id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18477 Boltz: PytorchStreamReader failed reading zip archive: failed finding central directory george.nyasha.chiduza@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.6-arm64-arm-64bit ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC) Description Replace this text with list of actions that caused this problem to occur 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 > ui tool show Boltz > boltz predict protein > MAKKNSQLPSTSEQILERSTTGATFLMMGQLFTKLVTFILNNLLIRFLSPRIFGITAFLEFIQGTVLFFSRDAIRLSTLRISDSGNGIIDDDDEEEYQETHYKSKVLQTAVNFAYIPFWIGFPLSIGLIAWQYRNINAYFITLPFFRWSIFLIWLSIIVELLSEPFFIVNQFMLNYAARSRFESIAVTTGCIVNFIVVYAVQQSRYPMGVVTSDIDKEGIAILAFALGKLAHSITLLACYYWDYLKNFKPKKLFSTRLTKIKTRENNELKKGYPKSTSYFFQNDILQHFKKVYFQLCFKHLLTEGDKLIINSLCTVEEQGIYALLSNYGSLLTRLLFAPIEESLRLFLARLLSSHNPKNLKLSIEVLVNLTRFYIYLSLMIIVFGPANSSFLLQFLIGSKWSTTSVLDTIRVYCFYIPFLSLNGIFEAFFQSVATGDQILKHSYFMMAFSGIFLLNSWLLIEKLKLSIEGLILSNIINMVLRILYCGVFLNKFHRELFTDSSFFFNFKDFKTVIIAGSTICLLDWWFIGYVKNLQQFVVNVLFAMGLLALILVKERQTIQSFINKRAVSNSKDV > ligandSmiles > CC(CCOP([O-])(=O)OP([O-])(=O)OC1OC(CO)C(OC2OC(CO)C(OC3OC(COC4OC(CO)C(O)C(O)C4O)C(O)C(OC4OC(CO)C(O)C(O)C4OC4OC(CO)C(O)C(O)C4OC4OC(CO)C(O)C(O)C4O)C3O)C(O)C2NC(C)=O)C(O)C1NC(C)=O)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C > name yeast_rft1_m5_crack Running Boltz prediction of protein with 574 residues, 1 ligands CC(CCOP([O-])(=O)OP([O-])(=O)OC1OC(CO)C(OC2OC(CO)C(OC3OC(COC4OC(CO)C(O)C(O)C4O)C(O)C(OC4OC(CO)C(O)C(O)C4OC4OC(CO)C(O)C(O)C4OC4OC(CO)C(O)C(O)C4O)C3O)C(O)C2NC(C)=O)C(O)C1NC(C)=O)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C on gpu Using multiple sequence alignment server https://api.colabfold.com Please cite Boltz-1 Democratizing Biomolecular Interaction Modeling. BioRxiv https://doi.org/10.1101/2024.11.19.624167 if you use these predictions. Running boltz prediction failed with exit code 1: command: /Users/n.e.xone/boltz/bin/boltz predict /Users/n.e.xone/Desktop/boltz_yeast_rft1_m5_crack/yeast_rft1_m5_crack.yaml --write_full_pae --use_msa_server --accelerator gpu --no_potentials stdout: Checking input data. Running predictions for 1 structure Processing input data. WARNING: RDKit ETKDGv3 failed to generate a conformer for molecule CC(=O)NC1C(OC2C(CO)OC(OP(=O)([O-])OP(=O)([O-])OCCC(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C)C(NC(C)=O)C2O)OC(CO)C(OC2OC(COC3OC(CO)C(O)C(O)C3O)C(O)C(OC3OC(CO)C(O)C(O)C3OC3OC(CO)C(O)C(O)C3OC3OC(CO)C(O)C(O)C3O)C2O)C1O, so the program will start with random coordinates. Note that the performance of the model under this behaviour was not tested. Generating MSA for /Users/n.e.xone/Desktop/boltz_yeast_rft1_m5_crack/yeast_rft1_m5_crack.yaml with 1 protein entities. stderr: 0%| | 0/1 [00:00 sys.exit(cli()) ^^^^^ File ""/Users/n.e.xone/boltz/lib/python3.11/site-packages/click/core.py"", line 1157, in __call__ return self.main(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/n.e.xone/boltz/lib/python3.11/site-packages/click/core.py"", line 1078, in main rv = self.invoke(ctx) ^^^^^^^^^^^^^^^^ File ""/Users/n.e.xone/boltz/lib/python3.11/site-packages/click/core.py"", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/n.e.xone/boltz/lib/python3.11/site-packages/click/core.py"", line 1434, in invoke return ctx.invoke(self.callback, **ctx.params) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/n.e.xone/boltz/lib/python3.11/site-packages/click/core.py"", line 783, in invoke return __callback(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/n.e.xone/boltz/lib/python3.11/site-packages/boltz/main.py"", line 744, in predict model_module: Boltz1 = Boltz1.load_from_checkpoint( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/n.e.xone/boltz/lib/python3.11/site- packages/pytorch_lightning/utilities/model_helpers.py"", line 125, in wrapper return self.method(cls, *args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/n.e.xone/boltz/lib/python3.11/site- packages/pytorch_lightning/core/module.py"", line 1582, in load_from_checkpoint loaded = _load_from_checkpoint( ^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/n.e.xone/boltz/lib/python3.11/site- packages/pytorch_lightning/core/saving.py"", line 63, in _load_from_checkpoint checkpoint = pl_load(checkpoint_path, map_location=map_location) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/n.e.xone/boltz/lib/python3.11/site- packages/lightning_fabric/utilities/cloud_io.py"", line 60, in _load return torch.load( ^^^^^^^^^^^ File ""/Users/n.e.xone/boltz/lib/python3.11/site- packages/torch/serialization.py"", line 1491, in load with _open_zipfile_reader(opened_file) as opened_zipfile: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/n.e.xone/boltz/lib/python3.11/site- packages/torch/serialization.py"", line 771, in __init__ super().__init__(torch._C.PyTorchFileReader(name_or_buffer)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ RuntimeError: PytorchStreamReader failed reading zip archive: failed finding central directory > open ""/Users/n.e.xone/Library/CloudStorage/Dropbox/ULB postdoc/Lab > work/Structural Bioinformatics/Glycosylation enzymes/yeast > rft1/omp/AF_P38206_F1_model_v4out.pdb"" AF_P38206_F1_model_v4out.pdb title: Protein RFT1 (P38206) [more info...] Chain information for AF_P38206_F1_model_v4out.pdb #1 --- Chain | Description | UniProt A | No description available | RFT1_YEAST 1-574 Non-standard residues in AF_P38206_F1_model_v4out.pdb #1 --- DUM — (DUM) Computing secondary structure > lighting soft > color bfactor palette alphafold 8097 atoms, 3983 residues, atom bfactor range 0 to 98.1 > set bgColor white > select ::name=""DUM"" 3409 atoms, 3409 residues, 1 model selected > surface sel > transparency (#!1 & sel) 70 > color (#!1 & sel) dim gray > transparency (#!1 & sel) 70 > color (#!1 & sel) dark gray > color (#!1 & sel) light gray > transparency (#!1 & sel) 70 > select clear > boltz predict protein > MAKKNSQLPSTSEQILERSTTGATFLMMGQLFTKLVTFILNNLLIRFLSPRIFGITAFLEFIQGTVLFFSRDAIRLSTLRISDSGNGIIDDDDEEEYQETHYKSKVLQTAVNFAYIPFWIGFPLSIGLIAWQYRNINAYFITLPFFRWSIFLIWLSIIVELLSEPFFIVNQFMLNYAARSRFESIAVTTGCIVNFIVVYAVQQSRYPMGVVTSDIDKEGIAILAFALGKLAHSITLLACYYWDYLKNFKPKKLFSTRLTKIKTRENNELKKGYPKSTSYFFQNDILQHFKKVYFQLCFKHLLTEGDKLIINSLCTVEEQGIYALLSNYGSLLTRLLFAPIEESLRLFLARLLSSHNPKNLKLSIEVLVNLTRFYIYLSLMIIVFGPANSSFLLQFLIGSKWSTTSVLDTIRVYCFYIPFLSLNGIFEAFFQSVATGDQILKHSYFMMAFSGIFLLNSWLLIEKLKLSIEGLILSNIINMVLRILYCGVFLNKFHRELFTDSSFFFNFKDFKTVIIAGSTICLLDWWFIGYVKNLQQFVVNVLFAMGLLALILVKERQTIQSFINKRAVSNSKDV > ligandSmiles > CC(CCOP([O-])(=O)OP([O-])(=O)OC1OC(CO)C(OC2OC(CO)C(OC3OC(COC4OC(CO)C(O)C(O)C4O)C(O)C(OC4OC(CO)C(O)C(O)C4OC4OC(CO)C(O)C(O)C4OC4OC(CO)C(O)C(O)C4O)C3O)C(O)C2NC(C)=O)C(O)C1NC(C)=O)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C > name yeast_rft1_m5_crack Running Boltz prediction of protein with 574 residues, 1 ligands CC(CCOP([O-])(=O)OP([O-])(=O)OC1OC(CO)C(OC2OC(CO)C(OC3OC(COC4OC(CO)C(O)C(O)C4O)C(O)C(OC4OC(CO)C(O)C(O)C4OC4OC(CO)C(O)C(O)C4OC4OC(CO)C(O)C(O)C4O)C3O)C(O)C2NC(C)=O)C(O)C1NC(C)=O)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C on gpu Using multiple sequence alignment server https://api.colabfold.com > ui tool show ""Side View"" > select /A 4688 atoms, 4803 bonds, 574 residues, 1 model selected > show sel surfaces > select clear Boltz prediction completed in 1639 seconds The Boltz prediction ran out of memory. The memory use depends on the number of protein and nucleic acid residues plus the number of ligand atoms. You can reduce the size of your molecular assembly to stay within the memory limits. > close session Traceback (most recent call last): File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/boltz/boltz_gui.py"", line 572, in _report_progress if not self.tool_window.shown: ^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/gui.py"", line 2343, in shown return self.__toolkit.shown ^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'shown' Error processing trigger ""new frame"": AttributeError: 'NoneType' object has no attribute 'shown' File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/gui.py"", line 2343, in shown return self.__toolkit.shown ^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M2 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 Air Model Identifier: Mac14,2 Model Number: MLY33B/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 11881.140.96 OS Loader Version: 11881.140.96 Software: System Software Overview: System Version: macOS 15.6 (24G84) Kernel Version: Darwin 24.6.0 Time since boot: 7 days, 22 hours, 33 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: PHL 242B1: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 75.00Hz Main Display: Yes Mirror: On Mirror Status: Master Mirror Online: Yes Rotation: Supported Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Mirror: On Mirror Status: Hardware Mirror Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 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: 2023.11.17 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 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 jupyter_client: 8.6.3 jupyter_core: 5.8.1 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.8 line_profiler: 4.2.0 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 numexpr: 2.11.0 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 ParmEd: 4.2.2 parso: 0.8.4 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 pluggy: 1.6.0 prompt_toolkit: 3.0.51 psutil: 7.0.0 ptyprocess: 0.7.0 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 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 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 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 tifffile: 2025.3.13 tinyarray: 1.2.4 tornado: 6.5.1 traitlets: 5.14.3 typing_extensions: 4.14.0 tzdata: 2025.2 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 }}} " defect closed normal Structure Prediction fixed all ChimeraX