id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
16204	AlphaFold PAE: list index out of range	chimera-bug-report@…	Tom Goddard	"The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.8.dev202401300915 (2024-01-30 09:15:05 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.8.dev202401300915 (2024-01-30)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

open ""D:/Dropbox/PME personal/희백 실험실 자료 -비공개/20240731 문선옥 박사님
리뷰/fold_tip2_udt_2pro/fold_tip2_udt_2pro_model_0.cif""

Chain information for fold_tip2_udt_2pro_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  


ui tool show ""AlphaFold Error Plot""

Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\pae.py"", line 100, in _structure_chosen  
self._guess_pae_file_or_database_id()  
File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\pae.py"", line 117, in
_guess_pae_file_or_database_id  
pae_path = _matching_pae_file(structure_path)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\pae.py"", line 315, in _matching_pae_file  
mfile = _longest_matching_prefix(filename, pkl_files, min_length = min_length)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\pae.py"", line 327, in _longest_matching_prefix  
mfilename = m[0][1] if m[0][0] >= min_length and m[0][0] > m[1][0] else None  
~^^^  
IndexError: list index out of range  

IndexError: list index out of range  

File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\pae.py"", line 327, in _longest_matching_prefix  
mfilename = m[0][1] if m[0][0] >= min_length and m[0][0] > m[1][0] else None  
~^^^  

See log for complete Python traceback.  


alphafold pae #1 file ""D:/Dropbox/PME personal/희백 실험실 자료 -비공개/20240731 문선옥
박사님 리뷰/fold_tip2_udt_2pro/fold_tip2_udt_2pro_full_data_0.json""

alphafold contacts /A toResidues /B

alphafold contacts /A toResidues /C

Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\cmd_line\tool.py"", line 319, in execute  
cmd.run(cmd_text)  
File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py"", line 2904, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\contacts.py"", line 100, in alphafold_contacts  
b = g.new_pseudobond(a1, a2)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molobject.py"", line 463, in new_pseudobond  
pb = f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)  
^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute '_c_pointer'  

AttributeError: 'NoneType' object has no attribute '_c_pointer'  

File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molobject.py"", line 463, in new_pseudobond  
pb = f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)  
^^^^^^^^^^^^^^^^  

See log for complete Python traceback.  


alphafold contacts /A toResidues /D

Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\cmd_line\tool.py"", line 319, in execute  
cmd.run(cmd_text)  
File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py"", line 2904, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\contacts.py"", line 100, in alphafold_contacts  
b = g.new_pseudobond(a1, a2)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molobject.py"", line 463, in new_pseudobond  
pb = f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)  
^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute '_c_pointer'  

AttributeError: 'NoneType' object has no attribute '_c_pointer'  

File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molobject.py"", line 463, in new_pseudobond  
pb = f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)  
^^^^^^^^^^^^^^^^  

See log for complete Python traceback.  


alphafold contacts /B toResidues /D

Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\cmd_line\tool.py"", line 319, in execute  
cmd.run(cmd_text)  
File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py"", line 2904, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\contacts.py"", line 100, in alphafold_contacts  
b = g.new_pseudobond(a1, a2)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molobject.py"", line 463, in new_pseudobond  
pb = f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)  
^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute '_c_pointer'  

AttributeError: 'NoneType' object has no attribute '_c_pointer'  

File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molobject.py"", line 463, in new_pseudobond  
pb = f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)  
^^^^^^^^^^^^^^^^  

See log for complete Python traceback.  


alphafold contacts /B toResidues /A

close #1

open ""D:/Dropbox/PME personal/희백 실험실 자료 -비공개/20240731 문선옥 박사님
리뷰/fold_2tip2_eatpro/fold_2tip2_eatpro_model_0.cif""

Chain information for fold_2tip2_eatpro_model_0.cif #1  
---  
Chain | Description  
A B | .  
C | .  


ui tool show ""AlphaFold Error Plot""

Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\pae.py"", line 100, in _structure_chosen  
self._guess_pae_file_or_database_id()  
File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\pae.py"", line 117, in
_guess_pae_file_or_database_id  
pae_path = _matching_pae_file(structure_path)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\pae.py"", line 315, in _matching_pae_file  
mfile = _longest_matching_prefix(filename, pkl_files, min_length = min_length)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\pae.py"", line 327, in _longest_matching_prefix  
mfilename = m[0][1] if m[0][0] >= min_length and m[0][0] > m[1][0] else None  
~^^^  
IndexError: list index out of range  

IndexError: list index out of range  

File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\pae.py"", line 327, in _longest_matching_prefix  
mfilename = m[0][1] if m[0][0] >= min_length and m[0][0] > m[1][0] else None  
~^^^  

See log for complete Python traceback.  


alphafold pae #1 file ""D:/Dropbox/PME personal/희백 실험실 자료 -비공개/20240731 문선옥
박사님 리뷰/fold_2tip2_eatpro/fold_2tip2_eatpro_full_data_0.json""

alphafold contacts /A toResidues /C

Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\cmd_line\tool.py"", line 319, in execute  
cmd.run(cmd_text)  
File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py"", line 2904, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\contacts.py"", line 100, in alphafold_contacts  
b = g.new_pseudobond(a1, a2)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molobject.py"", line 463, in new_pseudobond  
pb = f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)  
^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute '_c_pointer'  

AttributeError: 'NoneType' object has no attribute '_c_pointer'  

File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molobject.py"", line 463, in new_pseudobond  
pb = f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)  
^^^^^^^^^^^^^^^^  

See log for complete Python traceback.  


close #1

open ""D:/Dropbox/PME personal/희백 실험실 자료 -비공개/20240731 문선옥 박사님
리뷰/fold_eat_eat_2pro/fold_eat_eat_2pro_model_0.cif""

Chain information for fold_eat_eat_2pro_model_0.cif #1  
---  
Chain | Description  
A B | .  
C | .  
D | .  


ui tool show ""AlphaFold Error Plot""

Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\pae.py"", line 100, in _structure_chosen  
self._guess_pae_file_or_database_id()  
File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\pae.py"", line 117, in
_guess_pae_file_or_database_id  
pae_path = _matching_pae_file(structure_path)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\pae.py"", line 315, in _matching_pae_file  
mfile = _longest_matching_prefix(filename, pkl_files, min_length = min_length)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\pae.py"", line 327, in _longest_matching_prefix  
mfilename = m[0][1] if m[0][0] >= min_length and m[0][0] > m[1][0] else None  
~^^^  
IndexError: list index out of range  

IndexError: list index out of range  

File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\pae.py"", line 327, in _longest_matching_prefix  
mfilename = m[0][1] if m[0][0] >= min_length and m[0][0] > m[1][0] else None  
~^^^  

See log for complete Python traceback.  


alphafold pae #1 file ""D:/Dropbox/PME personal/희백 실험실 자료 -비공개/20240731 문선옥
박사님 리뷰/fold_eat_eat_2pro/fold_eat_eat_2pro_full_data_0.json""

alphafold contacts /A toResidues /C

Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\cmd_line\tool.py"", line 319, in execute  
cmd.run(cmd_text)  
File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py"", line 2904, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\contacts.py"", line 100, in alphafold_contacts  
b = g.new_pseudobond(a1, a2)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molobject.py"", line 463, in new_pseudobond  
pb = f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)  
^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute '_c_pointer'  

AttributeError: 'NoneType' object has no attribute '_c_pointer'  

File ""C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molobject.py"", line 463, in new_pseudobond  
pb = f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)  
^^^^^^^^^^^^^^^^  

See log for complete Python traceback.  





OpenGL version: 3.3.0 NVIDIA 457.51
OpenGL renderer: GeForce GTX 1660/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: ko_KR.cp949
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7B17
OS: Microsoft Windows 10 Education (Build 19045)
Memory: 17,114,308,608
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-9700K CPU @ 3.60GHz
OSLanguage: ko-KR

Installed Packages:
  alabaster: 0.7.16
  appdirs: 1.4.4
  asttokens: 2.4.1
  Babel: 2.14.0
  backcall: 0.2.0
  beautifulsoup4: 4.12.3
  blockdiag: 3.0.0
  blosc2: 2.5.1
  build: 1.0.3
  certifi: 2023.11.17
  cftime: 1.6.3
  charset-normalizer: 3.3.2
  ChimeraX-AddCharge: 1.5.15
  ChimeraX-AddH: 2.2.5
  ChimeraX-AlignmentAlgorithms: 2.0.1
  ChimeraX-AlignmentHdrs: 3.4.3
  ChimeraX-AlignmentMatrices: 2.1
  ChimeraX-Alignments: 2.12.3
  ChimeraX-AlphaFold: 1.0
  ChimeraX-AltlocExplorer: 1.1.1
  ChimeraX-AmberInfo: 1.0
  ChimeraX-Arrays: 1.1
  ChimeraX-Atomic: 1.52
  ChimeraX-AtomicLibrary: 12.1.10
  ChimeraX-AtomSearch: 2.0.1
  ChimeraX-AxesPlanes: 2.4
  ChimeraX-BasicActions: 1.1.2
  ChimeraX-BILD: 1.0
  ChimeraX-BlastProtein: 2.1.2
  ChimeraX-BondRot: 2.0.4
  ChimeraX-BugReporter: 1.0.1
  ChimeraX-BuildStructure: 2.11
  ChimeraX-Bumps: 1.0
  ChimeraX-BundleBuilder: 1.2.2
  ChimeraX-ButtonPanel: 1.0.1
  ChimeraX-CageBuilder: 1.0.1
  ChimeraX-CellPack: 1.0
  ChimeraX-Centroids: 1.4
  ChimeraX-ChangeChains: 1.1
  ChimeraX-CheckWaters: 1.3.2
  ChimeraX-ChemGroup: 2.0.1
  ChimeraX-Clashes: 2.2.4
  ChimeraX-ColorActions: 1.0.3
  ChimeraX-ColorGlobe: 1.0
  ChimeraX-ColorKey: 1.5.5
  ChimeraX-CommandLine: 1.2.5
  ChimeraX-ConnectStructure: 2.0.1
  ChimeraX-Contacts: 1.0.1
  ChimeraX-Core: 1.8.dev202401300915
  ChimeraX-CoreFormats: 1.2
  ChimeraX-coulombic: 1.4.3
  ChimeraX-Crosslinks: 1.0
  ChimeraX-Crystal: 1.0
  ChimeraX-CrystalContacts: 1.0.1
  ChimeraX-DataFormats: 1.2.3
  ChimeraX-Dicom: 1.2
  ChimeraX-DistMonitor: 1.4.1
  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: 1.1.1
  ChimeraX-Hbonds: 2.4
  ChimeraX-Help: 1.2.2
  ChimeraX-HKCage: 1.3
  ChimeraX-IHM: 1.1
  ChimeraX-ImageFormats: 1.2
  ChimeraX-IMOD: 1.0
  ChimeraX-IO: 1.0.1
  ChimeraX-ItemsInspection: 1.0.1
  ChimeraX-IUPAC: 1.0
  ChimeraX-Label: 1.1.9
  ChimeraX-ListInfo: 1.2.2
  ChimeraX-Log: 1.1.6
  ChimeraX-LookingGlass: 1.1
  ChimeraX-Maestro: 1.9.1
  ChimeraX-Map: 1.1.4
  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: 2.1.2
  ChimeraX-MCopy: 1.0
  ChimeraX-MDcrds: 2.6.2
  ChimeraX-MedicalToolbar: 1.0.2
  ChimeraX-Meeting: 1.0.1
  ChimeraX-MLP: 1.1.1
  ChimeraX-mmCIF: 2.12.2
  ChimeraX-MMTF: 2.2
  ChimeraX-Modeller: 1.5.15
  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: 1.1
  ChimeraX-NMRSTAR: 1.0.2
  ChimeraX-NRRD: 1.1
  ChimeraX-Nucleotides: 2.0.3
  ChimeraX-OpenCommand: 1.13.2
  ChimeraX-PDB: 2.7.3
  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
  ChimeraX-PubChem: 2.1
  ChimeraX-ReadPbonds: 1.0.1
  ChimeraX-Registration: 1.1.2
  ChimeraX-RemoteControl: 1.0
  ChimeraX-RenderByAttr: 1.2.1
  ChimeraX-RenumberResidues: 1.1
  ChimeraX-ResidueFit: 1.0.1
  ChimeraX-RestServer: 1.2
  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-SelInspector: 1.0
  ChimeraX-SeqView: 2.11.1
  ChimeraX-Shape: 1.0.1
  ChimeraX-Shell: 1.0.1
  ChimeraX-Shortcuts: 1.1.1
  ChimeraX-ShowSequences: 1.0.2
  ChimeraX-SideView: 1.0.1
  ChimeraX-Smiles: 2.1.2
  ChimeraX-SmoothLines: 1.0
  ChimeraX-SpaceNavigator: 1.0
  ChimeraX-StdCommands: 1.15
  ChimeraX-STL: 1.0.1
  ChimeraX-Storm: 1.0
  ChimeraX-StructMeasure: 1.1.2
  ChimeraX-Struts: 1.0.1
  ChimeraX-Surface: 1.0.1
  ChimeraX-SwapAA: 2.0.1
  ChimeraX-SwapRes: 2.2.2
  ChimeraX-TapeMeasure: 1.0
  ChimeraX-TaskManager: 1.0
  ChimeraX-Test: 1.0
  ChimeraX-Toolbar: 1.1.2
  ChimeraX-ToolshedUtils: 1.2.4
  ChimeraX-Topography: 1.0
  ChimeraX-ToQuest: 1.0
  ChimeraX-Tug: 1.0.1
  ChimeraX-UI: 1.33.5
  ChimeraX-uniprot: 2.3
  ChimeraX-UnitCell: 1.0.1
  ChimeraX-ViewDockX: 1.3.2
  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: 1.1.3
  ChimeraX-Zone: 1.0.1
  colorama: 0.4.6
  comm: 0.2.1
  comtypes: 1.2.1
  contourpy: 1.2.0
  cxservices: 1.2.2
  cycler: 0.12.1
  Cython: 3.0.8
  debugpy: 1.8.0
  decorator: 5.1.1
  docutils: 0.20.1
  executing: 2.0.1
  filelock: 3.13.1
  fonttools: 4.47.2
  funcparserlib: 2.0.0a0
  glfw: 2.6.5
  grako: 3.16.5
  h5py: 3.10.0
  html2text: 2020.1.16
  idna: 3.6
  ihm: 0.43
  imagecodecs: 2024.1.1
  imagesize: 1.4.1
  ipykernel: 6.23.2
  ipython: 8.14.0
  ipython-genutils: 0.2.0
  ipywidgets: 8.1.1
  jedi: 0.18.2
  Jinja2: 3.1.3
  jupyter-client: 8.2.0
  jupyter-core: 5.7.1
  jupyterlab-widgets: 3.0.9
  kiwisolver: 1.4.5
  line-profiler: 4.1.2
  lxml: 5.1.0
  lz4: 4.3.3
  MarkupSafe: 2.1.4
  matplotlib: 3.8.2
  matplotlib-inline: 0.1.6
  msgpack: 1.0.7
  ndindex: 1.7
  nest-asyncio: 1.6.0
  netCDF4: 1.6.5
  networkx: 3.2.1
  nibabel: 5.0.1
  nptyping: 2.5.0
  numexpr: 2.9.0
  numpy: 1.26.3
  openvr: 1.26.701
  packaging: 23.2
  ParmEd: 3.4.3
  parso: 0.8.3
  pep517: 0.13.1
  pickleshare: 0.7.5
  pillow: 10.2.0
  pip: 23.3.2
  pkginfo: 1.9.6
  platformdirs: 4.1.0
  prompt-toolkit: 3.0.43
  psutil: 5.9.8
  pure-eval: 0.2.2
  py-cpuinfo: 9.0.0
  pycollada: 0.8
  pydicom: 2.3.0
  pygments: 2.17.2
  pynmrstar: 3.3.2
  pynrrd: 1.0.0
  PyOpenGL: 3.1.7
  PyOpenGL-accelerate: 3.1.7
  pyopenxr: 1.0.3301
  pyparsing: 3.1.1
  pyproject-hooks: 1.0.0
  PyQt6-commercial: 6.3.1
  PyQt6-Qt6: 6.3.2
  PyQt6-sip: 13.6.0
  PyQt6-WebEngine-commercial: 6.3.1
  PyQt6-WebEngine-Qt6: 6.3.2
  python-dateutil: 2.8.2
  pytz: 2023.4
  pywin32: 306
  pyzmq: 25.1.2
  qtconsole: 5.4.3
  QtPy: 2.4.1
  RandomWords: 0.4.0
  requests: 2.31.0
  scipy: 1.11.4
  setuptools: 69.0.3
  sfftk-rw: 0.8.1
  six: 1.16.0
  snowballstemmer: 2.2.0
  sortedcontainers: 2.4.0
  soupsieve: 2.5
  sphinx: 7.2.6
  sphinx-autodoc-typehints: 1.25.3
  sphinxcontrib-applehelp: 1.0.8
  sphinxcontrib-blockdiag: 3.0.0
  sphinxcontrib-devhelp: 1.0.6
  sphinxcontrib-htmlhelp: 2.0.5
  sphinxcontrib-jsmath: 1.0.1
  sphinxcontrib-qthelp: 1.0.7
  sphinxcontrib-serializinghtml: 1.1.10
  stack-data: 0.6.3
  superqt: 0.6.1
  tables: 3.9.2
  tcia-utils: 1.5.1
  tifffile: 2023.12.9
  tinyarray: 1.2.4
  tornado: 6.4
  traitlets: 5.14.1
  typing-extensions: 4.9.0
  tzdata: 2023.4
  urllib3: 2.1.0
  wcwidth: 0.2.13
  webcolors: 1.13
  wheel: 0.42.0
  wheel-filename: 1.4.1
  widgetsnbextension: 4.0.9
  WMI: 1.5.1"	defect	closed	moderate		Structure Prediction		duplicate						all	ChimeraX