id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19040 Web services down lukas.bauer@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-15.7-arm64-arm-64bit ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC) Description Hi, I build a Plugin for unsing a GUI for sequence alignment. It was working until last Wednesday, however I get now this error: sequence chain #1/A Alignment identifier is 1/A save /Users/lbauer/ChopChop_output/chopchop_sequence1.fasta format fasta alignment 1/A FASTA file for P04637 downloaded successfully. sequence align MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD,MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD program muscle Alignment identifier is 1 Traceback (most recent call last): File ""/Users/lbauer/Library/Application Support/ChimeraX/1.10/lib/python/site-packages/chimerax/chopchop_mf/chopalignment.py"", line 367, in align run(self.session, ""sequence align {},{} program muscle"".format(sequence1, sequence2)) File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3221, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py"", line 506, in seqalign_align return session.alignments.new_alignment(realigned, None, name=title) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/manager.py"", line 262, in new_alignment alignment = Alignment(self.session, seqs, identify_as, attrs, markups, auto_destroy, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py"", line 93, in __init__ raise ValueError(""Cannot create alignment of zero sequences"") ValueError: Cannot create alignment of zero sequences ValueError: Cannot create alignment of zero sequences it must be something with the muscle alignent submission... since the script was working before... Thanks a lot! Lukas 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 > open /Users/lbauer/Downloads/ChimeraX/AlphaFold/AF-P04637-F1-model_v3.cif > format mmcif Chain information for AF-P04637-F1-model_v3.cif #1 --- Chain | Description | UniProt A | Cellular tumor antigen p53 | P53_HUMAN 1-393 Color AF-P04637-F1-model_v3.cif by residue attribute pLDDT_score Refreshing model list... Model list refreshed. > sequence chain #1/A Alignment identifier is 1/A > save /Users/lbauer/ChopChop_output/chopchop_sequence1.fasta format fasta > alignment 1/A FASTA file for P04637 downloaded successfully. > sequence align > MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD,MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD > program muscle Alignment identifier is 1 Traceback (most recent call last): File ""/Users/lbauer/Library/Application Support/ChimeraX/1.10/lib/python/site- packages/chimerax/chopchop_mf/chopalignment.py"", line 367, in align run(self.session, ""sequence align {},{} program muscle"".format(sequence1, sequence2)) File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3221, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/seqalign/cmd.py"", line 506, in seqalign_align return session.alignments.new_alignment(realigned, None, name=title) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/seqalign/manager.py"", line 262, in new_alignment alignment = Alignment(self.session, seqs, identify_as, attrs, markups, auto_destroy, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/seqalign/alignment.py"", line 93, in __init__ raise ValueError(""Cannot create alignment of zero sequences"") ValueError: Cannot create alignment of zero sequences ValueError: Cannot create alignment of zero sequences File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/seqalign/alignment.py"", line 93, in __init__ raise ValueError(""Cannot create alignment of zero sequences"") See log for complete Python traceback. Exception in thread Thread-14 (_run_function): Traceback (most recent call last): File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038, in _bootstrap_inner self.run() File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975, in run self._target(*self._args, **self._kwargs) File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/tasks.py"", line 300, in _run_function func(*args, **kw) File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/webservices/cxservices_job.py"", line 156, in run reason = json.loads(e.body)[""description""] ^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/json/__init__.py"", line 346, in loads return _default_decoder.decode(s) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/json/decoder.py"", line 337, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/json/decoder.py"", line 355, in raw_decode raise JSONDecodeError(""Expecting value"", s, err.value) from None json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0) OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M3 OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac15,3 Model Number: Z1A9000PKD/A Chip: Apple M3 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 13822.1.2 OS Loader Version: 11881.140.96 Software: System Software Overview: System Version: macOS 15.7 (24G222) Kernel Version: Darwin 24.6.0 Time since boot: 2 minutes, 55 seconds Graphics/Displays: Apple M3: Chipset Model: Apple M3 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: aiobotocore: 2.22.0 aiohappyeyeballs: 2.6.1 aiohttp: 3.11.18 aioitertools: 0.12.0 aiosignal: 1.3.2 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.8.0 appdirs: 1.4.4 appnope: 0.1.4 asciitree: 0.3.3 asttokens: 3.0.0 asyncssh: 2.21.0 attrs: 25.3.0 auditwheel: 6.4.0 autocommand: 2.2.2 babel: 2.17.0 backoff: 2.2.1 backports.tarfile: 1.2.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.5.0 boltons: 25.0.0 boto3: 1.37.3 botocore: 1.37.3 build: 1.2.2.post1 certifi: 2023.11.17 cffi: 1.17.1 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-AllMetal3D: 0.8 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.4 ChimeraX-Arrays: 1.1 ChimeraX-ArtiaX: 0.6.0 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-ChopChopMF: 3.0b0 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-copick: 1.4.1 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-EMalign: 0.1.3 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-InspectET: 0.0.6 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-OME-Zarr: 0.5.5 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-PICKLUSTER: 2.1 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 click: 8.2.0 cloudpickle: 3.1.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.2 copick: 1.2.0 coverage: 7.9.1 cryoet_alignment: 0.0.4 cryoet_data_portal: 4.4.1 cryptography: 44.0.3 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 dask: 2025.5.0 debugpy: 1.8.14 decorator: 5.2.1 deepmerge: 2.0 Deprecated: 1.2.18 distinctipy: 1.3.4 docutils: 0.21.2 executing: 2.2.0 fasteners: 0.19 filelock: 3.18.0 finufft: 2.3.1 fonticon-materialdesignicons7: 7.2.96 fonttools: 4.58.4 frozenlist: 1.6.0 fsspec: 2025.3.2 funcparserlib: 2.0.0a0 geomdl: 5.3.1 glfw: 2.9.0 gql: 3.5.3 gradio_client: 0.11.0 grako: 3.16.5 graphql-core: 3.2.6 h11: 0.14.0 h5py: 3.14.0 hatchling: 1.27.0 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 huggingface-hub: 0.29.2 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imageio: 2.37.0 imagesize: 1.4.1 importlib_metadata: 8.7.0 importlib_metadata: 8.0.0 inflect: 7.3.1 iniconfig: 2.1.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.7 jaraco.collections: 5.1.0 jaraco.context: 5.3.0 jaraco.functools: 4.0.1 jaraco.text: 3.12.1 jedi: 0.19.1 Jinja2: 3.1.6 jmespath: 1.0.1 jupyter_client: 8.6.3 jupyter_core: 5.8.1 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.8 lazy_loader: 0.4 line_profiler: 4.2.0 linkify-it-py: 2.0.3 locket: 1.0.0 lxml: 5.3.1 lz4: 4.4.4 markdown-it-py: 3.0.0 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 mdit-py-plugins: 0.4.2 mdurl: 0.1.2 more-itertools: 10.3.0 mrcfile: 1.5.4 msgpack: 1.1.0 multidict: 6.4.3 ndindex: 1.10.0 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numcodecs: 0.15.1 numexpr: 2.11.0 numpy: 1.26.4 ome-zarr: 0.11.1 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 packaging: 24.2 packaging: 24.2 pandas: 2.2.3 ParmEd: 4.2.2 parso: 0.8.4 partd: 1.4.2 pathspec: 0.12.1 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.8 platformdirs: 4.2.2 pluggy: 1.6.0 prompt_toolkit: 3.0.51 propcache: 0.3.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pyarrow: 19.0.1 pycollada: 0.8 pycparser: 2.22 pydantic: 2.10.6 pydantic_core: 2.27.2 pydicom: 2.4.4 pyelftools: 0.32 Pygments: 2.18.0 pynmrstar: 3.3.5 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 PyQt5: 5.15.11 PyQt5-Qt5: 5.15.16 PyQt5_sip: 12.16.1 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 pyspnego: 0.11.2 pytest: 8.4.1 pytest-cov: 6.2.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 PyYAML: 6.0.2 pyzmq: 27.0.0 qasync: 0.27.1 qt-async-threads: 0.6.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 requests-toolbelt: 1.0.0 rich: 14.0.0 roman-numerals-py: 3.1.0 s3fs: 2025.3.2 s3transfer: 0.11.3 scikit-image: 0.25.2 scipy: 1.14.0 setuptools: 78.1.0 sfftk-rw: 0.8.1 six: 1.16.0 smbprotocol: 1.15.0 sniffio: 1.3.1 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 sshfs: 2025.2.0 stack-data: 0.6.3 starfile: 0.5.12 strcase: 1.0.0 superqt: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 textual: 3.2.0 tifffile: 2025.3.13 tinyarray: 1.2.4 tomli: 2.0.1 toolz: 1.0.0 tornado: 6.5.1 tqdm: 4.67.1 traitlets: 5.14.3 trimesh: 4.6.10 trove-classifiers: 2025.5.9.12 typeguard: 4.3.0 typing_extensions: 4.14.0 typing_extensions: 4.12.2 tzdata: 2025.2 uc-micro-py: 1.0.3 urllib3: 2.5.0 wcwidth: 0.2.13 webcolors: 24.11.1 websockets: 11.0.3 wheel: 0.45.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 wrapt: 1.17.2 yarl: 1.20.0 zarr: 2.18.6 zipp: 3.21.0 zipp: 3.19.2 }}} " defect closed normal Web Services fixed all ChimeraX