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#19730 closed defect (fixed)
alphafold interfaces: bad log links
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Prediction | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
I am planning to set up systematic analysis of AF3 predictions. Here are the first two lines of the codes in my cxc script.
cd "C:/Users/hef/OneDrive - University Of Massachusetts Medical School/Documents/Feng_AF3_01_2026/fold_dcp1_dcp2_af3"
alphafold interfaces "C:/Users/hef/OneDrive - University Of Massachusetts Medical School/Documents/Feng_AF3_01_2026/fold_dcp1_dcp2_af3"
The codes appeared to be working as they point to the right folder and files.
cd "C:/Users/hef/OneDrive - University Of Massachusetts Medical School/Documents/Feng_AF3_01_2026/fold_dcp1_dcp2_af3"
Current working directory is: C:\Users\hef\OneDrive - University Of Massachusetts Medical School\Documents\Feng_AF3_01_2026\fold_dcp1_dcp2_af3
alphafold interfaces "C:\Users\hef\OneDrive - University Of Massachusetts Medical School\Documents\Feng_AF3_01_2026\fold_dcp1_dcp2_af3"
1 of 1 dimers have 10 or more confident residue interactions
spanning <= 4 Angstroms with predicted aligned error <= 5 Angstroms.
Sequences Models Confident pairs #Res1 #Res2
dcp1_dcp2_af3 5 61 29 23
Open best. Hide or show disordered loops (pLLDT <= 50).
executed feng-test2.cxc
However, the links in the log panels such as dcp1_dcp2_af3 and Open best are not working. I awalys got an error message "'\' has no suffix".
I am new to structural analysis software. Please help me.
Thanks,
Feng
Log:
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> help help:user
> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html
Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html
Downloading file ChimeraX_tutorial.html
> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html
Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html
> cd "C:/Users/hef/OneDrive - University Of Massachusetts Medical
> School/Documents/Feng_AF3_01_2026/Zip_files"
Current working directory is: C:\Users\hef\OneDrive - University Of
Massachusetts Medical School\Documents\Feng_AF3_01_2026\Zip_files
> alphafold interfaces ./AF_predictions
Missing or invalid "directory" argument: File './AF_predictions' does not
exist
> alphafold interfaces ./Zip_files
Missing or invalid "directory" argument: File './Zip_files' does not exist
> open "C:\Users\hef\OneDrive - University Of Massachusetts Medical
> School\Documents\Feng-12-2023\C22-AlphaFold-2023\Pat1Ebs1_18303.result\Pat1Ebs1_18303\Pat1Ebs1_18303_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb"
> format pdb
Chain information for
Pat1Ebs1_18303_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#1
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> alphafold interfaces ./AF_predictions
Missing or invalid "directory" argument: File './AF_predictions' does not
exist
> cd "C:/Users/hef/OneDrive - University Of Massachusetts Medical
> School/Documents/Feng_AF3_01_2026/fold_dcp1_dcp2_af3"
Current working directory is: C:\Users\hef\OneDrive - University Of
Massachusetts Medical School\Documents\Feng_AF3_01_2026\fold_dcp1_dcp2_af3
> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html
Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html
> close
> open "C:/Users/hef/OneDrive - University Of Massachusetts Medical
> School/Documents/feng-test2"
'C:/Users/hef/OneDrive - University Of Massachusetts Medical
School/Documents/feng-test2' has no suffix
> open "C:/Users/hef/OneDrive - University Of Massachusetts Medical
> School/Documents/feng-test2.cxc"
> cd "C:/Users/hef/OneDrive - University Of Massachusetts Medical
> School/Documents/Feng_AF3_01_2026/fold_dcp1_dcp2_af3"
Current working directory is: C:\Users\hef\OneDrive - University Of
Massachusetts Medical School\Documents\Feng_AF3_01_2026\fold_dcp1_dcp2_af3
> alphafold interfaces "C:/Users/hef/OneDrive - University Of Massachusetts
> Medical School/Documents/Feng_AF3_01_2026/fold_dcp1_dcp2_af3"
1 of 1 dimers have 10 or more confident residue interactions
spanning <= 4 Angstroms with predicted aligned error <= 5 Angstroms.
Sequences| Models| Confident pairs| #Res1| #Res2 | dcp1_dcp2_af3 | 5 | 61 | 29 | 23
---|---|---|---|---
Open best. Hide or show disordered loops (pLLDT <= 50).
executed feng-test2.cxc
> open \
'\' has no suffix
> open \
'\' has no suffix
> open \
'\' has no suffix
> open \
'\' has no suffix
> open \
'\' has no suffix
> open \
'\' has no suffix
> open "C:/Users/hef/OneDrive - University Of Massachusetts Medical
> School/Documents/feng-test2.cxc"
> cd "C:/Users/hef/OneDrive - University Of Massachusetts Medical
> School/Documents/Feng_AF3_01_2026/fold_dcp1_dcp2_af3"
Current working directory is: C:\Users\hef\OneDrive - University Of
Massachusetts Medical School\Documents\Feng_AF3_01_2026\fold_dcp1_dcp2_af3
> alphafold interfaces "C:/Users/hef/OneDrive - University Of Massachusetts
> Medical School/Documents/Feng_AF3_01_2026/fold_dcp1_dcp2_af3/...."
Cannot open files: [WinError 3] The system cannot find the path specified:
'C:/Users/hef/OneDrive - University Of Massachusetts Medical
School/Documents/Feng_AF3_01_2026/fold_dcp1_dcp2_af3/....'
> open "C:/Users/hef/OneDrive - University Of Massachusetts Medical
> School/Documents/feng-test2.cxc"
> cd "C:/Users/hef/OneDrive - University Of Massachusetts Medical
> School/Documents/Feng_AF3_01_2026/fold_dcp1_dcp2_af3"
Current working directory is: C:\Users\hef\OneDrive - University Of
Massachusetts Medical School\Documents\Feng_AF3_01_2026\fold_dcp1_dcp2_af3
> alphafold interfaces "C:/Users/hef/OneDrive - University Of Massachusetts
> Medical School/Documents/Feng_AF3_01_2026/fold_dcp1_dcp2_af3/."
1 of 1 dimers have 10 or more confident residue interactions
spanning <= 4 Angstroms with predicted aligned error <= 5 Angstroms.
Sequences| Models| Confident pairs| #Res1| #Res2 | dcp1_dcp2_af3 | 5 | 61 | 29 | 23
---|---|---|---|---
Open best. Hide or show disordered loops (pLLDT <= 50).
executed feng-test2.cxc
> open \
'\' has no suffix
> open "C:/Users/hef/OneDrive - University Of Massachusetts Medical
> School/Documents/feng-test2.cxc"
> cd "C:/Users/hef/OneDrive - University Of Massachusetts Medical
> School/Documents/Feng_AF3_01_2026/fold_dcp1_dcp2_af3"
Current working directory is: C:\Users\hef\OneDrive - University Of
Massachusetts Medical School\Documents\Feng_AF3_01_2026\fold_dcp1_dcp2_af3
> alphafold interfaces "C:/Users/hef/OneDrive - University Of Massachusetts
> Medical School/Documents/Feng_AF3_01_2026/fold_dcp1_dcp2_af3/..."
Cannot open files: [WinError 3] The system cannot find the path specified:
'C:/Users/hef/OneDrive - University Of Massachusetts Medical
School/Documents/Feng_AF3_01_2026/fold_dcp1_dcp2_af3/...'
> open "C:/Users/hef/OneDrive - University Of Massachusetts Medical
> School/Documents/feng-test2.cxc"
> cd "C:/Users/hef/OneDrive - University Of Massachusetts Medical
> School/Documents/Feng_AF3_01_2026/fold_dcp1_dcp2_af3"
Current working directory is: C:\Users\hef\OneDrive - University Of
Massachusetts Medical School\Documents\Feng_AF3_01_2026\fold_dcp1_dcp2_af3
> alphafold interfaces "C:/Users/hef/OneDrive - University Of Massachusetts
> Medical School/Documents/Feng_AF3_01_2026/fold_dcp1_dcp2_af3"
1 of 1 dimers have 10 or more confident residue interactions
spanning <= 4 Angstroms with predicted aligned error <= 5 Angstroms.
Sequences| Models| Confident pairs| #Res1| #Res2 | dcp1_dcp2_af3 | 5 | 61 | 29 | 23
---|---|---|---|---
Open best. Hide or show disordered loops (pLLDT <= 50).
executed feng-test2.cxc
> open \
'\' has no suffix
> help help:user/tools/log.html
> open "C:/Users/hef/OneDrive - University Of Massachusetts Medical
> School/Documents/feng-test2.cxc"
> cd "C:/Users/hef/OneDrive - University Of Massachusetts Medical
> School/Documents/Feng_AF3_01_2026/fold_dcp1_dcp2_af3"
Current working directory is: C:\Users\hef\OneDrive - University Of
Massachusetts Medical School\Documents\Feng_AF3_01_2026\fold_dcp1_dcp2_af3
> alphafold interfaces "C:\Users\hef/OneDrive - University Of Massachusetts
> Medical School\Documents\Feng_AF3_01_2026\fold_dcp1_dcp2_af3"
1 of 1 dimers have 10 or more confident residue interactions
spanning <= 4 Angstroms with predicted aligned error <= 5 Angstroms.
Sequences| Models| Confident pairs| #Res1| #Res2 | dcp1_dcp2_af3 | 5 | 61 | 29 | 23
---|---|---|---|---
Open best. Hide or show disordered loops (pLLDT <= 50).
executed feng-test2.cxc
> open \
'\' has no suffix
> open \
'\' has no suffix
> open \
'\' has no suffix
> open \
'\' has no suffix
> open \
'\' has no suffix
> open "C:/Users/hef/OneDrive - University Of Massachusetts Medical
> School/Documents/feng-test2.cxc"
> cd "C:/Users/hef/OneDrive - University Of Massachusetts Medical
> School/Documents/Feng_AF3_01_2026/fold_dcp1_dcp2_af3"
Current working directory is: C:\Users\hef\OneDrive - University Of
Massachusetts Medical School\Documents\Feng_AF3_01_2026\fold_dcp1_dcp2_af3
> alphafold interfaces "C:\Users\hef/OneDrive - University Of Massachusetts
> Medical School\Documents\Feng_AF3_01_2026\fold_dcp1_dcp2_af3\"
1 of 1 dimers have 10 or more confident residue interactions
spanning <= 4 Angstroms with predicted aligned error <= 5 Angstroms.
Sequences| Models| Confident pairs| #Res1| #Res2 | dcp1_dcp2_af3 | 5 | 61 | 29 | 23
---|---|---|---|---
Open best. Hide or show disordered loops (pLLDT <= 50).
executed feng-test2.cxc
> open \
'\' has no suffix
> open \
'\' has no suffix
> open \
'\' has no suffix
> open "C:/Users/hef/OneDrive - University Of Massachusetts Medical
> School/Documents/feng-test2.cxc"
> cd "C:/Users/hef/OneDrive - University Of Massachusetts Medical
> School/Documents/Feng_AF3_01_2026/fold_dcp1_dcp2_af3"
Current working directory is: C:\Users\hef\OneDrive - University Of
Massachusetts Medical School\Documents\Feng_AF3_01_2026\fold_dcp1_dcp2_af3
> alphafold interfaces "C:\Users\hef/OneDrive - University Of Massachusetts
> Medical School\Documents\Feng_AF3_01_2026\fold_dcp1_dcp2_af3"
1 of 1 dimers have 10 or more confident residue interactions
spanning <= 4 Angstroms with predicted aligned error <= 5 Angstroms.
Sequences| Models| Confident pairs| #Res1| #Res2 | dcp1_dcp2_af3 | 5 | 61 | 29 | 23
---|---|---|---|---
Open best. Hide or show disordered loops (pLLDT <= 50).
executed feng-test2.cxc
> open "C:/Users/hef/OneDrive - University Of Massachusetts Medical
> School/Documents/feng-test2.cxc"
> cd "C:/Users/hef/OneDrive - University Of Massachusetts Medical
> School/Documents/Feng_AF3_01_2026/fold_dcp1_dcp2_af3"
Current working directory is: C:\Users\hef\OneDrive - University Of
Massachusetts Medical School\Documents\Feng_AF3_01_2026\fold_dcp1_dcp2_af3
> alphafold interfaces "C:\Users\hef/OneDrive - University Of Massachusetts
> Medical School\Documents\Feng_AF3_01_2026\fold_dcp1_dcp2_af3"
1 of 1 dimers have 10 or more confident residue interactions
spanning <= 4 Angstroms with predicted aligned error <= 5 Angstroms.
Sequences| Models| Confident pairs| #Res1| #Res2 | dcp1_dcp2_af3 | 5 | 61 | 29 | 23
---|---|---|---|---
Open best. Hide or show disordered loops (pLLDT <= 50).
executed feng-test2.cxc
> open \
'\' has no suffix
> open \
'\' has no suffix
> open "C:/Users/hef/OneDrive - University Of Massachusetts Medical
> School/Documents/feng-test2.cxc"
> cd "C:/Users/hef/OneDrive - University Of Massachusetts Medical
> School/Documents/Feng_AF3_01_2026/fold_dcp1_dcp2_af3"
Current working directory is: C:\Users\hef\OneDrive - University Of
Massachusetts Medical School\Documents\Feng_AF3_01_2026\fold_dcp1_dcp2_af3
> alphafold interfaces "C:\Users\hef\OneDrive - University Of Massachusetts
> Medical School\Documents\Feng_AF3_01_2026\fold_dcp1_dcp2_af3"
1 of 1 dimers have 10 or more confident residue interactions
spanning <= 4 Angstroms with predicted aligned error <= 5 Angstroms.
Sequences| Models| Confident pairs| #Res1| #Res2 | dcp1_dcp2_af3 | 5 | 61 | 29 | 23
---|---|---|---|---
Open best. Hide or show disordered loops (pLLDT <= 50).
executed feng-test2.cxc
> open \
'\' has no suffix
> help help:contact.html
[Repeated 2 time(s)]
> open \
'\' has no suffix
OpenGL version: 3.3.13507 Core Profile Forward-Compatible Context 23.20.15032.11
OpenGL renderer: AMD Radeon R5 430
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows
Manufacturer: Dell Inc.
Model: OptiPlex 7050
OS: Microsoft Windows 10 Enterprise (Build 19045)
Memory: 34,210,705,408
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-7700 CPU @ 3.60GHz
OSLanguage: en-US
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.5.0
build: 1.2.2.post1
certifi: 2025.6.15
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.18
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
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: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
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: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.10
contourpy: 1.3.2
coverage: 7.9.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.4
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
joblib: 1.5.3
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
llvmlite: 0.46.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numba: 0.63.1
numexpr: 2.11.0
numpy: 1.26.4
nvidia-cuda-cupti-cu12: 12.9.79
nvidia-cuda-nvcc-cu12: 12.9.86
nvidia-cuda-nvrtc-cu12: 12.9.86
nvidia-cuda-runtime-cu12: 12.9.79
nvidia-cufft-cu12: 11.4.1.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynndescent: 0.5.13
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pywin32: 310
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scikit-learn: 1.8.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
threadpoolctl: 3.6.0
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
tqdm: 4.67.1
traitlets: 5.14.3
typing_extensions: 4.14.0
tzdata: 2025.2
umap-learn: 0.5.9.post2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
WMI: 1.5.1
Change History (4)
comment:1 by , 8 hours ago
| Component: | Unassigned → Structure Prediction |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → alphafold interfaces: bad log links |
comment:2 by , 5 hours ago
The links in the ChimeraX Log produced by the "alphafold interfaces" command are not working properly when the directory path containing your predictions includes space characters. A way to work around this ChimeraX bug is to copy your predictions to a directory on your computer that does not have any spaces in the path. I will try to fix this bug in ChimeraX today.
comment:3 by , 5 hours ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed in ChimeraX daily build Jan 14 or newer.
The alphafold interfaces code was using backslash quote (\") to escape quote marks in html for the command links. That is not the right way to include a quote mark in in html. Instead it needs to use "
Tested with alphafold predictions directory that contains space characters. Working now.
comment:4 by , 5 hours ago
Hi Tom,
Following your instructions, the issue has been resolved.
Thank you very much.
Feng
-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Wednesday, January 14, 2026 3:43 PM
To: goddard@cgl.ucsf.edu; He, Feng <Feng.He@umassmed.edu>
Subject: Re: [ChimeraX] #19730: alphafold interfaces: bad log links
#19730: alphafold interfaces: bad log links
-------------------------------------------+-------------------------
Reporter: feng.he@... | Owner: Tom Goddard
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Structure Prediction | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-------------------------------------------+-------------------------
Comment (by Tom Goddard):
The links in the ChimeraX Log produced by the "alphafold interfaces"
command are not working properly when the directory path containing your predictions includes space characters. A way to work around this ChimeraX bug is to copy your predictions to a directory on your computer that does not have any spaces in the path. I will try to fix this bug in ChimeraX today.
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/19730#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
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Reported by Feng He