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Opened 2 years ago
Closed 2 years ago
#9265 closed defect (fixed)
AlphaFold: Error running shell script install_openmm.sh
| 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-10-10.0.22621
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Having issues with google collab notebook off of chimeraX. If I run the notebook with PDB template and energy-minimization, I get this error:
Installing OpenMM
---------------------------------------------------------------------------
RuntimeError Traceback (most recent call last)
<ipython-input-8-657b9a61d1d2> in <cell line: 322>()
320 remove_from_list(seq_list, 'prokaryote') # Obsolete "prokaryote" flag
321
--> 322 run_prediction(seq_list, use_templates = use_templates, energy_minimize = not dont_minimize)
2 frames
<ipython-input-8-657b9a61d1d2> in run_shell_commands(commands, filename, install_log)
296 get_ipython().system('bash -x "{filename}" >> "{install_log}" 2>&1')
297 if _exit_code != 0:
--> 298 raise RuntimeError('Error running shell script %s, output in log file %s'
299 % (filename, install_log))
300
RuntimeError: Error running shell script install_openmm.sh, output in log file install_log.txt
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show AlphaFold
> alphafold predict
> MANDQRCASATERDWRARQRAFAAHLRDPRNAFAGIEERRLRIYRELFYNNVESCLASAFPVLRKLSSDAVWHARVRDFFTRHRCTAPQFHRLPEEFLRYLEAERGEHADDPPFLRELAHYEWVELALAIAPEDLPIEQADPEGDLLAGCPLLSPLAWPLVYAYPVHRIGPQFQPQAPGDSPTYLIVNRDREDRVRFLEINAVTARLVALIEAEPAASGRALLLRIAAELAHPDPQSVVAQGARILADLRARDIVLGTRR,MDIPRKPFAVALGAAFALGTAAAQASVFQASDLGAGYMVASAGEHAKSGEAKCGEGKCGEKKADAKAKEGKCGEGKCGEGKCGEKKADAKANEGKCGEGKCGENKTQ
Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.
Running AlphaFold prediction
> alphafold predict
> MANDQRCASATERDWRARQRAFAAHLRDPRNAFAGIEERRLRIYRELFYNNVESCLASAFPVLRKLSSDAVWHARVRDFFTRHRCTAPQFHRLPEEFLRYLEAERGEHADDPPFLRELAHYEWVELALAIAPEDLPIEQADPEGDLLAGCPLLSPLAWPLVYAYPVHRIGPQFQPQAPGDSPTYLIVNRDREDRVRFLEINAVTARLVALIEAEPAASGRALLLRIAAELAHPDPQSVVAQGARILADLRARDIVLGTRR,MDIPRKPFAVALGAAFALGTAAAQASVFQASDLGAGYMVASAGEHAKSGEAKCGEGKCGEKKADAKAKEGKCGEGKCGEGKCGEKKADAKANEGKCGEGKCGENKTQ
> minimize true templates true
Running AlphaFold prediction
> alphafold predict
> MANDQRCASATERDWRARQRAFAAHLRDPRNAFAGIEERRLRIYRELFYNNVESCLASAFPVLRKLSSDAVWHARVRDFFTRHRCTAPQFHRLPEEFLRYLEAERGEHADDPPFLRELAHYEWVELALAIAPEDLPIEQADPEGDLLAGCPLLSPLAWPLVYAYPVHRIGPQFQPQAPGDSPTYLIVNRDREDRVRFLEINAVTARLVALIEAEPAASGRALLLRIAAELAHPDPQSVVAQGARILADLRARDIVLGTRR,MDIPRKPFAVALGAAFALGTAAAQASVFQASDLGAGYMVASAGEHAKSGEAKCGEGKCGEKKADAKAKEGKCGEGKCGEGKCGEKKADAKANEGKCGEGKCGENKTQ
> minimize true templates true
Running AlphaFold prediction
> alphafold predict
> MANDQRCASATERDWRARQRAFAAHLRDPRNAFAGIEERRLRIYRELFYNNVESCLASAFPVLRKLSSDAVWHARVRDFFTRHRCTAPQFHRLPEEFLRYLEAERGEHADDPPFLRELAHYEWVELALAIAPEDLPIEQADPEGDLLAGCPLLSPLAWPLVYAYPVHRIGPQFQPQAPGDSPTYLIVNRDREDRVRFLEINAVTARLVALIEAEPAASGRALLLRIAAELAHPDPQSVVAQGARILADLRARDIVLGTRR,MDIPRKPFAVALGAAFALGTAAAQASVFQASDLGAGYMVASAGEHAKSGEAKCGEGKCGEKKADAKAKEGKCGEGKCGEGKCGEKKADAKANEGKCGEGKCGENKTQ
> minimize true templates true
Running AlphaFold prediction
> help help:user/tools/alphafold.html
> alphafold predict
> MANDQRCASATERDWRARQRAFAAHLRDPRNAFAGIEERRLRIYRELFYNNVESCLASAFPVLRKLSSDAVWHARVRDFFTRHRCTAPQFHRLPEEFLRYLEAERGEHADDPPFLRELAHYEWVELALAIAPEDLPIEQADPEGDLLAGCPLLSPLAWPLVYAYPVHRIGPQFQPQAPGDSPTYLIVNRDREDRVRFLEINAVTARLVALIEAEPAASGRALLLRIAAELAHPDPQSVVAQGARILADLRARDIVLGTRR
> minimize true templates true
Running AlphaFold prediction
Uncaught (in promise) TypeError: Cannot read properties of undefined (reading
'0')
> alphafold predict
> MANDQRCASATERDWRARQRAFAAHLRDPRNAFAGIEERRLRIYRELFYNNVESCLASAFPVLRKLSSDAVWHARVRDFFTRHRCTAPQFHRLPEEFLRYLEAERGEHADDPPFLRELAHYEWVELALAIAPEDLPIEQADPEGDLLAGCPLLSPLAWPLVYAYPVHRIGPQFQPQAPGDSPTYLIVNRDREDRVRFLEINAVTARLVALIEAEPAASGRALLLRIAAELAHPDPQSVVAQGARILADLRARDIVLGTRR
> minimize true templates true
Running AlphaFold prediction
OpenGL version: 3.3.0 NVIDIA 516.40
OpenGL renderer: NVIDIA GeForce RTX 3060 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows
Manufacturer: ASUSTeK COMPUTER INC.
Model: ROG Strix G513IM_G513IM
OS: Microsoft Windows 11 Home (Build 22621)
Memory: 33,738,051,584
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 4800H with Radeon Graphics
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
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: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
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
ChimeraX-DockPrep: 1.1.1
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: 1.2.1
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-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
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: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
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: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
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: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
comtypes: 1.1.14
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pywin32: 305
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
WMI: 1.5.1
zipp: 3.15.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Structure Prediction |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → AlphaFold: Error running shell script install_openmm.sh |
comment:2 by , 2 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed.
No need to update ChimeraX -- the fix is in the Colab AlphaFold prediction script that ChimeraX downloads each time a prediction is run.
If both PDB templates and optimization were enabled then installing hhsuite to use templates caused the subsequent installation of openmm to do energy minimization to fail. It failed because the hhsuite install updated conda to a new version (23.5.0) that apparently was not compatible with openmm (which wanted 23.3.1). When conda is installed it gets version 23.3.1 but then installing hhsuite updated it to 23.5.0. I'm not sure why it updated since the first install was supposed to get the most recent version. I suspect it is because the "bioconda" channel was enabled in the hhsuite install. I made the conda install of hhsuite not update the conda version to fix this.
Here is the install_log.txt from the failed openmm install
... + touch CONDA_READY + set -e + conda install -y -q -c conda-forge -c bioconda kalign2=2.04 hhsuite=3.3.0 python=3.10 + touch HH_READY + set -e + conda install -y -q -c conda-forge openmm=7.7.0 python=3.10 pdbfixer ResolvePackageNotFound: - conda==23.3.1
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Reported by Miriam Bregman