Trac Ticket Queries

In addition to reports, Trac provides support for custom ticket queries, which can be used to display tickets that meet specified criteria.

To configure and execute a custom query, switch to the View Tickets module from the navigation bar, and select the Custom Query link.

Filters

When you first go to the query page, the default filter will display tickets relevant to you:

• If logged in then all open tickets, it will display open tickets assigned to you.
• If not logged in but you have specified a name or email address in the preferences, then it will display all open tickets where your email (or name if email not defined) is in the CC list.
• If not logged in and no name/email is defined in the preferences, then all open issues are displayed.

Current filters can be removed by clicking the button to the left with the minus sign on the label. New filters are added from the pulldown lists at the bottom corners of the filters box; 'And' conditions on the left, 'Or' conditions on the right. Filters with either a text box or a pulldown menu of options can be added multiple times to perform an Or on the criteria.

You can use the fields just below the filters box to group the results based on a field, or display the full description for each ticket.

After you have edited your filters, click the Update button to refresh your results.

Some shortcuts can be used to manipulate checkbox filters.

• Clicking on a filter row label toggles all checkboxes.
• Pressing the modifier key while clicking on a filter row label inverts the state of all checkboxes.
• Pressing the modifier key while clicking on a checkbox selects the checkbox and deselects all other checkboxes in the filter.

The modifier key is platform and browser dependent. On Mac the modified key is Option/Alt or Command. On Linux the modifier key is Ctrl + Alt. Opera on Windows seems to use Ctrl + Alt, while Alt is effective for other Windows browsers.

Navigating Tickets

Clicking on one of the query results will take you to that ticket. You can navigate through the results by clicking the Next Ticket or Previous Ticket links just below the main menu bar, or click the Back to Query link to return to the query page.

You can safely edit any of the tickets and continue to navigate through the results using the Next/Previous/Back to Query links after saving your results. When you return to the query any tickets which were edited will be displayed with italicized text. If one of the tickets was edited such that it no longer matches the query criteria , the text will also be greyed. Lastly, if a new ticket matching the query criteria has been created, it will be shown in bold.

The query results can be refreshed and cleared of these status indicators by clicking the Update button again.

Saving Queries

Trac allows you to save the query as a named query accessible from the reports module. To save a query ensure that you have Updated the view and then click the Save query button displayed beneath the results. You can also save references to queries in Wiki content, as described below.

Note: one way to easily build queries like the ones below, you can build and test the queries in the Custom report module and when ready - click Save query. This will build the query string for you. All you need to do is remove the extra line breaks.

Note: you must have the REPORT_CREATE permission in order to save queries to the list of default reports. The Save query button will only appear if you are logged in as a user that has been granted this permission. If your account does not have permission to create reports, you can still use the methods below to save a query.

Using TracLinks

You may want to save some queries so that you can come back to them later. You can do this by making a link to the query from any Wiki page.

[query:status=new|assigned|reopened&version=1.0 Active tickets against 1.0]

Which is displayed as:

Active tickets against 1.0

This uses a very simple query language to specify the criteria, see Query Language.

Alternatively, you can copy the query string of a query and paste that into the Wiki link, including the leading ? character:

[query:?status=new&status=assigned&status=reopened&group=owner Assigned tickets by owner]

Which is displayed as:

Assigned tickets by owner

Customizing the table format

You can also customize the columns displayed in the table format (format=table) by using col=<field>. You can specify multiple fields and what order they are displayed in by placing pipes (|) between the columns:

[[TicketQuery(max=3,status=closed,order=id,desc=1,format=table,col=resolution|summary|owner|reporter)]]

This is displayed as:

Results (1 - 3 of 14119)

1 2 3 4 5 6 7 8 9 10 11 →

Ticket	Resolution	Summary	Owner	Reporter
#20782	not a bug	Python shell debugger warning	Tom Goddard	alexandra.zahradnikova@…
#20780	duplicate	Dock Prep: acc_phi_psi() takes 8 positional arguments but 9 were given	Eric Pettersen	chimerax-bug-report@…
#20777	duplicate	pyKVFinder install failed on Mac: '/usr/bin/clang' failed with exit code 1	Eric Pettersen	chimerax-bug-report@…

1 2 3 4 5 6 7 8 9 10 11 →

Full rows

In table format you can also have full rows by using rows=<field>:

[[TicketQuery(max=3,status=closed,order=id,desc=1,format=table,col=resolution|summary|owner|reporter,rows=description)]]

This is displayed as:

Results (1 - 3 of 14119)

1 2 3 4 5 6 7 8 9 10 11 →

Ticket	Resolution	Summary	Owner	Reporter
#20782	not a bug	Python shell debugger warning	Tom Goddard	alexandra.zahradnikova@…
Description	The following bug report has been submitted: Platform: Linux-6.8.0-124-generic-x86_64-with-glibc2.35 ChimeraX Version: 1.12.dev202604290127 (2026-04-29 01:27:48 UTC) Description 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. UCSF ChimeraX version: 1.12.dev202604290127 (2026-04-29) © 2016-2026 Regents of the University of California. All rights reserved. Log: > ui tool show Shell 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. UCSF ChimeraX version: 1.12.dev202604290127 (2026-04-29) © 2016-2026 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.5 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.4 OpenGL renderer: llvmpipe (LLVM 15.0.7, 256 bits) OpenGL vendor: Mesa Python: 3.11.13 Locale: en_US.UTF-8 Qt version: PyQt6 6.10.2, Qt 6.10.0 Qt runtime version: 6.10.1 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION=ubuntu XDG_SESSION_DESKTOP= XDG_CURRENT_DESKTOP=ubuntu:GNOME DISPLAY=:10.0 Manufacturer: Micro-Star International Co., Ltd. Model: Desktop MPG Z890 Infinite X3 AI 2nd OS: Ubuntu 22.04 Architecture: 64bit ELF Virtual Machine: none CPU: 20 Intel(R) Core(TM) Ultra 7 265KF Cache Size: 30720 KB Memory: total used free shared buff/cache available Mem: 62Gi 15Gi 33Gi 197Mi 14Gi 46Gi Swap: 2.0Gi 0B 2.0Gi Graphics: 02:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:2c05] (rev a1) Subsystem: Micro-Star International Co., Ltd. [MSI] Device [1462:5310] Kernel modules: nvidiafb, nouveau Installed Packages: accessible-pygments: 0.0.5 aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.13.0 appdirs: 1.4.4 asttokens: 3.0.1 attrs: 26.1.0 babel: 2.18.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 4.1.2 bs4: 0.0.2 build: 1.3.0 certifi: 2026.4.22 cftime: 1.6.5 charset-normalizer: 3.4.7 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.2 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.2 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: 1.67.1 ChimeraX-AtomicLibrary: 14.4 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: 1.12.dev202604290127 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: 1.2.1 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: 1.4.1 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: 1.8.2 ChimeraX-Label: 1.4 ChimeraX-LightingGUI: 1.0 ChimeraX-LinuxSupport: 1.0.1 ChimeraX-ListInfo: 1.3.1 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-MatchAlign: 1.1 ChimeraX-MatchMaker: 2.4 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.2.0 ChimeraX-MDcrds: 2.19 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.8 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.23 ChimeraX-ModelPanel: 1.6.1 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: 1.0.1 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: 1.15.4 ChimeraX-OpenFold: 1.0 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.13 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: 1.6 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.8.2 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: 3.5.12 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.18 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-SNFG: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.3 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: 1.50.5 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.6.1 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: 8.3.3 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.5 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.2.4 DateTime: 6.0 debugpy: 1.8.20 decorator: 5.2.1 distro: 1.9.0 docutils: 0.21.2 et_xmlfile: 2.0.0 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.62.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.16.0 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.13 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 2.0.0 iniconfig: 2.3.0 ipykernel: 7.1.0 ipython: 9.9.0 ipython_pygments_lexers: 1.1.1 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.8.0 jupyter_core: 5.9.1 kiwisolver: 1.5.0 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: 6.7.1 narwhals: 2.20.0 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: 8.4.0 OpenMM-CUDA-12: 8.4.0 openpyxl: 3.1.5 openvr: 1.26.701 packaging: 25.0 pandas: 3.0.2 ParmEd: 4.2.2 parso: 0.8.6 pathlib: 1.0.1 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: 4.9.6 plotly: 6.7.0 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: 2.13.3 pydantic-settings: 2.14.0 pydantic_core: 2.46.3 pydata-sphinx-theme: 0.17.1 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.5.1 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: 6.10.2 PyQt6-Qt6: 6.10.1 PyQt6-WebEngine: 6.10.0 PyQt6-WebEngine-Qt6: 6.10.1 PyQt6_sip: 13.10.3 pytest: 9.0.3 pytest-cov: 7.1.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.2 python-multipart: 0.0.27 pytz: 2026.1.post1 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 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: 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: 3.4.1 stack-data: 0.6.3 starlette: 1.0.0 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 3.2.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.5 tqdm: 4.67.3 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 Unidecode: 1.4.0 urllib3: 2.6.3 uvicorn: 0.46.0 wcwidth: 0.6.0 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 yarl: 1.23.0 zope.interface: 8.4
#20780	duplicate	Dock Prep: acc_phi_psi() takes 8 positional arguments but 9 were given	Eric Pettersen	chimerax-bug-report@…
Description	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. 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, 20 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: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.8.5 ChimeraX-Label: 1.5 ChimeraX-LightingGUI: 1.0 ChimeraX-ListInfo: 1.3.1 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.3 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-MatchAlign: 1.2.1 ChimeraX-MatchMaker: 2.4.1 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.2.0 ChimeraX-MDcrds: 2.19.2 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.4.3 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.17 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.24 ChimeraX-ModelPanel: 1.6.1 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: 1.0.1 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.16.2 ChimeraX-OpenFold: 1.0 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.13 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: 1.11 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.8.3 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: 1.5.3 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: 3.5.12 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.19.1 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-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
#20777	duplicate	pyKVFinder install failed on Mac: '/usr/bin/clang' failed with exit code 1	Eric Pettersen	chimerax-bug-report@…
Description	The following bug report has been submitted: Platform: macOS-14.8.5-arm64-arm-64bit ChimeraX Version: 1.12 (2026-06-12 03:42:34 UTC) Description Replace this text with list of actions that caused this problem to occur Log: UCSF ChimeraX version: 1.12 (2026-06-12) © 2016-2026 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > close session > open 4dpd Summary of feedback from opening 4dpd fetched from pdb --- notes | Fetching compressed mmCIF 4dpd from http://files.rcsb.org/download/4dpd.cif Fetching CCD DHF from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/F/DHF/DHF.cif Fetching CCD NAP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/NAP/NAP.cif Fetching CCD UMP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/UMP/UMP.cif 4dpd title: WILD TYPE PLASMODIUM FALCIPARUM DIHYDROFOLATE REDUCTASE-THYMIDYLATE SYNTHASE (PfDHFR-TS), DHF COMPLEX, NADP+, dUMP [more info...] Chain information for 4dpd #1 --- Chain | Description | UniProt A B | Bifunctional dihydrofolate reductase-thymidylate synthase | A7UD81_PLAFA 1-608 Non-standard residues in 4dpd #1 --- DHF — dihydrofolic acid NAP — nadp nicotinamide-adenine-dinucleotide phosphate (2'-monophosphoadenosine 5'-diphosphoribose) UMP — 2'-deoxyuridine 5'-monophosphate (DUMP) > select /B 4719 atoms, 4640 bonds, 2 pseudobonds, 729 residues, 2 models selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > select /B:2-605 Nothing selected > select ::name="DHF" 32 atoms, 34 bonds, 1 residue, 1 model selected > style sel sphere Changed 32 atom styles > color sel purple > open 4dpd Summary of feedback from opening 4dpd fetched from pdb --- warning | Cannot find consistent set of bond orders for ring system containing atom C12 in residue DHF /A:701 4dpd title: WILD TYPE PLASMODIUM FALCIPARUM DIHYDROFOLATE REDUCTASE-THYMIDYLATE SYNTHASE (PfDHFR-TS), DHF COMPLEX, NADP+, dUMP [more info...] Chain information for 4dpd #2 --- Chain | Description | UniProt A B | Bifunctional dihydrofolate reductase-thymidylate synthase | A7UD81_PLAFA 1-608 Non-standard residues in 4dpd #2 --- DHF — dihydrofolic acid NAP — nadp nicotinamide-adenine-dinucleotide phosphate (2'-monophosphoadenosine 5'-diphosphoribose) UMP — 2'-deoxyuridine 5'-monophosphate (DUMP) > select clear > select #2/B 4719 atoms, 4640 bonds, 2 pseudobonds, 729 residues, 2 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select #1/A:288 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:287 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:288 8 atoms, 7 bonds, 1 residue, 1 model selected > label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}" > label height 2 > surface sel > surface (#!1 & sel) > surface style solid > ui tool show "Color Actions" > color sel dark blue > select clear > surface > ui tool show "Color Actions" > color blue violet > select ::name="DHF" 64 atoms, 68 bonds, 2 residues, 2 models selected > select ::name="DHF" 64 atoms, 68 bonds, 2 residues, 2 models selected > select sel :< 5 472 atoms, 464 bonds, 48 residues, 2 models selected > show (#!1-2 & sel) target ab > color (#!1-2 & sel) red > select ::name="DHF" 64 atoms, 68 bonds, 2 residues, 2 models selected > ui tool show H-Bonds > hbonds sel restrict cross reveal true Cannot find consistent set of bond orders for ring system containing atom C12 in residue DHF /A:701 28 hydrogen bonds found > ui tool show Contacts > contacts sel restrict cross ignoreHiddenModels true 136 contacts > transparency sel 90 > ui tool show "Show Sequence Viewer" > sequence chain #1/A #2/A Alignment identifier is 1 > select > #1/A:4-9,33-37,51-64,66-82,106-117,132-136,145-156,166-176,286-294,308-318,324-339,376-388,392-399,405-416,429-437,454-466,478-485,516-536,556-564,582-589 > #2/A:4-9,33-37,51-64,66-82,106-117,132-136,145-156,166-176,286-294,308-318,324-339,376-388,392-399,405-416,429-437,454-466,478-485,516-536,556-564,582-589 3702 atoms, 3750 bonds, 438 residues, 2 models selected > select #1/A:299 #2/A:299 18 atoms, 16 bonds, 2 residues, 2 models selected > select #1/A:299-306 #2/A:299-306 134 atoms, 132 bonds, 16 residues, 2 models selected Bifunctional Dihydrofolate Reductase-Thymidylate Synthase [ID: 1] region 2 chains [299-306] RMSD: 0.000 > surface hidePatches (#!1-2 & sel) > select clear > transparency 70 > select #1/A:368-369 #2/A:368-369 32 atoms, 30 bonds, 4 residues, 2 models selected > select #1/A:368-369 #2/A:368-369 32 atoms, 30 bonds, 4 residues, 2 models selected Bifunctional Dihydrofolate Reductase-Thymidylate Synthase [ID: 1] region 2 chains [368-369] RMSD: 0.000 > open 1DHF Summary of feedback from opening 1DHF fetched from pdb --- notes | Fetching compressed mmCIF 1dhf from http://files.rcsb.org/download/1dhf.cif Fetching CCD FOL from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/FOL/FOL.cif 1dhf title: Crystal structures of recombinant human dihydrofolate reductase complexed with folate and 5-deazofolate [more info...] Chain information for 1dhf #5 --- Chain | Description | UniProt A B | DIHYDROFOLATE REDUCTASE | DYR_HUMAN 1-186 Non-standard residues in 1dhf #5 --- FOL — folic acid > select #5/B:4-185 1476 atoms, 1511 bonds, 182 residues, 1 model selected > delete atoms sel > delete bonds sel Drag select of 4dpd_A SES surface, 53 of 481140 triangles, 4dpd_A SES surface, 53 of 481140 triangles, 36 atoms, 34 bonds > delete atoms (#5 & sel) > delete bonds (#5 & sel) > surface hidePatches #1.3#2.2 > ui tool show Matchmaker > matchmaker #5#!2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 4dpd, chain A (#1) with 1dhf, chain A (#5), sequence alignment score = 313.5 RMSD between 148 pruned atom pairs is 0.835 angstroms; (across all 171 pairs: 1.723) Matchmaker 4dpd, chain A (#1) with 4dpd, chain A (#2), sequence alignment score = 3111.2 RMSD between 530 pruned atom pairs is 0.000 angstroms; (across all 530 pairs: 0.000) > save /Users/hkalin/Desktop/malaria.png width 930 height 675 supersample 3 > save /Users/hkalin/Desktop/4DPD_workshop_vr_HK.glb > color modify #*lightness 40 Missing or invalid "adjuster" argument: Should be one of 'blackness', 'blue', 'contrast', 'green', 'hue', 'lightness', 'red', 'saturation', or 'whiteness' > color modify #*lightness40 Missing or invalid "adjuster" argument: Should be one of 'blackness', 'blue', 'contrast', 'green', 'hue', 'lightness', 'red', 'saturation', or 'whiteness' > colormodify #*lightness40 Unknown command: colormodify #*lightness40 > colormodify #*lightness 40 Unknown command: colormodify #*lightness 40 > colormodify #*lightness 40 Unknown command: colormodify #*lightness 40 > color modify #*lightness 40 Missing or invalid "adjuster" argument: Should be one of 'blackness', 'blue', 'contrast', 'green', 'hue', 'lightness', 'red', 'saturation', or 'whiteness' > color modify #lightness 40 Missing or invalid "adjuster" argument: Should be one of 'blackness', 'blue', 'contrast', 'green', 'hue', 'lightness', 'red', 'saturation', or 'whiteness' > color modify #lightness +40 Missing or invalid "adjuster" argument: Should be one of 'blackness', 'blue', 'contrast', 'green', 'hue', 'lightness', 'red', 'saturation', or 'whiteness' > color modify #lightness -40 Missing or invalid "adjuster" argument: Should be one of 'blackness', 'blue', 'contrast', 'green', 'hue', 'lightness', 'red', 'saturation', or 'whiteness' > color modify #1 lightness -40 > color modify #1 lightness +40 > color modify #1 lightness +70 > color modify # lightness +70 Missing or invalid "adjuster" argument: Should be one of 'blackness', 'blue', 'contrast', 'green', 'hue', 'lightness', 'red', 'saturation', or 'whiteness' > color modify lightness +70 > color modify #2 lightness +70 > color modify #2 hue +70 > color modify #1 hue +70 > color modify lightness +70 > color modify lightness -70 > color modify lightness -10 > color modify lightness +50 > style ball Changed 11090 atom styles > style sphere Changed 11090 atom styles > style sphere Changed 11090 atom styles > style stick Changed 11090 atom styles > style sphere Changed 11090 atom styles > style sphere Changed 11090 atom styles > style ball Changed 11090 atom styles Drag select of 811 atoms, 1236 residues, 170 pseudobonds, 718 bonds > style sel sphere Changed 10509 atom styles > style sel ball Changed 10509 atom styles > style sel sphere Changed 10509 atom styles > set bgColor white > set bgColor black > style sel ball Changed 10509 atom styles > lighting simple > style sel sphere Changed 10509 atom styles > select #1/A#2/A 9470 atoms, 9248 bonds, 170 pseudobonds, 1510 residues, 6 models selected > select #1/A 4735 atoms, 4624 bonds, 44 pseudobonds, 755 residues, 4 models selected > select clear > select #1/A 4735 atoms, 4624 bonds, 44 pseudobonds, 755 residues, 4 models selected > select #5/A 1570 atoms, 1545 bonds, 245 residues, 1 model selected > close session > open 5WG8 Summary of feedback from opening 5WG8 fetched from pdb --- notes | Fetching compressed mmCIF 5wg8 from http://files.rcsb.org/download/5wg8.cif Fetching CCD LB1 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/1/LB1/LB1.cif Fetching CCD MN from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/MN/MN.cif Fetching CCD MPD from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/MPD/MPD.cif Fetching CCD MRD from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/MRD/MRD.cif 5wg8 title: Structure of PP5C with LB-100; 7-oxabicyclo[2.2.1]heptane-2,3-dicarbonyl moiety modeled in the density [more info...] Chain information for 5wg8 #1 --- Chain | Description | UniProt A | Serine/threonine-protein phosphatase 5 | PPP5_HUMAN 169-499 Non-standard residues in 5wg8 #1 --- LB1 — (1S,2R,3S,4R)-3-(4-methylpiperazine-1-carbonyl)-7-oxabicyclo[2.2.1]heptane-2-carboxylic acid MN — manganese (II) ion MPD — (4S)-2-methyl-2,4-pentanediol MRD — (4R)-2-methylpentane-2,4-diol 75 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 2553 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. Drag select of 118 atoms, 320 residues, 11 pseudobonds, 104 bonds No Surface models open > select clear No Surface models open [Repeated 1 time(s)] > select :LB1 11 atoms, 12 bonds, 1 residue, 1 model selected > select :MN 2 atoms, 2 residues, 1 model selected > select :MPD 8 atoms, 7 bonds, 1 residue, 1 model selected > select :MRD 8 atoms, 7 bonds, 1 residue, 1 model selected Drag select of 1 atoms > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 5wg8_A SES surface #1.2: minimum, 0.00, mean 0.00, maximum 0.00 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel Coulombic values for 5wg8_A SES surface #1.2: minimum, 0.00, mean 0.00, maximum 0.00 To also show corresponding color key, enter the above coulombic command and add key true > show sel surfaces > open 5WG8 fromDatabase pdb format mmcif 5wg8 title: Structure of PP5C with LB-100; 7-oxabicyclo[2.2.1]heptane-2,3-dicarbonyl moiety modeled in the density [more info...] Chain information for 5wg8 #2 --- Chain | Description | UniProt A | Serine/threonine-protein phosphatase 5 | PPP5_HUMAN 169-499 Non-standard residues in 5wg8 #2 --- LB1 — (1S,2R,3S,4R)-3-(4-methylpiperazine-1-carbonyl)-7-oxabicyclo[2.2.1]heptane-2-carboxylic acid MN — manganese (II) ion MPD — (4S)-2-methyl-2,4-pentanediol MRD — (4R)-2-methylpentane-2,4-diol 75 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 2553 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. > coulombic sel Coulombic values for 5wg8_A SES surface #1.2: minimum, 0.00, mean 0.00, maximum 0.00 To also show corresponding color key, enter the above coulombic command and add key true Drag select of 60 residues Drag select of 26 residues Drag select of 30 residues Drag select of 64 residues Drag select of 18 residues > color modify #1 lightness 40 > color modify #* lightness 40 > color modify #1 lightness 40 > color modify #2 lightness 40 > color modify #2 lightness +40 > color modify #2 hue +40 > color modify #* hue +40 [Repeated 2 time(s)] > color modify #* lightness +70 > select clear [Repeated 1 time(s)] > select #2/A 2815 atoms, 2613 bonds, 11 pseudobonds, 587 residues, 2 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > graphics silhouettes true > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > lighting full > lighting soft > lighting simple [Repeated 2 time(s)] > lighting soft > lighting simple > ui tool show "Side View" > view [Repeated 1 time(s)] > view orient > lighting flat > lighting simple > lighting shadows true > lighting shadows false > graphics silhouettes false Drag select of 106 atoms, 240 residues, 11 pseudobonds, 95 bonds Drag select of 5wg8_A SES surface, 118 atoms, 320 residues, 11 pseudobonds, 104 bonds > ui tool show "Find Cavities" pyKVFinder module not installed; fetching from PyPi repository... 'pip install pyKVFinder' failed. Error from pip: error: subprocess-exited- with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/gd/ww67f0hx1mg613mfry6rddqsxqlhrx/T/pip-build-env- jap6z4xt/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.12.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder Traceback (most recent call last): File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/kvfinder/__init__.py", line 48, in check_pyKVFinder import pyKVFinder ModuleNotFoundError: No module named 'pyKVFinder' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 571, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py", line 1400, in start_tool return cls._get_func(api, "start_tool")(session, ti.name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/kvfinder/__init__.py", line 42, in start_tool check_pyKVFinder(session.logger) File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/kvfinder/__init__.py", line 54, in check_pyKVFinder run(logger.session, pip_cmd, log=False) File "/Applications/ChimeraX-1.12.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-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/pip.py", line 84, in pip run_logged_pip(pip_cmd, session.logger) File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/python_utils.py", line 148, in run_logged_pip raise RuntimeError(s) RuntimeError: error: subprocess-exited-with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/gd/ww67f0hx1mg613mfry6rddqsxqlhrx/T/pip-build-env- jap6z4xt/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.12.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/gui.py", line 1955, in <lambda> run(ses, "ui tool show %s" % StringArg.unparse(tool_name))) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.12.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-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/cmd.py", line 219, in ui_tool_show return bi.start_tool(session, name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 578, in start_tool raise ToolshedError( chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find Cavities in bundle ChimeraX-KVFinder: error: subprocess-exited-with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/gd/ww67f0hx1mg613mfry6rddqsxqlhrx/T/pip-build-env- jap6z4xt/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.12.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find Cavities in bundle ChimeraX-KVFinder: error: subprocess-exited-with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/gd/ww67f0hx1mg613mfry6rddqsxqlhrx/T/pip-build-env- jap6z4xt/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.12.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 578, in start_tool raise ToolshedError( See log for complete Python traceback. > close session > open /Users/hkalin/Downloads/AF-P53041-F1-model_v4.pdb format pdb No such file/path: /Users/hkalin/Downloads/AF-P53041-F1-model_v4.pdb > open 5WG8 format mmcif fromDatabase pdb 5wg8 title: Structure of PP5C with LB-100; 7-oxabicyclo[2.2.1]heptane-2,3-dicarbonyl moiety modeled in the density [more info...] Chain information for 5wg8 #1 --- Chain | Description | UniProt A | Serine/threonine-protein phosphatase 5 | PPP5_HUMAN 169-499 Non-standard residues in 5wg8 #1 --- LB1 — (1S,2R,3S,4R)-3-(4-methylpiperazine-1-carbonyl)-7-oxabicyclo[2.2.1]heptane-2-carboxylic acid MN — manganese (II) ion MPD — (4S)-2-methyl-2,4-pentanediol MRD — (4R)-2-methylpentane-2,4-diol 75 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 2553 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. > close session > open /Users/hkalin/Desktop/4DPD_workshop_vr_HK.glb format gltf Opened glTF file containing 1 scenes, 29 nodes, 19 meshes > select water Expected an objects specifier or a keyword > close session > open > /Users/hkalin/Desktop/fold_ppp5c_alphafold3/fold_ppp5c_alphafold3_full_data_0.json Failed opening file /Users/hkalin/Desktop/fold_ppp5c_alphafold3/fold_ppp5c_alphafold3_full_data_0.json: Opening an AlphaFold PAE file requires first opening the predicted atomic model. Did not find an open atomic model from the same directory. If the atomic model is already open choose it using menu Tools / Structure Prediction / AlphaFold Error Plot or use the open command structure option, for example open /Users/hkalin/Desktop/fold_ppp5c_alphafold3/fold_ppp5c_alphafold3_full_data_0.json structure #1 If you are trying to open a JSON file that is not AlphaFold PAE data then you need to specify the specific JSON format such as open mole_channels.json format mole > open > /Users/hkalin/Desktop/fold_ppp5c_alphafold3/fold_ppp5c_alphafold3_model_4.cif > /Users/hkalin/Desktop/fold_ppp5c_alphafold3/fold_ppp5c_alphafold3_model_3.cif > /Users/hkalin/Desktop/fold_ppp5c_alphafold3/fold_ppp5c_alphafold3_model_2.cif > /Users/hkalin/Desktop/fold_ppp5c_alphafold3/fold_ppp5c_alphafold3_model_1.cif > /Users/hkalin/Desktop/fold_ppp5c_alphafold3/fold_ppp5c_alphafold3_model_0.cif Chain information for fold_ppp5c_alphafold3_model_4.cif #1 --- Chain | Description A | . Chain information for fold_ppp5c_alphafold3_model_3.cif #2 --- Chain | Description A | . Chain information for fold_ppp5c_alphafold3_model_2.cif #3 --- Chain | Description A | . Chain information for fold_ppp5c_alphafold3_model_1.cif #4 --- Chain | Description A | . Chain information for fold_ppp5c_alphafold3_model_0.cif #5 --- Chain | Description A | . Computing secondary structure [Repeated 4 time(s)] > select #1/A:1-499 3999 atoms, 4088 bonds, 499 residues, 1 model selected > select #2/A:1-499 3999 atoms, 4088 bonds, 499 residues, 1 model selected > select #3/A:1-499 3999 atoms, 4088 bonds, 499 residues, 1 model selected > select #4/A:1-499 3999 atoms, 4088 bonds, 499 residues, 1 model selected > select #5/A:1-499 3999 atoms, 4088 bonds, 499 residues, 1 model selected > select #1/A:1-499 3999 atoms, 4088 bonds, 499 residues, 1 model selected > select #5/A:1-499 3999 atoms, 4088 bonds, 499 residues, 1 model selected > select clear > select #2/A:1-499 3999 atoms, 4088 bonds, 499 residues, 1 model selected > select #2/A:1-499 3999 atoms, 4088 bonds, 499 residues, 1 model selected > delete atoms sel > delete bonds sel > select #2/A:1-499 Nothing selected > select #1/A:1-499 3999 atoms, 4088 bonds, 499 residues, 1 model selected > delete atoms sel > delete bonds sel > select #2/A:1-499 Nothing selected > select #1/A:1-499 Nothing selected > select #3/A:1-499 3999 atoms, 4088 bonds, 499 residues, 1 model selected > delete atoms sel > delete bonds sel > select #4/A:1-499 3999 atoms, 4088 bonds, 499 residues, 1 model selected > select #5/A:1-499 3999 atoms, 4088 bonds, 499 residues, 1 model selected > select #4/A:1-499 3999 atoms, 4088 bonds, 499 residues, 1 model selected > delete atoms sel > delete bonds sel > select clear [Repeated 1 time(s)] > open 5WG8 fromDatabase pdb format mmcif 5wg8 title: Structure of PP5C with LB-100; 7-oxabicyclo[2.2.1]heptane-2,3-dicarbonyl moiety modeled in the density [more info...] Chain information for 5wg8 #1 --- Chain | Description | UniProt A | Serine/threonine-protein phosphatase 5 | PPP5_HUMAN 169-499 Non-standard residues in 5wg8 #1 --- LB1 — (1S,2R,3S,4R)-3-(4-methylpiperazine-1-carbonyl)-7-oxabicyclo[2.2.1]heptane-2-carboxylic acid MN — manganese (II) ion MPD — (4S)-2-methyl-2,4-pentanediol MRD — (4R)-2-methylpentane-2,4-diol 75 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 2553 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. Drag select of 819 residues, 118 atoms, 11 pseudobonds, 104 bonds > Matchmaker #2 to #1 Unknown command: Matchmaker #2 to #1 > select clear > Matchmaker #2 to #1 Unknown command: Matchmaker #2 to #1 > Mmaker #2 to #1 Unknown command: Mmaker #2 to #1 > toolshed show > ui tool show Match→Align > msa3d #1/A#5/A Match→Align cutoff: 5.0, in column if within cutoff of: any 48 residue pairs aligned 48 fully populated columns Pairwise RMSDs across all fully populated columns --- Model | 1 | 5 1 | 0.000 | 3.100 5 | 3.100 | 0.000 Overall RMSD: 3.100 Sequence lengths: 320 499 SDM (cutoff 5.0): 155.607 Q-score: 0.007 Alignment identifier is MA-1 Showing conservation header ("seq_conservation" residue attribute) for alignment MA-1 Chains used in RMSD evaluation for alignment MA-1: 5wg8 #1/A, fold_ppp5c_alphafold3_model_0.cif #5/A Showing rmsd header ("seq_rmsd" residue attribute) for alignment MA-1 > select clear Drag select of 819 residues, 118 atoms, 11 pseudobonds, 104 bonds > Mmaker #2 to #1 Unknown command: Mmaker #2 to #1 > Mmaker #1 to #2 Unknown command: Mmaker #1 to #2 > select #5/A 3999 atoms, 4088 bonds, 499 residues, 1 model selected > ui tool show Matchmaker > matchmaker #5 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 5wg8, chain A (#1) with fold_ppp5c_alphafold3_model_0.cif, chain A (#5), sequence alignment score = 1693.4 RMSD between 314 pruned atom pairs is 0.284 angstroms; (across all 320 pairs: 0.782) > ui windowfill toggle [Repeated 2 time(s)] > ui mousemode right distance [Repeated 1 time(s)] > ui mousemode right "move label" [Repeated 1 time(s)]Drag select of 10 residues Drag select of 2 residues > select clear [Repeated 1 time(s)] > select #5/A:80 12 atoms, 12 bonds, 1 residue, 1 model selected > ui tool show "Find Cavities" pyKVFinder module not installed; fetching from PyPi repository... 'pip install pyKVFinder' failed. Error from pip: error: subprocess-exited- with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/gd/ww67f0hx1mg613mfry6rddqsxqlhrx/T/pip-build- env-n89hc9s1/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.12.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder Traceback (most recent call last): File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/kvfinder/__init__.py", line 48, in check_pyKVFinder import pyKVFinder ModuleNotFoundError: No module named 'pyKVFinder' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 571, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py", line 1400, in start_tool return cls._get_func(api, "start_tool")(session, ti.name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/kvfinder/__init__.py", line 42, in start_tool check_pyKVFinder(session.logger) File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/kvfinder/__init__.py", line 54, in check_pyKVFinder run(logger.session, pip_cmd, log=False) File "/Applications/ChimeraX-1.12.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-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/pip.py", line 84, in pip run_logged_pip(pip_cmd, session.logger) File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/python_utils.py", line 148, in run_logged_pip raise RuntimeError(s) RuntimeError: error: subprocess-exited-with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/gd/ww67f0hx1mg613mfry6rddqsxqlhrx/T/pip-build- env-n89hc9s1/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.12.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/gui.py", line 1955, in <lambda> run(ses, "ui tool show %s" % StringArg.unparse(tool_name))) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.12.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-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/cmd.py", line 219, in ui_tool_show return bi.start_tool(session, name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 578, in start_tool raise ToolshedError( chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find Cavities in bundle ChimeraX-KVFinder: error: subprocess-exited-with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/gd/ww67f0hx1mg613mfry6rddqsxqlhrx/T/pip-build- env-n89hc9s1/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.12.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find Cavities in bundle ChimeraX-KVFinder: error: subprocess-exited-with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/gd/ww67f0hx1mg613mfry6rddqsxqlhrx/T/pip-build- env-n89hc9s1/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.12.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 578, in start_tool raise ToolshedError( See log for complete Python traceback. OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M3 Pro OpenGL vendor: Apple Python: 3.11.9 Locale: 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 Pro Model Identifier: Mac15,6 Model Number: Z1AX0029VLL/A Chip: Apple M3 Pro Total Number of Cores: 12 (6 performance and 6 efficiency) Memory: 36 GB System Firmware Version: mBoot-18000.101.7 OS Loader Version: 10151.140.19.701.1 Software: System Software Overview: System Version: macOS 14.8.5 (23J423) Kernel Version: Darwin 23.6.0 Time since boot: 6 hours, 19 minutes Graphics/Displays: Apple M3 Pro: Chipset Model: Apple M3 Pro Type: GPU Bus: Built-In Total Number of Cores: 18 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: accessible-pygments: 0.0.5 aiohappyeyeballs: 2.6.2 aiohttp: 3.13.4 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.13.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 26.1.0 babel: 2.18.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 4.4.3 bs4: 0.0.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.7 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.2 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.2 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: 1.67.1 ChimeraX-AtomicLibrary: 14.4 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: 1.12 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: 1.2.2 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: 2.5.3 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: 1.8.2 ChimeraX-Label: 1.5 ChimeraX-LightingGUI: 1.0 ChimeraX-ListInfo: 1.3.1 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.3 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-MatchAlign: 1.2 ChimeraX-MatchMaker: 2.4.1 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.2.0 ChimeraX-MDcrds: 2.19 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.9 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.23 ChimeraX-ModelPanel: 1.6.1 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: 1.0.1 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: 1.15.4 ChimeraX-OpenFold: 1.0 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.13 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: 1.6 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.8.2 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: 3.5.12 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.18 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-SNFG: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.3 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: 1.50.8 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.6.2 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: 8.4.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.14.1 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: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.16.0 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.18 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 2.0.0 iniconfig: 2.3.0 ipykernel: 7.1.0 ipython: 9.9.0 ipython_pygments_lexers: 1.1.1 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.8.0 jupyter_core: 5.9.1 kiwisolver: 1.5.0 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: 0.2.2 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.1 narwhals: 2.22.1 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 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: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.10.0 plotly: 6.8.0 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 pydantic: 2.13.4 pydantic-settings: 2.14.1 pydantic_core: 2.46.4 pydata-sphinx-theme: 0.18.0 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.5.1 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-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: 9.0.3 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: 5.7.0 QtPy: 2.4.3 qtshim: 1.2.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 rpds-py: 2026.5.1 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.1.1 sortedcontainers: 2.4.0 soupsieve: 2.8.4 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: 3.4.4 stack-data: 0.6.3 starlette: 1.3.0 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 3.2.1 threadpoolctl: 3.6.0 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.7 tqdm: 4.68.2 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 Unidecode: 1.4.0 urllib3: 2.7.0 uvicorn: 0.49.0 wcwidth: 0.8.1 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 yarl: 1.24.2

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Query Language

query: TracLinks and the [[TicketQuery]] macro both use a mini “query language” for specifying query filters. Filters are separated by ampersands (&). Each filter consists of the ticket field name, an operator and one or more values. More than one value are separated by a pipe (|), meaning that the filter matches any of the values. To include a literal & or | in a value, escape the character with a backslash (\).

The available operators are:

=	the field content exactly matches one of the values
~=	the field content contains one or more of the values
^=	the field content starts with one of the values
$=	the field content ends with one of the values

All of these operators can also be negated:

!=	the field content matches none of the values
!~=	the field content does not contain any of the values
!^=	the field content does not start with any of the values
!$=	the field content does not end with any of the values

The date fields created and modified can be constrained by using the = operator and specifying a value containing two dates separated by two dots (..). Either end of the date range can be left empty, meaning that the corresponding end of the range is open. The date parser understands a few natural date specifications like "3 weeks ago", "last month" and "now", as well as Bugzilla-style date specifications like "1d", "2w", "3m" or "4y" for 1 day, 2 weeks, 3 months and 4 years, respectively. Spaces in date specifications can be omitted to avoid having to quote the query string.

created=2007-01-01..2008-01-01	query tickets created in 2007
created=lastmonth..thismonth	query tickets created during the previous month
modified=1weekago..	query tickets that have been modified in the last week
modified=..30daysago	query tickets that have been inactive for the last 30 days

---

See also: TracTickets, TracReports, TracGuide, TicketQuery