0.45889,-0.84035,0.28851,590.25,0.88461,-0.46247,0.059965,366.99

> view matrix models
> #1,0.083033,0.28273,0.9556,-437.24,-0.45889,-0.84035,0.28851,591.61,0.88461,-0.46247,0.059965,329.25

> hide #!2 models

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.052767,0.18246,0.9818,-409.67,-0.8274,-0.5425,0.14529,674.18,0.55913,-0.82001,0.12234,505.57

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.052767,0.18246,0.9818,-416.96,-0.8274,-0.5425,0.14529,671.95,0.55913,-0.82001,0.12234,519.55

> fitmap #1 inMap #3 resolution 16 metric correlation moveWholeMolecules false

Fit map penton.pdb map 16 in map run2_fromIter9_symm_c5_AvgVol_0P1440.mrc
scaled using 1924 points  
correlation = -0.2729, correlation about mean = 0.2194, overlap = -53.5  
steps = 120, shift = 48.7, angle = 60 degrees  
  
Position of penton.pdb map 16 (#2) relative to
run2_fromIter9_symm_c5_AvgVol_0P1440.mrc scaled (#3) coordinates:  
Matrix rotation and translation  
-0.49392245 0.08758082 0.86508393 -173.51401637  
-0.83690659 0.22198817 -0.50030852 871.82858596  
-0.23585583 -0.97110805 -0.03634797 852.43471271  
Axis -0.31122200 0.72777616 -0.61113234  
Axis point 399.61294399 -0.00000000 830.39393083  
Rotation angle (degrees) 130.85455765  
Shift along axis 167.54701635  
  
Average map value = -0.138 for 8722 atoms, 3616 outside contour  

> close #2

> close

> open
> /Users/yuliiamironova/Documents/writing/run2_fromIter9_symm_c5_AvgVol_0P1440.mrc
> format mrc

Summary of feedback from opening
/Users/yuliiamironova/Documents/writing/run2_fromIter9_symm_c5_AvgVol_0P1440.mrc  
---  
note | /Users/yuliiamironova/Documents/writing/run2_fromIter9_symm_c5_AvgVol_0P1440.mrc: invalid cell angles 0,0,0 must be between 0 and 180.  
  
Opened run2_fromIter9_symm_c5_AvgVol_0P1440.mrc as #1, grid size 48,48,48,
pixel 17.2, shown at level 2, step 1, values float32  

> vop scale #2 factor -1

> vop scale #1 factor -1

Opened run2_fromIter9_symm_c5_AvgVol_0P1440.mrc scaled as #2, grid size
48,48,48, pixel 17.2, shown at step 1, values float32  

> volume #2 level -0.03983

> volume #2 level -0.1176

> ui tool show "Segment Map"

> close #1

Segmenting run2_fromIter9_symm_c5_AvgVol_0P1440.mrc scaled, density threshold
-0.117633  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 389, in _segment  
self.Segment()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 2123, in Segment  
smod = self.SegmentAndGroup(show, group)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 2184, in SegmentAndGroup  
self.RegsDispUpdate ( task ) # Display region surfaces  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 1975, in RegsDispUpdate  
smod.display_regions(vis_mode, maxnr, task)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/regions.py", line 762, in display_regions  
reg.make_surface (None,None,self.regions_scale,bForce)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/regions.py", line 1173, in make_surface  
vertices, normals, triangles, level = gaussian_surface(pts, weights, res,
level = 0.1)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/gaussian.py", line 31, in gaussian_surface  
grid = bounding_grid(xyz, grid_spacing, pad)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
TypeError: bounding_grid() missing 1 required positional argument: 'cube'  
  
TypeError: bounding_grid() missing 1 required positional argument: 'cube'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/gaussian.py", line 31, in gaussian_surface  
grid = bounding_grid(xyz, grid_spacing, pad)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Showing run2_fromIter9_symm_c5_AvgVol_0P1440 scaled.seg - 18 regions, 0
surfaces  
Segmenting run2_fromIter9_symm_c5_AvgVol_0P1440.mrc scaled, density threshold
-0.117633  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 389, in _segment  
self.Segment()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 2123, in Segment  
smod = self.SegmentAndGroup(show, group)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 2184, in SegmentAndGroup  
self.RegsDispUpdate ( task ) # Display region surfaces  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 1975, in RegsDispUpdate  
smod.display_regions(vis_mode, maxnr, task)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/regions.py", line 762, in display_regions  
reg.make_surface (None,None,self.regions_scale,bForce)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/regions.py", line 1173, in make_surface  
vertices, normals, triangles, level = gaussian_surface(pts, weights, res,
level = 0.1)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/gaussian.py", line 31, in gaussian_surface  
grid = bounding_grid(xyz, grid_spacing, pad)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
TypeError: bounding_grid() missing 1 required positional argument: 'cube'  
  
TypeError: bounding_grid() missing 1 required positional argument: 'cube'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/gaussian.py", line 31, in gaussian_surface  
grid = bounding_grid(xyz, grid_spacing, pad)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Showing run2_fromIter9_symm_c5_AvgVol_0P1440 scaled.seg - 111 regions, 0
surfaces  

> ui tool show Segmentations

> ui view fourup

> segmentations mouseModes false

Mouse bindings not saved; ignoring 'mouseModes false'  

> ui view fourup

> segmentations mouseModes false

Mouse bindings not saved; ignoring 'mouseModes false'  

> ui view overunder

> segmentations create #2

Opened segmentation 1 of run2_fromIter9_symm_c5_AvgVol_0P1440.mrc scaled as
#6, grid size 48,48,48, pixel 17.2, shown at level 0.501, step 1, values
float64  




OpenGL version: 4.1 ATI-6.1.13
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2,3 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 2069.40.2.0.0 (iBridge: 22.16.11072.0.0,0)
      OS Loader Version: 582~2132

Software:

    System Software Overview:

      System Version: macOS 15.1 (24B83)
      Kernel Version: Darwin 24.1.0
      Time since boot: 2 days, 2 hours, 46 minutes

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-020
      Option ROM Version: 113-D32206U1-020
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL U2723QE:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 491L7P3     
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort
        DELL U2720Q:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: B9XVV13     
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.7.1
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.14
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.7
    ChimeraX-AtomicLibrary: 14.1.7
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.7
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.3.4
    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.dev202409210117
    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-DeepMutationalScan: 1.0
    ChimeraX-Dicom: 1.2.5
    ChimeraX-DiffPlot: 1.0
    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-Label: 1.1.11
    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: 2.7.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    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-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
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3
    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: 3.2.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.13
    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: 1.40.1
    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: 1.3.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.5
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.53.1
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    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: 2.1.5
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.1
    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: 3.0.47
    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
    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: 3.1.4
    pyproject_hooks: 1.1.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.2
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.2
    PyQt6-WebEngineSubwheel-Qt6: 6.7.2
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.1
    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
    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: 6.4.1
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.1
    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