Opened 8 days ago

Closed 7 days ago

#20110 closed defect (limitation)

boltz predict: ImportError: Unable to import required dependencies: pytz: No module named 'pytz'

Reported by: neha@… 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:        Linux-6.17.0-19-generic-x86_64-with-glibc2.39
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
boltz predict protein IQLQALSLPLVVIVHGNQDNNAKATILWDNAFSEMDRVPFVVAERVPWEKMCETLNLKFMAEVGTNRGLLPEHFLFLAQKIFNDNSLSMEAFQHRSVSWSQFNKEILLGRGFTFWQWFDGVLDLTKRCLRSYWSDRLIIGFISKQYVTSLLLNEPDGTFLLRFSDSEIGGITIAHVIRGQDGSPQIENIQPFSAKDLSIRSLGDRIRDLAQLKNLYPKKPKDEAFRSHYKPEQMGKDGRGYVPATIKMTVERDQPLPT ligandSmiles CN(C)C(=O)NC1=CC=C(CNC(=O)C2=NN(C)C3=CC=C(C4=CC=C(C5=NC=CN5C)C=C4)C=C32)C=C1 name test resultsDirectory /home/glpl/Documents/stat6/[name] useMsaCache false device gpu affinity CN(C)C(=O)NC1=CC=C(CNC(=O)C2=NN(C)C3=CC=C(C4=CC=C(C5=NC=CN5C)C=C4)C=C32)C=C1 steering true samples 3
Running Boltz prediction of protein with 258 residues, 1 ligands CN(C)C(=O)NC1=CC=C(CNC(=O)C2=NN(C)C3=CC=C(C4=CC=C(C5=NC=CN5C)C=C4)C=C32)C=C1 on gpu
Using multiple sequence alignment server https://api.colabfold.com
Running boltz prediction failed with exit code 1:
command:
/home/glpl/boltz22/bin/boltz predict /home/glpl/Documents/stat6/test_3/test.yaml --use_msa_server --use_potentials --accelerator gpu --diffusion_samples 3
stdout:

stderr:
Traceback (most recent call last):
File "/home/glpl/boltz22/bin/boltz", line 5, in <module>
from boltz.main import cli
File "/home/glpl/boltz22/lib/python3.11/site-packages/boltz/main.py", line 28, in <module>
from boltz.data.parse.csv import parse_csv
File "/home/glpl/boltz22/lib/python3.11/site-packages/boltz/data/parse/csv.py", line 5, in <module>
import pandas as pd
File "/home/glpl/boltz22/lib/python3.11/site-packages/pandas/__init__.py", line 19, in <module>
raise ImportError(
ImportError: Unable to import required dependencies:
pytz: No module named 'pytz'

Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show Boltz

> boltz predict protein
> IQLQALSLPLVVIVHGNQDNNAKATILWDNAFSEMDRVPFVVAERVPWEKMCETLNLKFMAEVGTNRGLLPEHFLFLAQKIFNDNSLSMEAFQHRSVSWSQFNKEILLGRGFTFWQWFDGVLDLTKRCLRSYWSDRLIIGFISKQYVTSLLLNEPDGTFLLRFSDSEIGGITIAHVIRGQDGSPQIENIQPFSAKDLSIRSLGDRIRDLAQLKNLYPKKPKDEAFRSHYKPEQMGKDGRGYVPATIKMTVERDQPLPT
> ligandSmiles
> CN(C)C(=O)NC1=CC=C(CNC(=O)C2=NN(C)C3=CC=C(C4=CC=C(C5=NC=CN5C)C=C4)C=C32)C=C1
> name test resultsDirectory /home/glpl/Documents/stat6/[name] steering true
> samples 3

Running Boltz prediction of protein with 258 residues, 1 ligands
CN(C)C(=O)NC1=CC=C(CNC(=O)C2=NN(C)C3=CC=C(C4=CC=C(C5=NC=CN5C)C=C4)C=C32)C=C1
on gpu  
Using multiple sequence alignment server https://api.colabfold.com  
Running boltz prediction failed with exit code 1:  
command:  
/home/glpl/boltz22/bin/boltz predict /home/glpl/Documents/stat6/test/test.yaml
--use_msa_server --use_potentials --accelerator gpu --diffusion_samples 3  
stdout:  
  
stderr:  
Traceback (most recent call last):  
File "/home/glpl/boltz22/bin/boltz", line 5, in <module>  
from boltz.main import cli  
File "/home/glpl/boltz22/lib/python3.11/site-packages/boltz/main.py", line 28,
in <module>  
from boltz.data.parse.csv import parse_csv  
File "/home/glpl/boltz22/lib/python3.11/site-
packages/boltz/data/parse/csv.py", line 5, in <module>  
import pandas as pd  
File "/home/glpl/boltz22/lib/python3.11/site-packages/pandas/__init__.py",
line 19, in <module>  
raise ImportError(  
ImportError: Unable to import required dependencies:  
pytz: No module named 'pytz'  
  

> boltz predict protein
> IQLQALSLPLVVIVHGNQDNNAKATILWDNAFSEMDRVPFVVAERVPWEKMCETLNLKFMAEVGTNRGLLPEHFLFLAQKIFNDNSLSMEAFQHRSVSWSQFNKEILLGRGFTFWQWFDGVLDLTKRCLRSYWSDRLIIGFISKQYVTSLLLNEPDGTFLLRFSDSEIGGITIAHVIRGQDGSPQIENIQPFSAKDLSIRSLGDRIRDLAQLKNLYPKKPKDEAFRSHYKPEQMGKDGRGYVPATIKMTVERDQPLPT
> ligandSmiles
> CN(C)C(=O)NC1=CC=C(CNC(=O)C2=NN(C)C3=CC=C(C4=CC=C(C5=NC=CN5C)C=C4)C=C32)C=C1
> name test resultsDirectory /home/glpl/Documents/stat6/[name] useMsaCache
> false device gpu steering true samples 3

Running Boltz prediction of protein with 258 residues, 1 ligands
CN(C)C(=O)NC1=CC=C(CNC(=O)C2=NN(C)C3=CC=C(C4=CC=C(C5=NC=CN5C)C=C4)C=C32)C=C1
on gpu  
Using multiple sequence alignment server https://api.colabfold.com  
Running boltz prediction failed with exit code 1:  
command:  
/home/glpl/boltz22/bin/boltz predict
/home/glpl/Documents/stat6/test_1/test.yaml --use_msa_server --use_potentials
--accelerator gpu --diffusion_samples 3  
stdout:  
  
stderr:  
Traceback (most recent call last):  
File "/home/glpl/boltz22/bin/boltz", line 5, in <module>  
from boltz.main import cli  
File "/home/glpl/boltz22/lib/python3.11/site-packages/boltz/main.py", line 28,
in <module>  
from boltz.data.parse.csv import parse_csv  
File "/home/glpl/boltz22/lib/python3.11/site-
packages/boltz/data/parse/csv.py", line 5, in <module>  
import pandas as pd  
File "/home/glpl/boltz22/lib/python3.11/site-packages/pandas/__init__.py",
line 19, in <module>  
raise ImportError(  
ImportError: Unable to import required dependencies:  
pytz: No module named 'pytz'  
  

> boltz predict protein
> IQLQALSLPLVVIVHGNQDNNAKATILWDNAFSEMDRVPFVVAERVPWEKMCETLNLKFMAEVGTNRGLLPEHFLFLAQKIFNDNSLSMEAFQHRSVSWSQFNKEILLGRGFTFWQWFDGVLDLTKRCLRSYWSDRLIIGFISKQYVTSLLLNEPDGTFLLRFSDSEIGGITIAHVIRGQDGSPQIENIQPFSAKDLSIRSLGDRIRDLAQLKNLYPKKPKDEAFRSHYKPEQMGKDGRGYVPATIKMTVERDQPLPT
> ligandSmiles
> CN(C)C(=O)NC1=CC=C(CNC(=O)C2=NN(C)C3=CC=C(C4=CC=C(C5=NC=CN5C)C=C4)C=C32)C=C1
> name test resultsDirectory /home/glpl/Documents/stat6/[name] useMsaCache
> false device gpu steering true samples 3

Running Boltz prediction of protein with 258 residues, 1 ligands
CN(C)C(=O)NC1=CC=C(CNC(=O)C2=NN(C)C3=CC=C(C4=CC=C(C5=NC=CN5C)C=C4)C=C32)C=C1
on gpu  
Using multiple sequence alignment server https://api.colabfold.com  
Running boltz prediction failed with exit code 1:  
command:  
/home/glpl/boltz22/bin/boltz predict
/home/glpl/Documents/stat6/test_2/test.yaml --use_msa_server --use_potentials
--accelerator gpu --diffusion_samples 3  
stdout:  
  
stderr:  
Traceback (most recent call last):  
File "/home/glpl/boltz22/bin/boltz", line 5, in <module>  
from boltz.main import cli  
File "/home/glpl/boltz22/lib/python3.11/site-packages/boltz/main.py", line 28,
in <module>  
from boltz.data.parse.csv import parse_csv  
File "/home/glpl/boltz22/lib/python3.11/site-
packages/boltz/data/parse/csv.py", line 5, in <module>  
import pandas as pd  
File "/home/glpl/boltz22/lib/python3.11/site-packages/pandas/__init__.py",
line 19, in <module>  
raise ImportError(  
ImportError: Unable to import required dependencies:  
pytz: No module named 'pytz'  
  

> boltz predict protein
> IQLQALSLPLVVIVHGNQDNNAKATILWDNAFSEMDRVPFVVAERVPWEKMCETLNLKFMAEVGTNRGLLPEHFLFLAQKIFNDNSLSMEAFQHRSVSWSQFNKEILLGRGFTFWQWFDGVLDLTKRCLRSYWSDRLIIGFISKQYVTSLLLNEPDGTFLLRFSDSEIGGITIAHVIRGQDGSPQIENIQPFSAKDLSIRSLGDRIRDLAQLKNLYPKKPKDEAFRSHYKPEQMGKDGRGYVPATIKMTVERDQPLPT
> ligandSmiles
> CN(C)C(=O)NC1=CC=C(CNC(=O)C2=NN(C)C3=CC=C(C4=CC=C(C5=NC=CN5C)C=C4)C=C32)C=C1
> name test resultsDirectory /home/glpl/Documents/stat6/[name] useMsaCache
> false device gpu affinity
> CN(C)C(=O)NC1=CC=C(CNC(=O)C2=NN(C)C3=CC=C(C4=CC=C(C5=NC=CN5C)C=C4)C=C32)C=C1
> steering true samples 3

Running Boltz prediction of protein with 258 residues, 1 ligands
CN(C)C(=O)NC1=CC=C(CNC(=O)C2=NN(C)C3=CC=C(C4=CC=C(C5=NC=CN5C)C=C4)C=C32)C=C1
on gpu  
Using multiple sequence alignment server https://api.colabfold.com  
Running boltz prediction failed with exit code 1:  
command:  
/home/glpl/boltz22/bin/boltz predict
/home/glpl/Documents/stat6/test_3/test.yaml --use_msa_server --use_potentials
--accelerator gpu --diffusion_samples 3  
stdout:  
  
stderr:  
Traceback (most recent call last):  
File "/home/glpl/boltz22/bin/boltz", line 5, in <module>  
from boltz.main import cli  
File "/home/glpl/boltz22/lib/python3.11/site-packages/boltz/main.py", line 28,
in <module>  
from boltz.data.parse.csv import parse_csv  
File "/home/glpl/boltz22/lib/python3.11/site-
packages/boltz/data/parse/csv.py", line 5, in <module>  
import pandas as pd  
File "/home/glpl/boltz22/lib/python3.11/site-packages/pandas/__init__.py",
line 19, in <module>  
raise ImportError(  
ImportError: Unable to import required dependencies:  
pytz: No module named 'pytz'  
  




OpenGL version: 4.5 (Core Profile) Mesa 25.0.7-0ubuntu0.24.04.2
OpenGL renderer: llvmpipe (LLVM 20.1.2, 256 bits)
OpenGL vendor: Mesa

Python: 3.11.13
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Gigabyte Technology Co., Ltd.
Model: B650M D3HP AX
OS: Ubuntu 24.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 24 AMD Ryzen 9 9900X 12-Core Processor
Cache Size: 1024 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            60Gi        12Gi        17Gi       195Mi        30Gi        48Gi
	Swap:          8.0Gi          0B       8.0Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation AD104GL [RTX 4500 Ada Generation] [10de:27b1] (rev a1)	
	Subsystem: NVIDIA Corporation AD104GL [RTX 4500 Ada Generation] [10de:180c]	
	Kernel driver in use: nvidia

Installed Packages:
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.12.1
    appdirs: 1.4.4
    asttokens: 3.0.1
    attrs: 25.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.12.2
    build: 1.3.0
    certifi: 2026.1.4
    cftime: 1.6.5
    charset-normalizer: 3.4.4
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.1.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.61.4
    ChimeraX-AtomicLibrary: 14.2.1
    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: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    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: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11.1
    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: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.7.3
    ChimeraX-Label: 1.2
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    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-MCPServer: 0.1.0
    ChimeraX-MDcrds: 2.17.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.6
    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: 1.0.1
    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: 1.15.2
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.12
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.4.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.5
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.10
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.3
    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: 1.49.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.5.2
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.3.1
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.13.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.4
    debugpy: 1.8.19
    decorator: 5.2.1
    distro: 1.9.0
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.61.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.15.1
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.11
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.3.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.8
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.6.3
    jupyter_core: 5.9.1
    jupyterlab_widgets: 3.0.16
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.1
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.0
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    numpy: 1.26.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.5
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.5.1
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.12.5
    pydantic-settings: 2.12.0
    pydantic_core: 2.41.5
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.6
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.2
    pyproject_hooks: 1.2.0
    PyQt6: 6.9.1
    PyQt6-Qt6: 6.9.2
    PyQt6-WebEngine: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.2
    PyQt6_sip: 13.10.2
    pytest: 9.0.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.1
    python-multipart: 0.0.21
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.1.0
    roman-numerals-py: 4.1.0
    rpds-py: 0.30.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8.3
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.2.0
    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
    sse-starlette: 3.2.0
    stack-data: 0.6.3
    starlette: 0.52.1
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.4
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    urllib3: 2.6.3
    uvicorn: 0.40.0
    wcwidth: 0.3.2
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.15
    yarl: 1.22.0

Change History (3)

comment:1 by Eric Pettersen, 8 days ago

Component: Unassigned → Structure Prediction
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → boltz predict: ImportError: Unable to import required dependencies: pytz: No module named 'pytz'

comment:2 by Tom Goddard, 7 days ago

I've seen this error before when you use ChimeraX 1.10 to install Boltz (in ~/boltz22) then you update to ChimeraX 1.11. The problem is that Boltz relied on ChimeraX 1.10 having the Python pytz package but that package was removed in ChimeraX 1.11. The solution is to delete the Boltz installation by removing ~/boltz22 and then reinstall Boltz in ChimeraX with the "Install Boltz" button on the ChimeraX 1.11.1 Boltz panel.

comment:3 by Tom Goddard, 7 days ago

Resolution: → limitation
Status: assigned → closed
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