sym: normalize_vector() takes 1 positional argument but 3 were given

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4.dev202203030220 (2022-03-03 02:20:09 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4.dev202203030220 (2022-03-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/egelmanlab01/Documents/milano/base_plate/cryosparc_P101_J190_003_volume_map_sharp-
> WINDOWED.mrc format mrc

Opened cryosparc_P101_J190_003_volume_map_sharp-WINDOWED.mrc as #1, grid size
448,448,448, pixel 1.08, shown at level 0.29, step 2, values float32  

> volume #1 step 1

> ui tool show "Side View"

> volume #1 color #797979

> ui tool show "Segment Map"

Segmenting cryosparc_P101_J190_003_volume_map_sharp-WINDOWED.mrc, density
threshold 0.290048  
Only showing 60 of 11092 regions.  
Showing 60 of 11092 region surfaces  
38000 watershed regions, grouped to 11092 regions  
Showing cryosparc_P101_J190_003_volume_map_sharp-WINDOWED.seg - 11092 regions,
60 surfaces  

> volume #1 level 0.25

> close #2

Segmenting cryosparc_P101_J190_003_volume_map_sharp-WINDOWED.mrc, density
threshold 0.250000  
Only showing 60 of 12587 regions.  
Showing 60 of 12587 region surfaces  
45927 watershed regions, grouped to 12587 regions  
Showing cryosparc_P101_J190_003_volume_map_sharp-WINDOWED.seg - 12587 regions,
60 surfaces  
Segmenting cryosparc_P101_J190_003_volume_map_sharp-WINDOWED.mrc, density
threshold 0.250000  
Only showing 60 of 11556 regions.  
Showing 60 of 11556 region surfaces  
45927 watershed regions, grouped to 11556 regions  
Showing cryosparc_P101_J190_003_volume_map_sharp-WINDOWED.seg - 11556 regions,
60 surfaces  
Ungrouped to 2 regions  
Segmenting cryosparc_P101_J190_003_volume_map_sharp-WINDOWED.mrc, density
threshold 0.250000  
Only showing 60 of 11556 regions.  
Showing 60 of 11556 region surfaces  
45927 watershed regions, grouped to 11556 regions  
Showing cryosparc_P101_J190_003_volume_map_sharp-WINDOWED.seg - 11556 regions,
60 surfaces  
Ungrouped to 2 regions  
Ungrouped to 2 regions, but did not show all surfaces, see Options  
[Repeated 1 time(s)]Segmenting cryosparc_P101_J190_003_volume_map_sharp-
WINDOWED.mrc, density threshold 0.250000  
Only showing 60 of 11721 regions.  
Showing 60 of 11721 region surfaces  
45927 watershed regions, grouped to 11721 regions  
Showing cryosparc_P101_J190_003_volume_map_sharp-WINDOWED.seg - 11721 regions,
60 surfaces  

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

Segmenting cryosparc_P101_J190_003_volume_map_sharp-WINDOWED.mrc, density
threshold 0.250000  
Only showing 60 of 11768 regions.  
Showing 60 of 11768 region surfaces  
45927 watershed regions, grouped to 11768 regions  
Showing cryosparc_P101_J190_003_volume_map_sharp-WINDOWED.seg - 11768 regions,
60 surfaces  
Segmenting cryosparc_P101_J190_003_volume_map_sharp-WINDOWED.mrc, density
threshold 0.250000  
Only showing 60 of 11556 regions.  
Showing 60 of 11556 region surfaces  
45927 watershed regions, grouped to 11556 regions  
Showing cryosparc_P101_J190_003_volume_map_sharp-WINDOWED.seg - 11556 regions,
60 surfaces  
Saving 1 regions to mrc file...  
Opened J190_region_80275.mrc as #3, grid size 93,94,83, pixel 1.08, shown at
step 1, values float32  
Wrote J190_region_80275.mrc  

> open /Users/egelmanlab01/Documents/milano/base_plate/J190_region_80275.mrc

Opened J190_region_80275.mrc as #4, grid size 93,94,83, pixel 1.08,1.08,1.08,
shown at level 0.4, step 1, values float32  

> hide #!2 models

> select add #2

61 models selected  

> volume #3 color silver

> volume #3 color white

> volume #3 color #212121

> volume #3 color #929000

> volume #3 level 0.255

> close #4

> open /Users/egelmanlab01/Desktop/051022_combine_baseFit.pdb

Chain information for 051022_combine_baseFit.pdb #4  
---  
Chain | Description  
1 J O f q v | No description available  
2 K P g r w | No description available  
A L Q h s x | No description available  
B C D E F G | No description available  
H M R i t y | No description available  
I N e p u z | No description available  
S T U V W X Y Z a b c d | No description available  
j k l m n o | No description available  
  

> hide cartoons

> hide atoms

> show cartoons

> hide #!4 models

> volume #3 level 0.431

> volume #3 level 0.3807

> open
> /Users/egelmanlab01/Documents/milano/base_plate/baseplate/C6_MFT7_baseFit.pdb

Chain information for C6_MFT7_baseFit.pdb #5  
---  
Chain | Description  
B C D E F G | No description available  
  

> hide #5 atoms

> show #5 cartoons

> show #!2 models

> hide #!2 models

Drag select of 5 residues  

> ui mousemode right "translate selected models"

> view matrix models #5,1,0,0,1.198,0,1,0,37.027,0,0,1,1.6604

> view matrix models
> #5,0.89404,0.44513,-0.050567,1.1363,-0.39759,0.84038,0.36835,37.476,0.20646,-0.30921,0.92831,1.573

> view matrix models
> #5,0.89404,0.44513,-0.050567,19.022,-0.39759,0.84038,0.36835,0.58257,0.20646,-0.30921,0.92831,11.496

> view matrix models
> #5,0.66279,0.69577,-0.27678,18.747,-0.61995,0.71719,0.31829,0.52158,0.41996,-0.039365,0.90669,11.469

> view matrix models
> #5,0.66279,0.69577,-0.27678,25.852,-0.61995,0.71719,0.31829,-22.726,0.41996,-0.039365,0.90669,27.079

> view matrix models
> #5,0.58615,0.63339,-0.50522,25.574,-0.78956,0.58642,-0.18084,-23.334,0.18172,0.5049,0.84383,27.003

> view matrix models
> #5,0.58615,0.63339,-0.50522,16.429,-0.78956,0.58642,-0.18084,-22.15,0.18172,0.5049,0.84383,21.09

> view matrix models
> #5,0.58615,0.63339,-0.50522,27.141,-0.78956,0.58642,-0.18084,-44.852,0.18172,0.5049,0.84383,37.377

> view matrix models
> #5,0.58615,0.63339,-0.50522,9.5924,-0.78956,0.58642,-0.18084,-49.641,0.18172,0.5049,0.84383,32.032

> view matrix models
> #5,0.63804,0.62438,-0.45062,9.659,-0.74493,0.64865,-0.15598,-49.611,0.1949,0.4352,0.87898,32.074

> view matrix models
> #5,0.22373,0.24105,-0.94437,9.0574,-0.90044,-0.31972,-0.29493,-49.78,-0.37303,0.91634,0.14552,31.181

> view matrix models
> #5,0.21806,0.23181,-0.94801,-46.413,-0.90582,-0.31348,-0.28501,-75.537,-0.36324,0.92087,0.14162,-1.4185

> view matrix models
> #5,-0.38286,0.68669,-0.61797,-46.011,-0.91298,-0.38337,0.13963,-75.019,-0.14103,0.61765,0.77371,-0.64844

> view matrix models
> #5,-0.38286,0.68669,-0.61797,-24.991,-0.91298,-0.38337,0.13963,-143.49,-0.14103,0.61765,0.77371,53.419

> view matrix models
> #5,-0.036462,0.99853,-0.040164,-24.287,-0.89244,-0.014451,0.45093,-143.11,0.44968,0.052286,0.89166,53.563

> view matrix models
> #5,-0.036462,0.99853,-0.040164,-15.751,-0.89244,-0.014451,0.45093,-84.186,0.44968,0.052286,0.89166,34.292

> view matrix models
> #5,0.062651,0.77447,-0.6295,-16.469,-0.99741,0.070841,-0.012113,-84.75,0.035214,0.62863,0.7769,34.152

> view matrix models
> #5,0.062651,0.77447,-0.6295,-11.461,-0.99741,0.070841,-0.012113,-86.448,0.035214,0.62863,0.7769,37.444

> view matrix models
> #5,0.062651,0.77447,-0.6295,-10.292,-0.99741,0.070841,-0.012113,-90.208,0.035214,0.62863,0.7769,31.628

> close #5

> open
> /Users/egelmanlab01/Documents/milano/base_plate/baseplate/C6_MFQ9_tentetive_baseFit.pdb

Chain information for C6_MFQ9_tentetive_baseFit.pdb #5  
---  
Chain | Description  
C D E F G H | No description available  
  

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> hide #5 atoms

> show #5 cartoons

> hide #5 models

> open
> /Users/egelmanlab01/Documents/milano/base_plate/baseplate/MFU4/MFU4_combo_dif_chain_ID.pdb

Chain information for MFU4_combo_dif_chain_ID.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> close #6

> hide #!3 models

> show #!1 models

> open
> /Users/egelmanlab01/Documents/milano/base_plate/baseplate/MFU4/MFU4_combo_dif_chain_ID.pdb

Chain information for MFU4_combo_dif_chain_ID.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> volume zone #1 nearAtoms #6 range 6.48

> hide #6 atoms

> show #6 cartoons

[Repeated 1 time(s)]

> show #5 models

> hide #5 models

> open /Users/egelmanlab01/Documents/milano/base_plate/J190_region_80275.mrc

Opened J190_region_80275.mrc as #7, grid size 93,94,83, pixel 1.08,1.08,1.08,
shown at level 0.4, step 1, values float32  

> show #!2 models

> hide #!2 models

> open
> /Users/egelmanlab01/Documents/milano/base_plate/baseplate/rotation_axis_Base.pdb

Summary of feedback from opening
/Users/egelmanlab01/Documents/milano/base_plate/baseplate/rotation_axis_Base.pdb  
---  
warning | Cannot find LINK/SSBOND residue mar (1 )  
  
Chain information for rotation_axis_Base.pdb #8  
---  
Chain | Description  
kM | No description available  
  

> sym #6 C6 axis #8 ceter #8

Expected a keyword  

> sym #6 C6 axis #8 center #8

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 302, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/sym.py", line 87, in sym  
transforms = symmetry.positions(center, axis, coordinate_system,
structures[0])  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/args.py", line 428, in positions  
return parse_symmetry(self.session, self.group, c, a, molecule)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/args.py", line 447, in parse_symmetry  
tf = vector_rotation(axis, (0,0,1)) * tf  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 466, in vector_rotation  
return Place(m34.vector_rotation_transform(u, v))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/matrix.py", line 337, in vector_rotation_transform  
ax, ay, az = normalize_vector(-n0[1], n0[0], 0)  
TypeError: normalize_vector() takes 1 positional argument but 3 were given  
  
TypeError: normalize_vector() takes 1 positional argument but 3 were given  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/matrix.py", line 337, in vector_rotation_transform  
ax, ay, az = normalize_vector(-n0[1], n0[0], 0)  
  
See log for complete Python traceback.  
  

> sym #6 C6 axis #8 center #8

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 302, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/sym.py", line 87, in sym  
transforms = symmetry.positions(center, axis, coordinate_system,
structures[0])  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/args.py", line 428, in positions  
return parse_symmetry(self.session, self.group, c, a, molecule)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/args.py", line 447, in parse_symmetry  
tf = vector_rotation(axis, (0,0,1)) * tf  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 466, in vector_rotation  
return Place(m34.vector_rotation_transform(u, v))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/matrix.py", line 337, in vector_rotation_transform  
ax, ay, az = normalize_vector(-n0[1], n0[0], 0)  
TypeError: normalize_vector() takes 1 positional argument but 3 were given  
  
TypeError: normalize_vector() takes 1 positional argument but 3 were given  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/matrix.py", line 337, in vector_rotation_transform  
ax, ay, az = normalize_vector(-n0[1], n0[0], 0)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.8.15
OpenGL renderer: AMD Radeon Pro 5300 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Locale: UTF-8
Qt version: PyQt5 5.15.2, Qt 5.15.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac20,1
      Processor Name: 6-Core Intel Core i5
      Processor Speed: 3.3 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 12 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 1731.100.130.0.0 (iBridge: 19.16.14243.0.0,0)
      OS Loader Version: 540.100.7~23

Software:

    System Software Overview:

      System Version: macOS 12.3.1 (21E258)
      Kernel Version: Darwin 21.4.0
      Time since boot: 41 days 12:02

Graphics/Displays:

    AMD Radeon Pro 5300:

      Chipset Model: AMD Radeon Pro 5300
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0047
      ROM Revision: 113-D3220I-231
      VBIOS Version: 113-D322A1XL-012
      Option ROM Version: 113-D322A1XL-012
      EFI Driver Version: 01.01.231
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.5.30
    cftime: 1.5.2
    charset-normalizer: 2.0.12
    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: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.36.2
    ChimeraX-AtomicLibrary: 6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.1
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4.dev202203030220
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.2
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.8
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    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
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.7.7
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.16.2
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.5.1
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.29.1
    funcparserlib: 1.0.0a0
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.26
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.9.2
    kiwisolver: 1.3.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.0
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.4
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.0
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.28
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.2.2
    QtPy: 2.0.1
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    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
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.8
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

[Tom Goddard]

Fixed in 1.4.

The vector_rotation() routine was wrong in some corner case code where two vector arguments were in opposite directions.