AlphaFold PAE: list index out of range

[chimera-bug-report@…]

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)

<sup>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'</sup>

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)

<sup>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'</sup>

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)

<sup>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'</sup>

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)

<sup>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'</sup>

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)

<sup>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'</sup>

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

[Tom Goddard]

Was fixed in ChimeraX 1.8.