The following bug report has been submitted:
Platform: macOS-14.4.1-arm64-arm-64bit
ChimeraX Version: 1.8.dev202405031817 (2024-05-03 18:17:29 UTC)
Description
Tried alphafold error plot on an AlphaFold 3 prediction. Clicking on the menu to load from "file (.json or .pkl)" gave this error, apparently trying to populate the entry field by scanning the directory. The directory has files
ls -1 ~/Downloads/fold_2024_05_08_15_09
fold_2024_05_08_15_09_full_data_0.json
fold_2024_05_08_15_09_full_data_1.json
fold_2024_05_08_15_09_full_data_2.json
fold_2024_05_08_15_09_full_data_3.json
fold_2024_05_08_15_09_full_data_4.json
fold_2024_05_08_15_09_job_request.json
fold_2024_05_08_15_09_model_0.cif
fold_2024_05_08_15_09_model_1.cif
fold_2024_05_08_15_09_model_2.cif
fold_2024_05_08_15_09_model_3.cif
fold_2024_05_08_15_09_model_4.cif
fold_2024_05_08_15_09_summary_confidences_0.json
fold_2024_05_08_15_09_summary_confidences_1.json
fold_2024_05_08_15_09_summary_confidences_2.json
fold_2024_05_08_15_09_summary_confidences_3.json
fold_2024_05_08_15_09_summary_confidences_4.json
terms_of_use.md
Log:
UCSF ChimeraX version: 1.8.dev202405031817 (2024-05-03)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> registration file ~/Desktop/registration.txt
Expected name of a file to open/read; a name of 'browse' will bring up a file
browser or a keyword
> registration file /Users/goddard/Desktop/registration.txt
Expected name of a file to open/read; a name of 'browse' will bring up a file
browser or a keyword
> registration file /Users/goddard/registration.txt
/Users/goddard/registration.txt: no registration data found
> registration file /Users/goddard/Desktop/reg.html
Thank you for registering your copy of ChimeraX. By providing the information
requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.
> registration file ~/Desktop/reg2.html
Expected name of a file to open/read; a name of 'browse' will bring up a file
browser or a keyword
> open 4xv9
Summary of feedback from opening 4xv9 fetched from pdb
---
warning | Cannot find consistent set of bond orders for ring system containing atom C19 in residue 1OO /A:801
4xv9 title:
B-Raf Kinase domain in complex with PLX5568 [more info...]
Chain information for 4xv9 #1
---
Chain | Description | UniProt
A | Serine/threonine-protein kinase B-raf | BRAF_HUMAN 442-705
Non-standard residues in 4xv9 #1
---
1OO —
N-{3-[(5-chloro-1H-pyrrolo[2,3-b]pyridin-3-yl)carbonyl]-2,4-difluorophenyl}-4-(trifluoromethyl)benzenesulfonamide
SO4 — sulfate ion
4xv9 mmCIF Assemblies
---
1| author_defined_assembly
53 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> close
> open 8jk9
Summary of feedback from opening 8jk9 fetched from pdb
---
note | Fetching compressed mmCIF 8jk9 from http://files.rcsb.org/download/8jk9.cif
8jk9 title:
SP1746 in complex with GDP [more info...]
Chain information for 8jk9 #1
---
Chain | Description | UniProt
A | bis(5'-nucleosyl)-tetraphosphatase (symmetrical) | A0A0H2URF8_STRPN 1-197
Non-standard residues in 8jk9 #1
---
FE — Fe (III) ion
GDP — guanosine-5'-diphosphate
GOL — glycerol (glycerin; propane-1,2,3-triol)
MG — magnesium ion
8jk9 mmCIF Assemblies
---
1| author_and_software_defined_assembly
15 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select :FE
2 atoms, 2 residues, 1 model selected
> select :GDP
28 atoms, 30 bonds, 1 residue, 1 model selected
> select :MG
2 atoms, 2 residues, 1 model selected
> open
> /Users/goddard/Downloads/fold_2024_05_08_15_09/fold_2024_05_08_15_09_model_0.cif
Chain information for fold_2024_05_08_15_09_model_0.cif #2
---
Chain | Description
A B | .
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8jk9, chain A (#1) with fold_2024_05_08_15_09_model_0.cif, chain A
(#2), sequence alignment score = 1114.4
RMSD between 194 pruned atom pairs is 0.339 angstroms; (across all 195 pairs:
0.385)
> sym #1 assembly 1
Made 2 copies for 8jk9 assembly 1
> view
> hide #!3 models
> show #!3 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #!3 models
> hide #2 models
> show #2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> ui tool show "AlphaFold Error Plot"
Traceback (most recent call last):
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 62, in <lambda>
sf.widget.menu().triggered.connect(lambda action, self=self:
self._guess_for_source())
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 132, in _guess_for_source
pae_path = _matching_pae_file(structure_path)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 316, in _matching_pae_file
mfile = _longest_matching_prefix(filename, pkl_files, min_length = min_length)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 328, 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
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 328, 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.
> ui tool show "AlphaFold Error Plot"
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac Studio
Model Identifier: Mac14,14
Model Number: Z1800003VLL/A
Chip: Apple M2 Ultra
Total Number of Cores: 24 (16 performance and 8 efficiency)
Memory: 64 GB
System Firmware Version: 10151.101.3
OS Loader Version: 10151.101.3
Software:
System Software Overview:
System Version: macOS 14.4.1 (23E224)
Kernel Version: Darwin 23.4.0
Time since boot: 1 day, 19 hours, 18 minutes
Graphics/Displays:
Apple M2 Ultra:
Chipset Model: Apple M2 Ultra
Type: GPU
Bus: Built-In
Total Number of Cores: 60
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
PHL 278B1:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
aiobotocore: 2.12.3
aiohttp: 3.9.5
aioitertools: 0.11.0
aiosignal: 1.3.1
alabaster: 0.7.16
alphashape: 1.3.1
annotated-types: 0.6.0
appdirs: 1.4.4
appnope: 0.1.4
asciitree: 0.3.3
asttokens: 2.4.1
attrs: 23.2.0
Babel: 2.14.0
beautifulsoup4: 4.12.3
biopython: 1.83
blockdiag: 3.0.0
blosc2: 2.0.0
botocore: 1.34.69
build: 1.2.1
certifi: 2023.11.17
cffi: 1.16.0
cftime: 1.6.3
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: 2.12.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-ArtiaX: 0.4.5
ChimeraX-Atomic: 1.57
ChimeraX-AtomicLibrary: 14.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.5
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.3
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: 2.2.4
ChimeraX-Clipper: 0.23.0
ChimeraX-ColorActions: 1.0.4
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-copick: 0.1.0
ChimeraX-Core: 1.8.dev202405031817
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-crai: 0.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
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: 1.1.1
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: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
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-NIHPresets: 1.1.17
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OME-Zarr: 0.5.3
ChimeraX-OpenCommand: 1.13.4
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.2.2
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
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-Segmentations: 1.0.4
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.4
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-TetraScapeCommand: 0.1
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: 1.38
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.1
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
click: 8.1.7
click-log: 0.4.0
cloudpickle: 3.0.0
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
copick: 0.1.dev45+g5a19260
cripser: 0.0.13
cryptography: 42.0.5
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
dask: 2024.4.2
debugpy: 1.8.1
decorator: 5.1.1
distributed: 2024.4.2
docutils: 0.20.1
executing: 2.0.1
fasteners: 0.19
filelock: 3.13.4
fonttools: 4.51.0
frozenlist: 1.4.1
fsspec: 2024.3.1
funcparserlib: 2.0.0a0
geomdl: 5.3.1
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
hatchling: 1.24.2
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imageio: 2.34.1
imagesize: 1.4.1
importlib-metadata: 7.1.0
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
Jinja2: 3.1.3
jmespath: 1.0.1
joblib: 1.4.0
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
lazy-loader: 0.4
line-profiler: 4.1.2
llvmlite: 0.42.0
locket: 1.0.0
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
mpmath: 1.3.0
mrcfile: 1.5.0
msgpack: 1.0.8
multidict: 6.0.5
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numba: 0.59.1
numcodecs: 0.12.1
numexpr: 2.10.0
numpy: 1.26.4
ome-zarr: 0.8.3
openvr: 1.26.701
packaging: 23.2
pandas: 2.2.2
ParmEd: 4.2.2
parso: 0.8.4
partd: 1.4.1
pathspec: 0.12.1
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.1
pluggy: 1.5.0
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pyarrow: 16.0.0
pycollada: 0.8
pycparser: 2.22
pydantic: 2.7.1
pydantic-core: 2.18.2
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynndescent: 0.5.12
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
pyspnego: 0.10.2
python-dateutil: 2.9.0.post0
pytz: 2024.1
PyYAML: 6.0.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
Rtree: 1.1.0
s3fs: 2024.3.1
scikit-image: 0.23.2
scikit-learn: 1.4.2
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
shapely: 2.0.2
six: 1.16.0
smbprotocol: 1.13.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
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
starfile: 0.5.6
superqt: 0.6.3
sympy: 1.12
tables: 3.8.0
tblib: 3.0.0
tcia-utils: 1.5.1
threadpoolctl: 3.4.0
tifffile: 2024.1.30
tinyarray: 1.2.4
toolz: 0.12.1
torch: 2.2.2
tornado: 6.4
tqdm: 4.66.2
traitlets: 5.14.2
trimesh: 4.0.10
trove-classifiers: 2024.4.10
typing-extensions: 4.11.0
tzdata: 2024.1
umap-learn: 0.5.6
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
wrapt: 1.16.0
yarl: 1.9.4
zarr: 2.17.2
zict: 3.0.0
zipp: 3.18.1
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Fixed in 1.9 and 1.8.
Code to find the .json or .pkl file with the longest prefix assumed that if no .json match is found then some .pkl files exist. Made code handle cases where no .pkl files are present.
Also made code find .json file names produced by AlphaFold 3 Server, although the code still needs to be fixed to handle those files when ligands, ions, or nucleic acids are present.