id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20781 Dock Prep: acc_phi_psi() takes 8 positional arguments but 9 were given shreyasukar@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-15.4.1-arm64-arm-64bit-Mach-O ChimeraX Version: 1.13.dev202607201743 (2026-07-20 17:43:16 UTC) Description Replace this text with list of actions that caused this problem to occur Log: UCSF ChimeraX version: 1.13.dev202607201743 (2026-07-20) © 2016-2026 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/reyyverie/Downloads/pdb4kxq.ent pdb4kxq.ent title: Structure of nad-dependent protein deacetylase sirtuin-1 (closed state, 1.85 A) [more info...] Chain information for pdb4kxq.ent #1 --- Chain | Description | UniProt A | nad-dependent protein deacetylase sirtuin-1 | SIR1_HUMAN 234-510 B | nad-dependent protein deacetylase sirtuin-1 | SIR1_HUMAN 641-663 Non-standard residues in pdb4kxq.ent #1 --- APR — adenosine-5-diphosphoribose BME — β-mercaptoethanol GOL — glycerol (glycerin; propane-1,2,3-triol) ZN — zinc ion 127 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open /Users/reyyverie/Downloads/pdb4kxq.ent pdb4kxq.ent title: Structure of nad-dependent protein deacetylase sirtuin-1 (closed state, 1.85 A) [more info...] Chain information for pdb4kxq.ent #2 --- Chain | Description | UniProt A | nad-dependent protein deacetylase sirtuin-1 | SIR1_HUMAN 234-510 B | nad-dependent protein deacetylase sirtuin-1 | SIR1_HUMAN 641-663 Non-standard residues in pdb4kxq.ent #2 --- APR — adenosine-5-diphosphoribose BME — β-mercaptoethanol GOL — glycerol (glycerin; propane-1,2,3-triol) ZN — zinc ion 127 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > close > open /Users/reyyverie/SIRT1_clean.pdb Chain information for SIRT1_clean.pdb #1 --- Chain | Description A | No description available B | No description available 254 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Computing secondary structure > ui tool show ""Dock Prep"" Populating font family aliases took 113 ms. Replace uses of missing font family ""Times"" with one that exists to avoid this cost. Starting dock prep Deleting solvent Deleting non-metal-complex ions Deleting non-current alt locs Filling out missing side chains /A HIS 232: phi none, psi 101.8 trans /A SER 275: phi -78.9, psi 171.4 trans /A ARG 282: phi -65.3, psi -37.3 trans /A CYS 326: phi -60.3, psi -47.1 trans /A LYS 377: phi -116.3, psi 137.3 trans /A ARG 384: phi -60.0, psi -44.7 trans /A LYS 430: phi -51.9, psi -45.4 trans /A ILE 510: phi -63.5, psi none trans /B GLN 641: phi -102.9, psi 149.9 trans /B ASP 660: phi -114.2, psi none trans /A SER 275 OG has bad number of bonds (3) donor: /A SER 1 N acceptor: /A SER 275 O Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site- packages/chimerax/dock_prep/tool.py"", line 168, in dock_prep self.dock_prep_info['callback'](self.structures, tool_settings=params) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site- packages/chimerax/dock_prep/tool.py"", line 27, in callback dock_prep_caller(session, structures, _from_tool=True, **tool_settings) ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site- packages/chimerax/dock_prep/cmd.py"", line 146, in dock_prep_caller run_steps(session, state, structures) ~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site- packages/chimerax/dock_prep/cmd.py"", line 161, in run_steps step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'], state['memorize_name'], ~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ structures, kw_dict) ^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site- packages/chimerax/dock_prep/prep.py"", line 139, in prep swap_aa(session, targets, ""same"", rot_lib=style) ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site- packages/chimerax/swap_res/swap_res.py"", line 122, in swap_aa process_hbonds(session, res, by_alt_loc, False, None, None, hbond_relax, ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ hbond_dist_slop, hbond_angle_slop, False, None, ignore_other_models, cache_da=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site- packages/chimerax/swap_res/swap_res.py"", line 807, in process_hbonds hbonds = { hb: color for hb in find_hbonds(session, target_models, intra_model=False, ~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ dist_slop=dist_slop, angle_slop=angle_slop, cache_da=cache_da, status=False) } ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site- packages/chimerax/hbonds/hbond.py"", line 615, in find_hbonds if not geom_func(donor_atom, donor_hyds, *args): ~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site- packages/chimerax/hbonds/hbond.py"", line 615, in find_hbonds if not geom_func(donor_atom, donor_hyds, *args): ~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. > ui tool show ""Dock Prep"" Starting dock prep Deleting solvent Deleting non-metal-complex ions Deleting non-current alt locs Filling out missing side chains /A HIS 232: phi none, psi 101.8 trans /A SER 275: phi -78.9, psi 171.4 trans /A ARG 282: phi -65.3, psi -37.3 trans /A CYS 326: phi -60.3, psi -47.1 trans /A LYS 377: phi -116.3, psi 137.3 trans /A ARG 384: phi -60.0, psi -44.7 trans /A LYS 430: phi -51.9, psi -45.4 trans /A ILE 510: phi -63.5, psi none trans /B GLN 641: phi -102.9, psi 149.9 trans /B ASP 660: phi -114.2, psi none trans donor: /A SER 1 N acceptor: /A SER 275 O Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site- packages/chimerax/dock_prep/tool.py"", line 168, in dock_prep self.dock_prep_info['callback'](self.structures, tool_settings=params) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site- packages/chimerax/dock_prep/tool.py"", line 27, in callback dock_prep_caller(session, structures, _from_tool=True, **tool_settings) ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site- packages/chimerax/dock_prep/cmd.py"", line 146, in dock_prep_caller run_steps(session, state, structures) ~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site- packages/chimerax/dock_prep/cmd.py"", line 161, in run_steps step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'], state['memorize_name'], ~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ structures, kw_dict) ^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site- packages/chimerax/dock_prep/prep.py"", line 139, in prep swap_aa(session, targets, ""same"", rot_lib=style) ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site- packages/chimerax/swap_res/swap_res.py"", line 122, in swap_aa process_hbonds(session, res, by_alt_loc, False, None, None, hbond_relax, ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ hbond_dist_slop, hbond_angle_slop, False, None, ignore_other_models, cache_da=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site- packages/chimerax/swap_res/swap_res.py"", line 807, in process_hbonds hbonds = { hb: color for hb in find_hbonds(session, target_models, intra_model=False, ~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ dist_slop=dist_slop, angle_slop=angle_slop, cache_da=cache_da, status=False) } ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site- packages/chimerax/hbonds/hbond.py"", line 615, in find_hbonds if not geom_func(donor_atom, donor_hyds, *args): ~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site- packages/chimerax/hbonds/hbond.py"", line 615, in find_hbonds if not geom_func(donor_atom, donor_hyds, *args): ~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. > ui tool show ""Dock Prep"" Starting dock prep Deleting solvent Deleting non-metal-complex ions Deleting non-current alt locs Filling out missing side chains /A HIS 232: phi none, psi 101.8 trans /A SER 275: phi -78.9, psi 171.4 trans /A ARG 282: phi -65.3, psi -37.3 trans /A CYS 326: phi -60.3, psi -47.1 trans /A LYS 377: phi -116.3, psi 137.3 trans /A ARG 384: phi -60.0, psi -44.7 trans /A LYS 430: phi -51.9, psi -45.4 trans /A ILE 510: phi -63.5, psi none trans /B GLN 641: phi -102.9, psi 149.9 trans /B ASP 660: phi -114.2, psi none trans donor: /A SER 1 N acceptor: /A SER 275 O Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site- packages/chimerax/dock_prep/tool.py"", line 168, in dock_prep self.dock_prep_info['callback'](self.structures, tool_settings=params) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site- packages/chimerax/dock_prep/tool.py"", line 27, in callback dock_prep_caller(session, structures, _from_tool=True, **tool_settings) ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site- packages/chimerax/dock_prep/cmd.py"", line 146, in dock_prep_caller run_steps(session, state, structures) ~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site- packages/chimerax/dock_prep/cmd.py"", line 161, in run_steps step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'], state['memorize_name'], ~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ structures, kw_dict) ^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site- packages/chimerax/dock_prep/prep.py"", line 139, in prep swap_aa(session, targets, ""same"", rot_lib=style) ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site- packages/chimerax/swap_res/swap_res.py"", line 122, in swap_aa process_hbonds(session, res, by_alt_loc, False, None, None, hbond_relax, ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ hbond_dist_slop, hbond_angle_slop, False, None, ignore_other_models, cache_da=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site- packages/chimerax/swap_res/swap_res.py"", line 807, in process_hbonds hbonds = { hb: color for hb in find_hbonds(session, target_models, intra_model=False, ~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ dist_slop=dist_slop, angle_slop=angle_slop, cache_da=cache_da, status=False) } ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site- packages/chimerax/hbonds/hbond.py"", line 615, in find_hbonds if not geom_func(donor_atom, donor_hyds, *args): ~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site- packages/chimerax/hbonds/hbond.py"", line 615, in find_hbonds if not geom_func(donor_atom, donor_hyds, *args): ~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M4 OpenGL vendor: Apple Python: 3.14.6 Locale: C.UTF-8 Qt version: PyQt6 6.10.2, Qt 6.10.0 Qt runtime version: 6.10.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac16,12 Model Number: MW0Y3HN/A Chip: Apple M4 Total Number of Cores: 10 (4 performance and 6 efficiency) Memory: 16 GB System Firmware Version: 11881.101.1 OS Loader Version: 11881.101.1 Software: System Software Overview: System Version: macOS 15.4.1 (24E263) Kernel Version: Darwin 24.4.0 Time since boot: 49 days, 18 hours, 21 minutes Graphics/Displays: Apple M4: Chipset Model: Apple M4 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: accessible-pygments: 0.0.5 aiohappyeyeballs: 2.7.1 aiohttp: 3.11.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.14.2 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.2 attrs: 26.1.0 babel: 2.18.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 4.9.1 build: 1.5.0 certifi: 2026.6.17 cffi: 2.1.0 cftime: 1.6.5 charset-normalizer: 3.4.9 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.3.1 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.2 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.2.2 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: 1.70.2 ChimeraX-AtomicLibrary: 14.4.2 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: 1.4.1 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.4 ChimeraX-Cluster: 1.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.1 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.13.dev202607201743 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.6 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.3 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.2.2 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: 2.5.4 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: 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ChimeraX-SmoothLines: 1.0 ChimeraX-SNFG: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.20 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: 2.5.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.4 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.53.2 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.6.5 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: 8.4.2 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.15.2 cryptography: 49.0.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.2.4 debugpy: 1.8.21 decorator: 5.3.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.63.0 frozenlist: 1.8.0 funcparserlib: 1.0.1 glfw: 2.10.1 grako: 3.16.5 h11: 0.16.0 h2: 4.3.0 h5py: 3.16.0 hpack: 4.2.0 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 hyperframe: 6.1.0 idna: 3.18 ihm: 2.2 imagecodecs: 2026.6.26 imagesize: 2.0.0 iniconfig: 2.3.0 ipykernel: 7.3.0 ipython: 9.14.1 ipython_pygments_lexers: 1.1.1 jedi: 0.20.0 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.9.1 jupyter_core: 5.9.1 kiwisolver: 1.5.0 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.4.5 Markdown: 3.8.2 markdown-it-py: 4.2.0 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.2 mcp: 1.28.1 mdurl: 0.1.2 msgpack: 1.1.1 multidict: 6.7.1 ndindex: 1.10.1 nest-asyncio2: 1.7.2 netCDF4: 1.7.4 networkx: 3.3 numexpr: 2.14.2 numpy: 2.4.6 OpenMM: 8.4.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.7 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 12.3.0 pip: 26.1.2 pkginfo: 1.12.1.2 platformdirs: 4.10.1 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.5.2 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 pycparser: 3.0 pydantic: 2.13.4 pydantic-settings: 2.14.2 pydantic_core: 2.46.4 pydata-sphinx-theme: 0.20.0 Pygments: 2.18.0 PyJWT: 2.13.0 pynmrstar: 3.5.1 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.10.2 PyQt6-Qt6: 6.10.2 PyQt6-WebEngine-commercial: 6.10.0 PyQt6-WebEngine-Qt6: 6.10.2 PyQt6_sip: 13.10.3 pytest: 9.1.1 pytest-cov: 7.1.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.2 python-multipart: 0.0.32 pyzmq: 27.1.0 qtconsole: 5.7.2 QtPy: 2.4.3 qtshim: 1.2.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 rich: 15.0.0 roman-numerals: 4.1.0 rpds-py: 2026.6.3 scipy: 1.18.0 setuptools: 82.0.1 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.1.1 sortedcontainers: 2.4.0 soupsieve: 2.9 Sphinx: 9.0.4 sphinx-autodoc-typehints: 3.6.1 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: 3.4.6 stack-data: 0.6.3 starlette: 1.3.1 superqt: 0.7.6 tables: 3.11.1 threadpoolctl: 3.6.0 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.7 tqdm: 4.69.0 traitlets: 5.15.1 typing-inspection: 0.4.2 typing_extensions: 4.16.0 urllib3: 2.7.0 uv: 0.11.26 uvicorn: 0.51.0 wcwidth: 0.8.2 webcolors: 24.11.1 wheel: 0.47.0 wheel-filename: 1.4.2 yarl: 1.24.5 }}} " defect assigned normal Structure Analysis all ChimeraX