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

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-12.2.1-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:
> volume #2 transparency 0

> lighting soft

> show #!1 models

> select #1

2 models selected  

> view matrix models
> #1,0.69232,0.68453,0.22827,-51.695,-0.54005,0.70134,-0.46526,134.83,-0.47858,0.19883,0.85524,49.79

> view matrix models
> #1,0.64087,0.34474,-0.68589,72.238,-0.72574,-0.019091,-0.6877,246.68,-0.25017,0.9385,0.23796,9.3352

> view matrix models
> #1,0.22485,-0.26043,-0.93895,202.52,-0.78741,-0.61618,-0.017652,249.1,-0.57396,0.7433,-0.34361,119.92

> view matrix models
> #1,0.11798,-0.18704,-0.97524,211.21,-0.80804,-0.58894,0.015202,245.8,-0.5772,0.78624,-0.22062,104.69

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.11798,-0.18704,-0.97524,201.79,-0.80804,-0.58894,0.015202,235.84,-0.5772,0.78624,-0.22062,119.29

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.23915,0.015601,-0.97086,167.75,-0.63725,-0.75189,-0.16906,248.93,-0.73261,0.65911,-0.16987,144.87

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.23915,0.015601,-0.97086,166.56,-0.63725,-0.75189,-0.16906,263.01,-0.73261,0.65911,-0.16987,138.56

> view matrix models
> #1,0.23915,0.015601,-0.97086,171.54,-0.63725,-0.75189,-0.16906,256.96,-0.73261,0.65911,-0.16987,136.09

> volume #1 level 0.02772

> view matrix models
> #1,0.23915,0.015601,-0.97086,169.81,-0.63725,-0.75189,-0.16906,256.98,-0.73261,0.65911,-0.16987,138.81

> view matrix models
> #1,0.23915,0.015601,-0.97086,166.82,-0.63725,-0.75189,-0.16906,253.79,-0.73261,0.65911,-0.16987,139.61

> volume #1 transparency 0.5

> view matrix models
> #1,0.23915,0.015601,-0.97086,217.2,-0.63725,-0.75189,-0.16906,324.49,-0.73261,0.65911,-0.16987,147.14

> view matrix models
> #1,0.23915,0.015601,-0.97086,219.7,-0.63725,-0.75189,-0.16906,327.19,-0.73261,0.65911,-0.16987,147.51

> volume #1 level 0.02558

> view matrix models
> #1,0.23915,0.015601,-0.97086,234.85,-0.63725,-0.75189,-0.16906,286.15,-0.73261,0.65911,-0.16987,150.75

> view matrix models
> #1,0.23915,0.015601,-0.97086,235.42,-0.63725,-0.75189,-0.16906,286.09,-0.73261,0.65911,-0.16987,149.11

> view matrix models
> #1,0.23915,0.015601,-0.97086,178.41,-0.63725,-0.75189,-0.16906,251.82,-0.73261,0.65911,-0.16987,145.09

> view matrix models
> #1,0.23915,0.015601,-0.97086,173.8,-0.63725,-0.75189,-0.16906,248.8,-0.73261,0.65911,-0.16987,143.59

> select clear

> fitmap #1 inMap #2

Fit map emdb 31448 in map cryosparc_P21_J1977_004_volume_map_sharp.mrc using
28182 points  
correlation = 0.321, correlation about mean = 0.04871, overlap = 206.3  
steps = 80, shift = 2.07, angle = 5.66 degrees  
  
Position of emdb 31448 (#1) relative to
cryosparc_P21_J1977_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.46278883 -0.05175227 -0.88495661 284.58069597  
-0.21507981 -0.96191024 0.16872869 225.91915444  
-0.85998091 0.26842206 0.43403044 160.59925490  
Axis 0.51661917 -0.12942610 -0.84637670  
Axis point 197.69098500 92.28304945 0.00000000  
Rotation angle (degrees) 174.46312735  
Shift along axis -18.14745914  
  

> select #1

2 models selected  

> view matrix models
> #1,0.18097,-0.054246,-0.98199,189.98,-0.62912,-0.77385,-0.073192,251.46,-0.75595,0.63104,-0.17417,145.25

> el clear

Unknown command: el clear  

> select clear

> select #1

2 models selected  

> view matrix models
> #1,0.18097,-0.054246,-0.98199,188.3,-0.62912,-0.77385,-0.073192,255.19,-0.75595,0.63104,-0.17417,143.71

> select subtract #1

Nothing selected  

> select add #1

2 models selected  

> view matrix models
> #1,0.18097,-0.054246,-0.98199,182.26,-0.62912,-0.77385,-0.073192,251.21,-0.75595,0.63104,-0.17417,145.3

> select subtract #1

Nothing selected  

> color #2 bule

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color #2 bychain

> volume #2 transparency 0.5

> select add #1

2 models selected  

> view matrix models
> #1,0.18097,-0.054246,-0.98199,180.31,-0.62912,-0.77385,-0.073192,252.12,-0.75595,0.63104,-0.17417,135.86

> select subtract #1

Nothing selected  

> volume #2 transparency 0

> volume #2 level 1.566

> volume #1 level 0.04029

> select add #1

2 models selected  

> view matrix models
> #1,0.18097,-0.054246,-0.98199,180.61,-0.62912,-0.77385,-0.073192,253.52,-0.75595,0.63104,-0.17417,136.27

> view matrix models
> #1,0.18097,-0.054246,-0.98199,183.43,-0.62912,-0.77385,-0.073192,254.88,-0.75595,0.63104,-0.17417,138.09

> undo

> fitmap #2 inMap #1

Fit map cryosparc_P21_J1977_004_volume_map_sharp.mrc in map emdb 31448 using
9430 points  
correlation = 0.674, correlation about mean = 0.08344, overlap = 270.9  
steps = 380, shift = 7.1, angle = 23.1 degrees  
  
Position of cryosparc_P21_J1977_004_volume_map_sharp.mrc (#2) relative to emdb
31448 (#1) coordinates:  
Matrix rotation and translation  
-0.35029167 -0.30744457 -0.88474492 321.71170569  
-0.36256340 -0.82644776 0.43073411 211.33578142  
-0.86362233 0.47165870 0.17802962 124.51221511  
Axis 0.56976866 -0.29407731 -0.76738661  
Axis point 209.64124606 78.21567991 0.00000000  
Rotation angle (degrees) 177.94187478  
Shift along axis 25.60318391  
  

> select subtract #1

Nothing selected  

> volume #2 level 0.852

> volume #1 level 0.02236

> volume #1 level 0.02558

> volume #2 level 0.6443

> select add #1

2 models selected  

> view matrix models
> #1,0.18097,-0.054246,-0.98199,180.49,-0.62912,-0.77385,-0.073192,254.07,-0.75595,0.63104,-0.17417,137.75

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.22236,-0.06024,-0.9731,175.54,-0.59169,-0.80161,-0.085581,253.76,-0.77489,0.5948,-0.21389,147.28

> view matrix models
> #1,0.28242,-0.012542,-0.95921,162.78,-0.58808,-0.79225,-0.16279,259.96,-0.75789,0.61007,-0.23112,145.56

> view matrix models
> #1,0.54834,0.4485,-0.70581,63.329,-0.68346,-0.24598,-0.68729,268.67,-0.48187,0.85927,0.17165,51.014

> view matrix models
> #1,0.5641,0.48344,-0.66938,54.61,-0.67924,-0.18925,-0.70909,264.81,-0.46948,0.85468,0.22162,45.199

> ui mousemode right "move picked models"

> view matrix models
> #1,0.5641,0.48344,-0.66938,50.735,-0.67924,-0.18925,-0.70909,268.49,-0.46948,0.85468,0.22162,41.218

> view matrix models
> #1,0.5641,0.48344,-0.66938,55.643,-0.67924,-0.18925,-0.70909,263.49,-0.46948,0.85468,0.22162,51.885

> fitmap #2 inMap #1

Fit map cryosparc_P21_J1977_004_volume_map_sharp.mrc in map emdb 31448 using
34620 points  
correlation = 0.642, correlation about mean = 0.07085, overlap = 489.7  
steps = 376, shift = 8.35, angle = 30.1 degrees  
  
Position of cryosparc_P21_J1977_004_volume_map_sharp.mrc (#2) relative to emdb
31448 (#1) coordinates:  
Matrix rotation and translation  
0.01112037 -0.89938441 -0.43701718 297.24493295  
0.15402464 -0.43028764 0.88945430 17.83021720  
-0.98800443 -0.07720248 0.13374240 231.41566541  
Axis -0.63088846 0.35960178 0.68750732  
Axis point 246.06848561 44.50017874 0.00000000  
Rotation angle (degrees) 129.99437747  
Shift along axis -22.01665534  
  

> select subtract #1

Nothing selected  

> select add #1

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.5641,0.48344,-0.66938,58.675,-0.67924,-0.18925,-0.70909,268.45,-0.46948,0.85468,0.22162,40.852

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.047994,0.99166,-0.11957,24.691,0.20509,-0.10738,-0.97283,186.54,-0.97757,-0.071214,-0.19823,228.99

> view matrix models
> #1,0.12405,0.60974,0.78283,-45.436,-0.070939,0.79236,-0.60592,94.442,-0.98974,0.019632,0.14155,188.44

> view matrix models
> #1,-0.070558,0.7556,-0.65122,101.95,-0.57891,-0.56268,-0.59014,281.86,-0.81234,0.33536,0.47712,105.08

> view matrix models
> #1,-0.61834,-0.48057,-0.62186,280.98,-0.30509,-0.58243,0.75346,122.1,-0.72428,0.65561,0.21352,89.699

> view matrix models
> #1,-0.44578,-0.034848,-0.89446,244.76,-0.57578,-0.75393,0.31633,211.84,-0.68539,0.65603,0.31602,75.295

> view matrix models
> #1,-0.34608,0.20471,-0.9156,212.29,-0.66654,-0.74044,0.086389,243.14,-0.66027,0.64018,0.3927,66.539

> select subtract #1

Nothing selected  

> select add #2

2 models selected  

> view matrix models
> #2,0.66468,-0.72885,0.16422,89.191,0.73747,0.67527,0.012087,-102.53,-0.1197,0.11308,0.98635,-27.861

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.66468,-0.72885,0.16422,87.105,0.73747,0.67527,0.012087,-155.64,-0.1197,0.11308,0.98635,-7.8537

> view matrix models
> #2,0.66468,-0.72885,0.16422,102.43,0.73747,0.67527,0.012087,-37.707,-0.1197,0.11308,0.98635,-5.6411

> select subtract #2

Nothing selected  

> select add #1

2 models selected  

> view matrix models
> #1,-0.34608,0.20471,-0.9156,227.06,-0.66654,-0.74044,0.086389,225.99,-0.66027,0.64018,0.3927,93.781

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.0093268,0.63434,-0.773,131.36,-0.73165,-0.5226,-0.43769,263.18,-0.68161,0.56965,0.45924,96.563

> view matrix models
> #1,0.037802,0.66799,-0.74321,121.98,-0.72968,-0.4897,-0.47725,263.61,-0.68275,0.56035,0.4689,96.655

> view matrix models
> #1,0.08323,0.58383,-0.8076,131.32,-0.69566,-0.54623,-0.46657,264.24,-0.71353,0.60065,0.36068,106.74

> view matrix models
> #1,-0.16196,0.63104,-0.75866,149.59,-0.33894,-0.75761,-0.55781,253.48,-0.92676,0.1668,0.33659,175.29

> view matrix models
> #1,-0.1854,0.62911,-0.75488,152.05,-0.30129,-0.7676,-0.56571,250.98,-0.93534,0.12256,0.33186,181.02

> view matrix models
> #1,-0.28488,0.67614,-0.67947,151.34,-0.37192,-0.73128,-0.57176,255.99,-0.88347,0.089827,0.4598,165.9

> view matrix models
> #1,-0.3217,0.69652,-0.64138,149.8,-0.40181,-0.71379,-0.57363,257.84,-0.85736,0.073181,0.50949,159.73

> view matrix models
> #1,-0.38014,0.67063,-0.63698,158.47,-0.40509,-0.73983,-0.53717,257.19,-0.8315,0.053836,0.55291,154.47

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.38014,0.67063,-0.63698,125.48,-0.40509,-0.73983,-0.53717,312.63,-0.8315,0.053836,0.55291,162.49

> view matrix models
> #1,-0.38014,0.67063,-0.63698,125.55,-0.40509,-0.73983,-0.53717,312.81,-0.8315,0.053836,0.55291,162.43

> view matrix models
> #1,-0.38014,0.67063,-0.63698,140.43,-0.40509,-0.73983,-0.53717,341.8,-0.8315,0.053836,0.55291,163.35

> select subtract #1

Nothing selected  

> fitmap #2 inMap #1

Fit map cryosparc_P21_J1977_004_volume_map_sharp.mrc in map emdb 31448 using
34620 points  
correlation = 0.6513, correlation about mean = 0.103, overlap = 565  
steps = 384, shift = 13.3, angle = 30.2 degrees  
  
Position of cryosparc_P21_J1977_004_volume_map_sharp.mrc (#2) relative to emdb
31448 (#1) coordinates:  
Matrix rotation and translation  
-0.38435624 -0.31585165 -0.86747219 325.22045819  
-0.43194711 -0.76892501 0.47135551 209.18000694  
-0.81589948 0.55587054 0.15910992 110.11773154  
Axis 0.55390594 -0.33800415 -0.76088199  
Axis point 208.16058835 72.32407525 0.00000000  
Rotation angle (degrees) 175.62465052  
Shift along axis 25.65123637  
  

> select add #1

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.011374,0.91757,-0.3974,48.986,-0.48619,-0.34221,-0.80406,338.27,-0.87378,0.20236,0.44223,164.46

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.011374,0.91757,-0.3974,43.762,-0.48619,-0.34221,-0.80406,348.17,-0.87378,0.20236,0.44223,174.84

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.43834,0.79651,-0.41645,108.05,-0.074909,-0.49409,-0.86618,322.65,-0.89568,-0.34848,0.27624,247.02

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.43834,0.79651,-0.41645,118.47,-0.074909,-0.49409,-0.86618,308.85,-0.89568,-0.34848,0.27624,238.02

> view matrix models
> #1,-0.43834,0.79651,-0.41645,123.87,-0.074909,-0.49409,-0.86618,309.79,-0.89568,-0.34848,0.27624,235.61

> select subtract #1

Nothing selected  

> volume subtract #1 #2 minRms true

Opened volume difference as #4, grid size 200,200,200, pixel 1.04, shown at
step 1, values float32  
Minimum RMS scale factor for "cryosparc_P21_J1977_004_volume_map_sharp.mrc #2"
above level 0.64426 is 0.0068191  
  

> hide #!4 models

> show #!4 models

> volume #4 color pink transparency 0

> hide atoms

> show ribbons

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 Pro
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: MacBook Pro
      Model Identifier: MacBookPro18,3
      Chip: Apple M1 Pro
      Total Number of Cores: 8 (6 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 7429.81.3
      OS Loader Version: 7429.81.3

Software:

    System Software Overview:

      System Version: macOS 12.2.1 (21D62)
      Kernel Version: Darwin 21.3.0
      Time since boot: 60 days 13:47

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 14
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


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