wiki:TracQuery

Trac Ticket Queries

Table of Contents

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.

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.

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 13674)

1 2 3 4 5 6 7 8 9 10 11 →
Ticket Resolution Summary Owner Reporter
#20141 can't reproduce UniProt fetch failure Eric Pettersen vijayapillaik@…
#20138 not a bug Binary file opened as PDB Eric Pettersen chimerax-bug-report@…
#20137 duplicate Crash on Mac waking from sleep Eric Pettersen bhogeba@…
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 13674)

1 2 3 4 5 6 7 8 9 10 11 →
Ticket Resolution Summary Owner Reporter
#20141 can't reproduce UniProt fetch failure Eric Pettersen vijayapillaik@…
Description 
The following bug report has been submitted:
Platform:        Windows-10-10.0.26200
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
issue faced regarding the process of generating the loop

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

> open C:/Users/HP/Downloads/3pjc.pdb

3pjc.pdb title:  
Crystal structure of JAK3 complexed with A potent atp site inhibitor showing
high selectivity within the janus kinase family [more info...]  
  
Chain information for 3pjc.pdb #1  
---  
Chain | Description | UniProt  
A | tyrosine-protein kinase JAK3 | JAK3_HUMAN 812-1124  
  
Non-standard residues in 3pjc.pdb #1  
---  
PJC —
3-(1H-indol-3-yl)-4-[2-(4-oxopiperidin-1-yl)-5-(trifluoromethyl)pyrimidin-4-yl]-1H-pyrrole-2,5-dione  
  

> select ::name="HOH"::name="PJC"

172 atoms, 37 bonds, 140 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> open P52333 fromDatabase uniprot associate #1/A

Error from UniProt web server while checking job status: HTTP Error 400:  
  
Try again later. If you then still get the error, you could use Help->Report a
Bug to report the error to the ChimeraX team. They may be able to help you
work around the problem.  

Failed to send bug report. Possibly no internet connection.  

[Repeated 1 time(s)]




OpenGL version: 3.3.0 - Build 31.0.101.5186
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel

Python: 3.11.9
Locale: en_US.cp1252
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: windows

Manufacturer: HP
Model: HP Laptop 15-dy2xxx
OS: Microsoft Windows 11 Home (Build 26200)
Memory: 8,215,126,016
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i7-1165G7 @ 2.80GHz
OSLanguage: en-US

Installed Packages:
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.12.1
    appdirs: 1.4.4
    asttokens: 3.0.1
    attrs: 25.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.12.2
    build: 1.3.0
    certifi: 2026.1.4
    cftime: 1.6.5
    charset-normalizer: 3.4.4
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.1.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.61.4
    ChimeraX-AtomicLibrary: 14.2.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.7.3
    ChimeraX-Label: 1.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.1.0
    ChimeraX-MDcrds: 2.17.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0.1
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.15.2
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.12
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.4.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.5
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.10
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.3
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.49.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.5.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.3.1
    colorama: 0.4.6
    comm: 0.2.3
    comtypes: 1.4.11
    contourpy: 1.3.3
    coverage: 7.13.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.4
    debugpy: 1.8.19
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.61.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.15.1
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.11
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.3.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.8
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.6.3
    jupyter_core: 5.9.1
    jupyterlab_widgets: 3.0.16
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.1
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.0
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    numpy: 1.26.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.5
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.5.1
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.12.5
    pydantic-settings: 2.12.0
    pydantic_core: 2.41.5
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.6
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.2
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.9.1
    PyQt6-Qt6: 6.9.2
    PyQt6-WebEngine-commercial: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.2
    PyQt6_sip: 13.10.2
    pytest: 9.0.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.1
    python-multipart: 0.0.21
    pywin32: 311
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.1.0
    roman-numerals-py: 4.1.0
    rpds-py: 0.30.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.0.1
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    soupsieve: 2.8.3
    Sphinx: 8.2.3
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    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
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    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
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    stack-data: 0.6.3
    starlette: 0.52.1
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.4
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    tzdata: 2025.3
    urllib3: 2.6.3
    uvicorn: 0.40.0
    wcwidth: 0.3.2
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.15
    WMI: 1.5.1
    yarl: 1.22.0
File attachment: 3pjc achain.pdb

3pjc achain.pdb​

#20138 not a bug Binary file opened as PDB Eric Pettersen chimerax-bug-report@…
Description 
The following bug report has been submitted:
Platform:        macOS-26.2-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Replace this text with list of actions that caused this problem to occur

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

> open /Users/sarahsiregar/Desktop/S818958_results.tar.bz2.pdb

Summary of feedback from opening
/Users/sarahsiregar/Desktop/S818958_results.tar.bz2.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
404 Not Found  
Ignored bad PDB record found on line 2  
  
  
Ignored bad PDB record found on line 3  
  
  
Ignored bad PDB record found on line 4  
The?equested?RL?as??(f?)?n?his?erver.??  
  
Ignored bad PDB record found on line 5  
  
  
1 messages similar to the above omitted  
  

> open /Users/sarahsiregar/Desktop/S818958_results.tar.bz2.pdb format pdb

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 316, in interceptRequest  
self._callback(info)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 349, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 455, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 527, in thread_safe  
func(*args, **kw)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 442, in defer  
cxcmd(session, topic)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 464, in cxcmd  
run(session, cmd)  
File
"/Applications/ChimeraX-1.11.1.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-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 216, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 527, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 498, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/pdb/__init__.py", line 45, in open  
return pdb.open_pdb(session, data, file_name, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/pdb/pdb.py", line 89, in open_pdb  
pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic,
segid_chains,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "<frozen codecs>", line 322, in decode  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd4 in position 37:
invalid continuation byte  
  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd4 in position 37:
invalid continuation byte  
  
File "", line 322, in decode  
  
See log for complete Python traceback.  
  

> open "/Users/sarahsiregar/Desktop/COL1A2PORCINE_SPECIFIC_578fa
> 2/COL1A2PORCINE_SPECIFIC_578fa_unrelaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb"
> format pdb

Chain information for
COL1A2PORCINE_SPECIFIC_578fa_unrelaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb
#1  
---  
Chain | Description  
A | No description available  
  

> open /Users/sarahsiregar/Desktop/model1.pdb_1786c043.pdb

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 355, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/Applications/ChimeraX-1.11.1.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-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 216, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 527, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 498, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/pdb/__init__.py", line 45, in open  
return pdb.open_pdb(session, data, file_name, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/pdb/pdb.py", line 89, in open_pdb  
pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic,
segid_chains,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "<frozen codecs>", line 322, in decode  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd4 in position 37:
invalid continuation byte  
  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd4 in position 37:
invalid continuation byte  
  
File "", line 322, in decode  
  
See log for complete Python traceback.  
  

> open /Users/sarahsiregar/Desktop/model1.pdb_1786c043.pdb

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 355, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/Applications/ChimeraX-1.11.1.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-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 216, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 527, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 498, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/pdb/__init__.py", line 45, in open  
return pdb.open_pdb(session, data, file_name, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/pdb/pdb.py", line 89, in open_pdb  
pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic,
segid_chains,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "<frozen codecs>", line 322, in decode  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd4 in position 37:
invalid continuation byte  
  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd4 in position 37:
invalid continuation byte  
  
File "", line 322, in decode  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir10,1
      Model Number: MGND3ZP/A
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 13822.61.10
      OS Loader Version: 13822.61.10

Software:

    System Software Overview:

      System Version: macOS 26.2 (25C56)
      Kernel Version: Darwin 25.2.0
      Time since boot: 11 hours, 52 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 7
      Vendor: Apple (0x106b)
      Metal Support: Metal 4
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.12.1
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.1
    attrs: 25.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.12.2
    build: 1.3.0
    certifi: 2025.7.14
    cftime: 1.6.5
    charset-normalizer: 3.4.4
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.1.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.61.4
    ChimeraX-AtomicLibrary: 14.2.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.7.3
    ChimeraX-Label: 1.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.1.0
    ChimeraX-MDcrds: 2.17.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0.1
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.15.2
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.12
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.4.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.5
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.10
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.3
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.49.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.5.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.3.1
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.13.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.4
    debugpy: 1.8.19
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.61.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.15.1
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.11
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.3.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.8
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.6.3
    jupyter_core: 5.9.1
    jupyterlab_widgets: 3.0.16
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.1
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.0
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.5
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.5.1
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.12.5
    pydantic-settings: 2.12.0
    pydantic_core: 2.41.5
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.6
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.2
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.9.1
    PyQt6-Qt6: 6.9.2
    PyQt6-WebEngine-commercial: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.2
    PyQt6_sip: 13.10.2
    pytest: 9.0.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.1
    python-multipart: 0.0.21
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    referencing: 0.37.0
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#20137 duplicate Crash on Mac waking from sleep Eric Pettersen bhogeba@…
Description 
The following bug report has been submitted:
Platform:        macOS-26.3.1-arm64-arm-64bit
ChimeraX Version: 1.10rc202506100450 (2025-06-10 04:50:02 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault

Current thread 0x0000000206eff100 (most recent call first):
 File "/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
 File "/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
 File "/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 in 
 File "", line 88 in _run_code
 File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, psutil._psutil_osx, psutil._psutil_posix, chimerax.surface._surface, chimerax.map._map, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.graphics._graphics, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 61)


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{
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 "procRole" : "Background",
 "version" : 2,
 "userID" : 1533080713,
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   "build" : "25D2128",
   "releaseType" : "User"
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 "captureTime" : "2026-04-05 11:36:26.1042 -0400",
 "codeSigningMonitor" : 2,
 "incident" : "824EADAE-27B8-49BF-BA67-792C8DFA8D20",
 "pid" : 22775,
 "translated" : false,
 "cpuType" : "ARM-64",
 "procLaunch" : "2026-04-02 22:47:26.0355 -0400",
 "procStartAbsTime" : 5193175762842,
 "procExitAbsTime" : 6722574093641,
 "procName" : "ChimeraX",
 "procPath" : "\/Applications\/ChimeraX-1.10-rc2025.06.10.app\/Contents\/MacOS\/ChimeraX",
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 "crashReporterKey" : "70228687-E509-459D-AB31-FABE2482F60C",
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 "developerMode" : 1,
 "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
 "codeSigningTeamID" : "LWV8X224YF",
 "codeSigningFlags" : 570491649,
 "codeSigningValidationCategory" : 6,
 "codeSigningTrustLevel" : 4294967295,
 "codeSigningAuxiliaryInfo" : 0,
 "instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRFOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkQng\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
 "bootSessionUUID" : "8589CC38-99E9-4D39-A76C-779C2F48B65D",
 "wakeTime" : 24,
 "sleepWakeUUID" : "F313F6DB-8DAE-4EBC-AA16-F54504747946",
 "sip" : "enabled",
 "vmRegionInfo" : "0xffffb2833dd137ec is not in any region.  \n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      UNUSED SPACE AT END",
 "exception" : {"codes":"0x0000000000000001, 0x3bf5b2833dd137ec","rawCodes":[1,4320555694279440364],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x3bf5b2833dd137ec -> 0xffffb2833dd137ec (possible pointer authentication failure)"},
 "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":22775},
 "vmregioninfo" : "0xffffb2833dd137ec is not in any region.  \n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      UNUSED SPACE AT END",
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===== Log before crash start =====
UCSF ChimeraX version: 1.10rc202506100450 (2025-06-10)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/bhogeba/T4_dimeric
> tRNA/Ecoli_M1RNP/3'UAA_T4_tRNA/M1_Holo_T4dimer_ternary/Intermediates_and
> active conformer_publication.cxs"

Opened cryosparc_P23_J2582_006_volume_map.mrc as #2, grid size 456,456,456,
pixel 0.909, shown at level 0.103, step 2, values float32  
Opened cryosparc_P23_J2372_006_volume_map.mrc as #3, grid size 456,456,456,
pixel 0.909, shown at level 0.139, step 2, values float32  
Opened Productive_Ser_5mM_Ca_HoloM1_J1524_map_1.mrc as #6, grid size
384,384,384, pixel 0.999, shown at level 0.0712, step 2, values float32  

> view name session-start

opened ChimeraX session  

> show #!7 models

> select #1/A

8068 atoms, 9036 bonds, 375 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #5#!7 to #1 & sel

Using Nucleic matrix instead of BLOSUM-62 for matching  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
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 Int_2_5mM_Mg_3UAA_Ser_J2582-coot-1.pdb, chain A (#1) with
Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb, chain A (#5), sequence alignment score
= 1496  
RMSD between 156 pruned atom pairs is 1.086 angstroms; (across all 374 pairs:
3.812)  

Matchmaker Int_2_5mM_Mg_3UAA_Ser_J2582-coot-1.pdb, chain A (#1) with
Int_1_5mM_Mg_UAA_J2372_1-coot-1_real_space_refined_001.pdb, chain A (#7),
sequence alignment score = 1491.1  
RMSD between 208 pruned atom pairs is 0.979 angstroms; (across all 374 pairs:
3.576)  


> matchmaker #5#!7 to #1 & sel

Using Nucleic matrix instead of BLOSUM-62 for matching  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
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 Int_2_5mM_Mg_3UAA_Ser_J2582-coot-1.pdb, chain A (#1) with
Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb, chain A (#5), sequence alignment score
= 1496  
RMSD between 156 pruned atom pairs is 1.086 angstroms; (across all 374 pairs:
3.812)  

Matchmaker Int_2_5mM_Mg_3UAA_Ser_J2582-coot-1.pdb, chain A (#1) with
Int_1_5mM_Mg_UAA_J2372_1-coot-1_real_space_refined_001.pdb, chain A (#7),
sequence alignment score = 1491.1  
RMSD between 208 pruned atom pairs is 0.979 angstroms; (across all 374 pairs:
3.576)  


> select clear

Drag select of 394 atoms, 698 residues, 412 bonds  

> hide sel atoms

> select clear

Drag select of 238 atoms, 708 residues, 250 bonds  

> hide sel atoms

> select clear

> hide #!7 models

Drag select of 120 atoms, 200 residues, 125 bonds  

> hide sel atoms

> select clear

> select add #1/C:0

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #1/C:-1

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select add #1/C:-2

62 atoms, 66 bonds, 3 residues, 1 model selected  

> hide sel atoms

> select add #1/A:333

84 atoms, 90 bonds, 4 residues, 1 model selected  

> select add #1/C:76

104 atoms, 111 bonds, 5 residues, 1 model selected  

> select add #1/C:75

124 atoms, 132 bonds, 6 residues, 1 model selected  

> hide sel atoms

> select add #1/A:254

146 atoms, 156 bonds, 7 residues, 1 model selected  

> hide sel atoms

> select add #1/A:332

169 atoms, 181 bonds, 8 residues, 1 model selected  

> hide sel atoms

Drag select of 31 atoms, 150 residues, 28 bonds  

> ~label sel residues

> select clear

> select add #1/C:-1

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #1/C:-2

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select add #1/C:0

62 atoms, 66 bonds, 3 residues, 1 model selected  

> select add #1/C:75

82 atoms, 87 bonds, 4 residues, 1 model selected  

> select add #1/A:295

104 atoms, 111 bonds, 5 residues, 1 model selected  

> select add #1/C:76

124 atoms, 132 bonds, 6 residues, 1 model selected  

> select add #1/A:296

147 atoms, 157 bonds, 7 residues, 1 model selected  

> select add #1/A:332

170 atoms, 182 bonds, 8 residues, 1 model selected  

> ~label sel residues

> select add #1/C:77

193 atoms, 207 bonds, 9 residues, 1 model selected  

> select clear

> select #1/C:77

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #1/C:76

43 atoms, 46 bonds, 2 residues, 1 model selected  

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> hide sel atoms

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> show sel atoms

> hide sel atoms

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> select clear

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 23 atom styles  

> select clear

> select add #1/A:68

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #1/A:67

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select add #1/A:69

65 atoms, 70 bonds, 3 residues, 1 model selected  

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> select add #1/C:77@O3'

66 atoms, 70 bonds, 4 residues, 1 model selected  

> select up

88 atoms, 97 bonds, 4 residues, 1 model selected  

> select up

90 atoms, 99 bonds, 5 residues, 1 model selected  

> select up

108 atoms, 119 bonds, 5 residues, 1 model selected  

> select add #1/A:352

130 atoms, 143 bonds, 6 residues, 1 model selected  

> select add #1/A:351

152 atoms, 167 bonds, 7 residues, 1 model selected  

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> hide sel atoms

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> color sel byhetero

> show (sel-residues & sidechain) target ab

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> hide sel atoms

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 152 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 152 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 152 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 152 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 152 atom styles  

> nucleotides sel tube/slab shape box

> nucleotides sel ladder

> label sel text "{0.name} {0.number}{0.insertion_code}"

> select Mg

26 atoms, 26 residues, 2 models selected  

> show (#!1 & sel) target ab

> select clear

> select add #1/D:14@MG

1 atom, 1 residue, 1 model selected  

> select add #1/C:77@OP2

2 atoms, 2 residues, 1 model selected  

> ui tool show Distances

> distance #1/D:14@MG #1/C:77@OP2

Distance between Int_2_5mM_Mg_3UAA_Ser_J2582-coot-1.pdb #1/D MG 14 MG and /C G
77 OP2: 11.76Å  

> select clear

> select #1/D:14@MG

1 atom, 1 residue, 1 model selected  

> color sel red

> color sel blue

> color sel cyan

> color sel orange

> color sel light sea green

> color sel forest green

> ui tool show "Color Actions"

> color sel magenta

> select clear

> hide #!1 models

> show #!1 models

> show #!7 models

> hide #!1 models

> hide #!4 models

> hide #4.1 models

> show #!4 models

> show #4.1 models

> select add #7/A:248

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select clear

> select add #7/A:248

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #7/A:254

44 atoms, 48 bonds, 2 residues, 1 model selected  

> select add #7/A:295

66 atoms, 72 bonds, 3 residues, 1 model selected  

> select add #7/C:76

86 atoms, 93 bonds, 4 residues, 1 model selected  
Drag select of 2 atoms, 5 residues, 2 bonds  

> select clear

Drag select of 115 atoms, 198 residues, 122 bonds  

> hide sel atoms

> ~label sel residues

> select #7/A:339

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select clear

> select add #7/A:248

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #7/C:165

44 atoms, 48 bonds, 2 residues, 1 model selected  

> select add #7/C:166

66 atoms, 72 bonds, 3 residues, 1 model selected  

> select add #7/A:253

86 atoms, 93 bonds, 4 residues, 1 model selected  

> select subtract #7/A:253

66 atoms, 72 bonds, 3 residues, 1 model selected  

> select add #7/A:333

88 atoms, 96 bonds, 4 residues, 1 model selected  

> select add #7/A:332

111 atoms, 121 bonds, 5 residues, 1 model selected  

> hide sel atoms

> select add #7/B:17

122 atoms, 132 bonds, 6 residues, 1 model selected  

> select add #7/B:86

133 atoms, 142 bonds, 7 residues, 1 model selected  

> select add #7/B:26

144 atoms, 152 bonds, 8 residues, 1 model selected  

> select add #7/B:25

152 atoms, 159 bonds, 9 residues, 1 model selected  

> select add #7/B:13

163 atoms, 170 bonds, 10 residues, 1 model selected  

> hide sel atoms

> select clear

> show #!1 models

> hide #!1 models

> select clear

> select Mg

26 atoms, 26 residues, 2 models selected  

> show (#!7 & sel) target ab

> select clear

> select #7/D:14@MG

1 atom, 1 residue, 1 model selected  

> color sel magenta

> select clear

> select add #7/C:76

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #7/C:77

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select add #7/A:68

66 atoms, 71 bonds, 3 residues, 1 model selected  

> select add #7/A:67

88 atoms, 95 bonds, 4 residues, 1 model selected  

> select add #7/A:69

108 atoms, 116 bonds, 5 residues, 1 model selected  

> select add #7/A:352

130 atoms, 140 bonds, 6 residues, 1 model selected  

> select add #7/A:351

152 atoms, 164 bonds, 7 residues, 1 model selected  

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> show #!1 models

> hide #!1 models

> color sel byhetero

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> transparency #7/a 80 rings

> transparency #7/a 0 rings

> transparency #7/b 0 rings

> transparency #7/c 0 rings

> show #!1 models

> hide #!1 models

> label sel text "{0.name} {0.number}{0.insertion_code}"

> show #!1 models

> hide #!1 models

> show #5 models

> hide #!7 models

> select add #7

12689 atoms, 14097 bonds, 670 residues, 2 models selected  

> transparency #7/c 80 ribbons

> transparency #5/c 80 ribbons

> transparency #5/a 80 ribbons

> transparency #5/b 80 ribbons

> hide #5 atoms

> select clear

> select Ca

5 atoms, 5 residues, 1 model selected  

> show sel target ab

> select clear

> select #5/F:5@CA

1 atom, 1 residue, 1 model selected  

> select add #5/A:68

24 atoms, 25 bonds, 2 residues, 1 model selected  

> select add #5/A:67

46 atoms, 49 bonds, 3 residues, 1 model selected  

> select add #5/A:69

66 atoms, 70 bonds, 4 residues, 1 model selected  

> select add #5/C:77

89 atoms, 95 bonds, 5 residues, 1 model selected  

> select add #5/C:76

109 atoms, 116 bonds, 6 residues, 1 model selected  

> select add #5/A:351

131 atoms, 140 bonds, 7 residues, 1 model selected  

> select add #5/A:352

153 atoms, 164 bonds, 8 residues, 1 model selected  

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> label sel text "{0.name} {0.number}{0.insertion_code}"

> select #5/F:5@CA

1 atom, 1 residue, 1 model selected  

> ~label sel residues

> select clear

> select #5/F:5@CA

1 atom, 1 residue, 1 model selected  

> color sel magenta

> select clear

> show #!1 models

> show #!7 models

> hide #!1 models

> hide #!5 models

> hide #!7 models

> show #!5 models

> select clear

> select #5/C:77@OP1

1 atom, 1 residue, 1 model selected  

> select up

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #5/C:76@O3'

24 atoms, 25 bonds, 2 residues, 1 model selected  

> select up

43 atoms, 47 bonds, 2 residues, 1 model selected  

> select add #5/A:67@P

44 atoms, 47 bonds, 3 residues, 1 model selected  

> select up

65 atoms, 71 bonds, 3 residues, 1 model selected  

> select add #5/A:68@OP1

66 atoms, 71 bonds, 4 residues, 1 model selected  

> select up

88 atoms, 97 bonds, 4 residues, 1 model selected  

> select add #5/A:351@O3'

89 atoms, 97 bonds, 5 residues, 1 model selected  

> select up

110 atoms, 121 bonds, 5 residues, 1 model selected  

> select add #5/A:352@C4'

111 atoms, 122 bonds, 6 residues, 1 model selected  

> select subtract #5/A:352@C4'

110 atoms, 121 bonds, 5 residues, 1 model selected  

> select add #5/A:352@C4'

111 atoms, 121 bonds, 6 residues, 1 model selected  

> select up

132 atoms, 146 bonds, 6 residues, 1 model selected  

> select add #5/A:69@O5'

133 atoms, 146 bonds, 7 residues, 1 model selected  

> select up

152 atoms, 168 bonds, 7 residues, 1 model selected  

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> color sel byhetero

> select clear

> select #5/F:5@CA

1 atom, 1 residue, 1 model selected  

> select add #5/C:77@OP1

2 atoms, 2 residues, 1 model selected  

> distance #5/F:5@CA #5/C:77@OP1

Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/F CA 5 CA and /C G
77 OP1: 2.14Å  

> select clear

> show #!1 models

> show #!7 models

> hide #!5 models

> hide #!1 models

> select add #7/C:77@OP1

1 atom, 1 residue, 1 model selected  

> select add #7/D:14@MG

2 atoms, 2 residues, 1 model selected  

> distance #7/C:77@OP1 #7/D:14@MG

Distance between Int_1_5mM_Mg_UAA_J2372_1-coot-1_real_space_refined_001.pdb
#7/C G 77 OP1 and /D MG 14 MG: 10.79Å  

> show #!1 models

> show #!5 models

> hide #!1 models

> hide #!7 models

> hide #!5 models

> show #!1 models

> show #!7 models

> hide #!4 models

> show #!4 models

> hide #!1 models

> show #!1 models

> show #!5 models

> hide #!1 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!7 models

> show #!1 models

> hide #!5 models

> hide #!1 models

> show #!5 models

> hide #!5 models

> show #!5 models

> show #!6 models

> hide #!6 models

> show #!7 models

> hide #!5 models

> show #!1 models

> hide #!1 models

> save /Users/bhogeba/Desktop/image4.png supersample 3

> hide #!7 models

> show #!1 models

> show #!5 models

> hide #!1 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!5 models

> hide #!7 models

> show #!5 models

> save /Users/bhogeba/Desktop/image5.png supersample 3

> show #!1 models

> hide #!5 models

> save /Users/bhogeba/Desktop/image6.png supersample 3

> hide #!1 models

> show #!6 models

> show #!7 models

> hide #!6 models

> save /Users/bhogeba/Desktop/image7.png supersample 3

> show #!5 models

> hide #!7 models

> select add #7

12689 atoms, 14097 bonds, 1 pseudobond, 670 residues, 3 models selected  

> select subtract #7

Nothing selected  

> select #5/C:161

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #5/C:162

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select add #5/C:163

63 atoms, 67 bonds, 3 residues, 1 model selected  

> select add #5/C:164

83 atoms, 88 bonds, 4 residues, 1 model selected  

> select add #5/C:165

105 atoms, 112 bonds, 5 residues, 1 model selected  

> select subtract #5/C:161

85 atoms, 91 bonds, 4 residues, 1 model selected  

> select subtract #5/C:162

65 atoms, 70 bonds, 3 residues, 1 model selected  

> show sel atoms

> nucleotides sel ladder

> nucleotides sel atoms

> style nucleic & sel stick

Changed 65 atom styles  

> select add #5/A:294

85 atoms, 91 bonds, 4 residues, 1 model selected  

> select add #5/A:295

107 atoms, 115 bonds, 5 residues, 1 model selected  

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 107 atom styles  

> select add #5/A:293

130 atoms, 140 bonds, 6 residues, 1 model selected  

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 130 atom styles  

> select #5/A:50

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select clear

> select #5/A:296

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #5/A:297

46 atoms, 50 bonds, 2 residues, 1 model selected  

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 46 atom styles  

> hide sel atoms

> select clear

> select #5/A:295

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #5/A:294

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select add #5/A:293

65 atoms, 70 bonds, 3 residues, 1 model selected  

> select add #5/C:165

87 atoms, 94 bonds, 4 residues, 1 model selected  

> select add #5/C:164

107 atoms, 115 bonds, 5 residues, 1 model selected  

> select add #5/C:163

130 atoms, 140 bonds, 6 residues, 1 model selected  

> select subtract #5/C:164

110 atoms, 119 bonds, 5 residues, 1 model selected  

> select add #5/C:164

130 atoms, 140 bonds, 6 residues, 1 model selected  

> select subtract #5/C:163

107 atoms, 115 bonds, 5 residues, 1 model selected  

> select add #5/C:163

130 atoms, 140 bonds, 6 residues, 1 model selected  

> color sel byhetero

> select clear

> select add #5/C:164

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #5/C:165

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select subtract #5/C:165

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #5/A:293

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select add #5/A:294

63 atoms, 67 bonds, 3 residues, 1 model selected  

> select add #5/A:295

85 atoms, 91 bonds, 4 residues, 1 model selected  

> label sel text "{0.name} {0.number}{0.insertion_code}"

> select add #5/C:163

108 atoms, 116 bonds, 5 residues, 1 model selected  

> select add #5/C:165

130 atoms, 140 bonds, 6 residues, 1 model selected  

> label sel text "{0.name} {0.number}{0.insertion_code}"

> select #5/C:164@O2

1 atom, 1 residue, 1 model selected  

> select add #5/A:295@N6

2 atoms, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 select true reveal true retainCurrent true

0 hydrogen bonds found  

> select clear

> select add #5/C:164@O4

1 atom, 1 residue, 1 model selected  

> select add #5/A:295@N6

2 atoms, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 select true reveal true retainCurrent true

0 hydrogen bonds found  

> select clear

> select #5/C:164@O2

1 atom, 1 residue, 1 model selected  

> select add #5/A:294@O2

2 atoms, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 select true reveal true retainCurrent true

0 hydrogen bonds found  

> select #5/A:295@N1

1 atom, 1 residue, 1 model selected  

> select add #5/C:164@N3

2 atoms, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 select true reveal true retainCurrent true

1 hydrogen bonds found  

> select clear

> select add #5/C:163@O2'

1 atom, 1 residue, 1 model selected  

> select clear

> select #5/C:163@O2'

1 atom, 1 residue, 1 model selected  

> select add #5/C:164@O2

2 atoms, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 select true reveal true retainCurrent true

1 hydrogen bonds found  

> select clear

> select add #5/C:165@O4'

1 atom, 1 residue, 1 model selected  

> select add #5/A:293@O6

2 atoms, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 select true reveal true retainCurrent true

1 hydrogen bonds found  

> hbonds sel dashes 6 select true reveal true retainCurrent true

1 hydrogen bonds found  

> select #5/A:295

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #5/A:294

20 atoms, 21 bonds, 1 residue, 1 model selected  

> save /Users/bhogeba/Desktop/image8.png supersample 3

> select clear

> select #5/A:294

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #5/C:164

40 atoms, 42 bonds, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 select true reveal true retainCurrent true

8 hydrogen bonds found  

> hbonds sel dashes 6 select true reveal true retainCurrent true

15 hydrogen bonds found  

> select clear

> select #5/A:295

22 atoms, 24 bonds, 1 residue, 1 model selected  

> ui tool show H-Bonds

> select clear

> select add #5/A:294@O2'

1 atom, 1 pseudobond, 1 residue, 2 models selected  

> select add #5/A:295

23 atoms, 24 bonds, 1 pseudobond, 2 residues, 2 models selected  

> hbonds delete

> select clear

> select #5/C:164@N3

1 atom, 1 residue, 1 model selected  

> select add #5/A:294@O2

2 atoms, 2 residues, 1 model selected  

> hbonds select

Missing "select" keyword's argument  

> ui tool show H-Bonds

> hbonds sel restrict both select true reveal true

0 hydrogen bonds found  

> select #5/C:163@O2'

1 atom, 1 residue, 1 model selected  

> select add #5/C:164@N3

2 atoms, 2 residues, 1 model selected  

> hbonds sel restrict both select true reveal true

0 hydrogen bonds found  

> select #5/A:294@O2

1 atom, 1 residue, 1 model selected  

> select #5/A:294@N3

1 atom, 1 residue, 1 model selected  

> select #5/A:294

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #5/C:164@N3

1 atom, 1 residue, 1 model selected  

> select add #5/A:294@O2

2 atoms, 2 residues, 1 model selected  

> hbonds sel restrict both select true reveal true

0 hydrogen bonds found  

> select add #5/C:164@N3

1 atom, 1 residue, 1 model selected  

> select #5/C:164@O4

1 atom, 1 residue, 1 model selected  

> select add #5/A:295@N1

2 atoms, 2 residues, 1 model selected  

> select clear

> select #5/A:295@N1

1 atom, 1 residue, 1 model selected  

> select add #5/C:164@N3

2 atoms, 2 residues, 1 model selected  

> hbonds sel restrict both select true reveal true

1 hydrogen bonds found  

> select clear

> select #5/C:163@O2'

1 atom, 1 residue, 1 model selected  

> select clear

> select #5/C:164@O2'

1 atom, 1 residue, 1 model selected  

> select add #5/A:293@N2

2 atoms, 2 residues, 1 model selected  

> hbonds sel restrict both select true reveal true

0 hydrogen bonds found  

> select #5/A:295@N1

1 atom, 1 residue, 1 model selected  

> select add #5/C:164@N3

2 atoms, 2 residues, 1 model selected  

> hbonds sel restrict both select true reveal true

1 hydrogen bonds found  

> select clear

> save /Users/bhogeba/Desktop/image9.png supersample 3

> save /Users/bhogeba/Desktop/image10.png supersample 3

> select add #5/C:0

22 atoms, 24 bonds, 1 residue, 1 model selected  

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 22 atom styles  

> select clear

> select #5/C:158

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #5/C:159

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select add #5/C:157

63 atoms, 67 bonds, 3 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> select clear

> select #5/C:0

22 atoms, 24 bonds, 1 residue, 1 model selected  

> color sel byhetero

> save /Users/bhogeba/Desktop/image11.png supersample 3

> ui tool show "Model Panel"

> ui tool show "Side View"

> select clear

> select #5/F:2@CA

1 atom, 1 residue, 1 model selected  

> color sel hot pink

> color sel orange

> color sel red

> color sel orange red

> color sel orange

> color sel yellow

> color sel orange

> color sel cornflower blue

> color sel light sea green

> color sel dodger blue

> color sel blue

> color sel pale violet red

> color sel deep pink

> color sel magenta

> color sel rebecca purple

> color sel dark slate blue

> color sel slate blue

> color sel medium slate blue

> color sel dim gray

> color sel pale green

> color sel light green

> color sel burly wood

> color sel light coral

> color sel burly wood

> color sel tan

> color sel burly wood

> color sel aquamarine

> color sel sky blue

> color sel light sky blue

> color sel light blue

> color sel light steel blue

> color sel silver

> color sel thistle

> color sel rosy brown

> ui tool show Distances

> select #5/F:5@CA

1 atom, 1 residue, 1 model selected  

> select add #5/A:67@OP1

2 atoms, 2 residues, 1 model selected  

> distance #5/F:5@CA #5/A:67@OP1

Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/F CA 5 CA and /A A
67 OP1: 1.88Å  

> select clear

> select #5/A:67@OP2

1 atom, 1 residue, 1 model selected  

> select add #5/F:2@CA

2 atoms, 2 residues, 1 model selected  

> distance #5/A:67@OP2 #5/F:2@CA

Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/A A 67 OP2 and /F
CA 2 CA: 2.12Å  

> select #5/F:5@CA

1 atom, 1 residue, 1 model selected  

> select add #5/A:352@OP2

2 atoms, 2 residues, 1 model selected  

> distance #5/F:5@CA #5/A:352@OP2

Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/F CA 5 CA and /A A
352 OP2: 1.95Å  

> select #5/F:5@CA

1 atom, 1 residue, 1 model selected  

> select add #5/A:351@OP1

2 atoms, 2 residues, 1 model selected  

> distance #5/F:5@CA #5/A:351@OP1

Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/F CA 5 CA and /A A
351 OP1: 1.91Å  

> distance style symbol false

> distance style symbol true

> label size 2

> label size 1

> label size 150

> label height 1.5

> label height 1

> label height 0.5

> select #5/F:5@CA

1 atom, 1 residue, 1 model selected  

> select add #5/C:76@O3'

2 atoms, 2 residues, 1 model selected  

> distance #5/F:5@CA #5/C:76@O3'

Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/F CA 5 CA and /C U
76 O3': 2.21Å  

> label height 0.5

> select #5/F:2@CA

1 atom, 1 residue, 1 model selected  

> select add #5/C:77@OP1

2 atoms, 2 residues, 1 model selected  

> distance #5/F:2@CA #5/C:77@OP1

Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/F CA 2 CA and /C G
77 OP1: 2.71Å  

> label height 0.5

> select #5/A:68@OP2

1 atom, 1 residue, 1 model selected  

> select add #5/F:2@CA

2 atoms, 2 residues, 1 model selected  

> distance #5/A:68@OP2 #5/F:2@CA

Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/A G 68 OP2 and /F
CA 2 CA: 2.89Å  

> label height 0.5

> select add #5/F:2@CA

21 atoms, 2 residues, 1 model selected  
Exactly two atoms must be selected!  

> select clear

> nucleotides sel atoms

> style nucleic & sel stick

Changed 20 atom styles  

> show sel atoms

> select clear

> select #5/A:69@O4

1 atom, 1 residue, 1 model selected  

> select add #5/F:2@CA

2 atoms, 2 residues, 1 model selected  

> distance #5/A:69@O4 #5/F:2@CA

Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/A U 69 O4 and /F CA
2 CA: 1.91Å  

> label height 0.5

> select clear

> select #5/F:2@CA

1 atom, 1 residue, 1 model selected  

> ui tool show "Selection Inspector"

> style sel ball

Changed 1 atom style  

> style sel stick

Changed 1 atom style  

> style sel ball

Changed 1 atom style  

> style sel sphere

Changed 1 atom style  

> select down

1 atom, 1 residue, 1 model selected  


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.10rc202506100450 (2025-06-10)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/bhogeba/T4_dimeric tRNA/Gst_RNP/J1387_GstRNR.pdb"

Chain information for J1387_GstRNR.pdb #1  
---  
Chain | Description  
A | No description available  

Computing secondary structure  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

   Hardware Overview:

     Model Name: MacBook Pro
     Model Identifier: Mac15,6
     Model Number: Z1AU00299LL/A
     Chip: Apple M3 Pro
     Total Number of Cores: 11 (5 Performance and 6 Efficiency)
     Memory: 18 GB
     System Firmware Version: 13822.81.10
     OS Loader Version: 13822.81.10

Software:

   System Software Overview:

     System Version: macOS 26.3.1 (25D2128)
     Kernel Version: Darwin 25.3.0
     Time since boot: 9 days, 19 hours, 58 minutes

Graphics/Displays:

   Apple M3 Pro:

     Chipset Model: Apple M3 Pro
     Type: GPU
     Bus: Built-In
     Total Number of Cores: 14
     Vendor: Apple (0x106b)
     Metal Support: Metal 4
     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
       DELL P2715Q:
         Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
         UI Looks like: 1920 x 1080 @ 30.00Hz
         Mirror: Off
         Online: Yes
         Rotation: Supported
       DELL P2715Q:
         Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
         UI Looks like: 1920 x 1080 @ 60.00Hz
         Mirror: Off
         Online: Yes
         Rotation: Supported


Installed Packages:
   alabaster: 1.0.0
   appdirs: 1.4.4
   appnope: 0.1.4
   asttokens: 3.0.0
   auditwheel: 6.4.0
   babel: 2.17.0
   beautifulsoup4: 4.13.3
   blockdiag: 3.0.0
   blosc2: 3.3.4
   build: 1.2.2.post1
   certifi: 2023.11.17
   cftime: 1.6.4.post1
   charset-normalizer: 3.4.2
   ChimeraX-AddCharge: 1.5.19
   ChimeraX-AddH: 2.2.7
   ChimeraX-AlignmentAlgorithms: 2.0.2
   ChimeraX-AlignmentHdrs: 3.6.1
   ChimeraX-AlignmentMatrices: 2.1
   ChimeraX-Alignments: 2.20.2
   ChimeraX-AlphaFold: 1.0.1
   ChimeraX-AltlocExplorer: 1.1.2
   ChimeraX-AmberInfo: 1.0
   ChimeraX-Aniso: 1.1.4
   ChimeraX-Arrays: 1.1
   ChimeraX-Atomic: 1.60.7
   ChimeraX-AtomicLibrary: 14.1.18
   ChimeraX-AtomSearch: 2.0.1
   ChimeraX-AxesPlanes: 2.4
   ChimeraX-BasicActions: 1.1.3
   ChimeraX-BILD: 1.0
   ChimeraX-BlastProtein: 3.0.0
   ChimeraX-Boltz: 1.0
   ChimeraX-BondRot: 2.0.4
   ChimeraX-BugReporter: 1.0.2
   ChimeraX-BuildStructure: 2.13.1
   ChimeraX-Bumps: 1.0
   ChimeraX-BundleBuilder: 1.5.1
   ChimeraX-ButtonPanel: 1.0.1
   ChimeraX-CageBuilder: 1.0.1
   ChimeraX-CellPack: 1.0
   ChimeraX-Centroids: 1.4
   ChimeraX-ChangeChains: 1.1
   ChimeraX-CheckWaters: 1.5
   ChimeraX-ChemGroup: 2.0.2
   ChimeraX-Clashes: 2.3
   ChimeraX-ColorActions: 1.0.5
   ChimeraX-ColorGlobe: 1.0
   ChimeraX-ColorKey: 1.5.8
   ChimeraX-CommandLine: 1.3
   ChimeraX-ConnectStructure: 2.0.1
   ChimeraX-Contacts: 1.0.1
   ChimeraX-Core: 1.10rc202506100450
   ChimeraX-CoreFormats: 1.2
   ChimeraX-coulombic: 1.4.5
   ChimeraX-Crosslinks: 1.0
   ChimeraX-Crystal: 1.0
   ChimeraX-CrystalContacts: 1.0.1
   ChimeraX-DataFormats: 1.2.4
   ChimeraX-Dicom: 1.2.7
   ChimeraX-DistMonitor: 1.4.2
   ChimeraX-DockPrep: 1.1.4
   ChimeraX-Dssp: 2.0
   ChimeraX-EMDB-SFF: 1.0
   ChimeraX-ESMFold: 1.0
   ChimeraX-FileHistory: 1.0.1
   ChimeraX-FunctionKey: 1.0.1
   ChimeraX-Geometry: 1.3
   ChimeraX-gltf: 1.0
   ChimeraX-Graphics: 1.4.1
   ChimeraX-Hbonds: 2.5.1
   ChimeraX-Help: 1.3
   ChimeraX-HKCage: 1.3
   ChimeraX-IHM: 1.1
   ChimeraX-ImageFormats: 1.2
   ChimeraX-IMOD: 1.0
   ChimeraX-IO: 1.0.3
   ChimeraX-ItemsInspection: 1.0.1
   ChimeraX-IUPAC: 1.0
   ChimeraX-KVFinder: 1.6.2
   ChimeraX-Label: 1.1.14
   ChimeraX-ListInfo: 1.2.2
   ChimeraX-Log: 1.2
   ChimeraX-LookingGlass: 1.1
   ChimeraX-Maestro: 1.9.1
   ChimeraX-Map: 1.3
   ChimeraX-MapData: 2.0
   ChimeraX-MapEraser: 1.0.1
   ChimeraX-MapFilter: 2.0.1
   ChimeraX-MapFit: 2.0
   ChimeraX-MapSeries: 2.1.1
   ChimeraX-Markers: 1.0.1
   ChimeraX-Mask: 1.0.2
   ChimeraX-MatchMaker: 2.2.1
   ChimeraX-MCopy: 1.0
   ChimeraX-MDcrds: 2.10.1
   ChimeraX-MedicalToolbar: 1.1
   ChimeraX-Meeting: 1.0.1
   ChimeraX-MLP: 1.1.1
   ChimeraX-mmCIF: 2.16
   ChimeraX-MMTF: 2.2
   ChimeraX-ModelArchive: 1.0
   ChimeraX-Modeller: 1.5.19
   ChimeraX-ModelPanel: 1.5.1
   ChimeraX-ModelSeries: 1.0.1
   ChimeraX-Mol2: 2.0.3
   ChimeraX-Mole: 1.0
   ChimeraX-Morph: 1.0.2
   ChimeraX-MouseModes: 1.2
   ChimeraX-Movie: 1.0
   ChimeraX-MutationScores: 1.0
   ChimeraX-Neuron: 1.0
   ChimeraX-Nifti: 1.2
   ChimeraX-NMRSTAR: 1.0.2
   ChimeraX-NRRD: 1.2
   ChimeraX-Nucleotides: 2.0.3
   ChimeraX-OpenCommand: 1.14.1
   ChimeraX-OrthoPick: 1.0.1
   ChimeraX-PDB: 2.7.10
   ChimeraX-PDBBio: 1.0.1
   ChimeraX-PDBLibrary: 1.0.4
   ChimeraX-PDBMatrices: 1.0
   ChimeraX-PickBlobs: 1.0.1
   ChimeraX-Positions: 1.0
   ChimeraX-PresetMgr: 1.1.3
   ChimeraX-ProfileGrids: 1.1.2
   ChimeraX-PubChem: 2.2
   ChimeraX-QScore: 1.2
   ChimeraX-ReadPbonds: 1.0.1
   ChimeraX-Registration: 1.1.2
   ChimeraX-RemoteControl: 1.0
   ChimeraX-RenderByAttr: 1.6.3
   ChimeraX-RenumberResidues: 1.1
   ChimeraX-ResidueFit: 1.0.1
   ChimeraX-RestServer: 1.3.1
   ChimeraX-RNALayout: 1.0
   ChimeraX-RotamerLibMgr: 4.0
   ChimeraX-RotamerLibsDunbrack: 2.0
   ChimeraX-RotamerLibsDynameomics: 2.0
   ChimeraX-RotamerLibsRichardson: 2.0
   ChimeraX-SaveCommand: 1.5.1
   ChimeraX-SchemeMgr: 1.0
   ChimeraX-SDF: 2.0.3
   ChimeraX-Segger: 1.0
   ChimeraX-Segment: 1.0.1
   ChimeraX-Segmentations: 3.5.7
   ChimeraX-SelInspector: 1.0
   ChimeraX-SeqView: 2.17.1
   ChimeraX-Shape: 1.1
   ChimeraX-Shell: 1.0.1
   ChimeraX-Shortcuts: 1.2.1
   ChimeraX-ShowSequences: 1.0.3
   ChimeraX-SideView: 1.0.1
   ChimeraX-SimilarStructures: 1.0.1
   ChimeraX-Smiles: 2.1.2
   ChimeraX-SmoothLines: 1.0
   ChimeraX-SpaceNavigator: 1.0
   ChimeraX-StdCommands: 1.19.1
   ChimeraX-STL: 1.0.1
   ChimeraX-Storm: 1.0
   ChimeraX-StructMeasure: 1.2.1
   ChimeraX-Struts: 1.0.1
   ChimeraX-Surface: 1.0.1
   ChimeraX-SwapAA: 2.0.1
   ChimeraX-SwapRes: 2.5.2
   ChimeraX-TapeMeasure: 1.0
   ChimeraX-TaskManager: 1.0
   ChimeraX-Test: 1.0
   ChimeraX-Toolbar: 1.2.3
   ChimeraX-ToolshedUtils: 1.2.4
   ChimeraX-Topography: 1.0
   ChimeraX-ToQuest: 1.0
   ChimeraX-Tug: 1.0.1
   ChimeraX-UI: 1.45.1
   ChimeraX-Umap: 1.0
   ChimeraX-uniprot: 2.3.1
   ChimeraX-UnitCell: 1.0.1
   ChimeraX-ViewDockX: 1.4.4
   ChimeraX-VIPERdb: 1.0
   ChimeraX-Vive: 1.1
   ChimeraX-VolumeMenu: 1.0.1
   ChimeraX-vrml: 1.0
   ChimeraX-VTK: 1.0
   ChimeraX-WavefrontOBJ: 1.0
   ChimeraX-WebCam: 1.0.2
   ChimeraX-WebServices: 1.1.5
   ChimeraX-Zone: 1.0.1
   colorama: 0.4.6
   comm: 0.2.2
   contourpy: 1.3.2
   coverage: 7.8.2
   cxservices: 1.2.3
   cycler: 0.12.1
   Cython: 3.0.12
   debugpy: 1.8.14
   decorator: 5.2.1
   docutils: 0.21.2
   executing: 2.2.0
   filelock: 3.18.0
   fonttools: 4.58.2
   funcparserlib: 2.0.0a0
   glfw: 2.9.0
   grako: 3.16.5
   h5py: 3.14.0
   html2text: 2024.2.26
   idna: 3.10
   ihm: 2.2
   imagecodecs: 2024.6.1
   imagesize: 1.4.1
   iniconfig: 2.1.0
   ipykernel: 6.29.5
   ipython: 8.26.0
   ipywidgets: 8.1.7
   jedi: 0.19.1
   Jinja2: 3.1.6
   jupyter_client: 8.6.3
   jupyter_core: 5.8.1
   jupyterlab_widgets: 3.0.15
   kiwisolver: 1.4.8
   line_profiler: 4.2.0
   lxml: 5.3.1
   lz4: 4.4.4
   MarkupSafe: 3.0.2
   matplotlib: 3.10.1
   matplotlib-inline: 0.1.7
   msgpack: 1.1.0
   ndindex: 1.10.0
   nest-asyncio: 1.6.0
   netCDF4: 1.6.5
   networkx: 3.3
   nibabel: 5.2.0
   nptyping: 2.5.0
   numexpr: 2.11.0
   numpy: 1.26.4
   OpenMM: 8.2.0
   openvr: 1.26.701
   packaging: 24.2
   ParmEd: 4.2.2
   parso: 0.8.4
   pep517: 0.13.1
   pexpect: 4.9.0
   pickleshare: 0.7.5
   pillow: 10.4.0
   pip: 25.0.1
   pkginfo: 1.11.1
   platformdirs: 4.3.8
   pluggy: 1.6.0
   prompt_toolkit: 3.0.51
   psutil: 7.0.0
   ptyprocess: 0.7.0
   pure_eval: 0.2.3
   py-cpuinfo: 9.0.0
   pycollada: 0.8
   pydicom: 2.4.4
   pyelftools: 0.32
   Pygments: 2.18.0
   pynmrstar: 3.3.5
   pynrrd: 1.0.0
   PyOpenGL: 3.1.9
   PyOpenGL-accelerate: 3.1.9
   pyopenxr: 1.1.4501
   pyparsing: 3.2.3
   pyproject_hooks: 1.2.0
   PyQt6-commercial: 6.8.1
   PyQt6-Qt6: 6.8.2
   PyQt6-WebEngine-commercial: 6.8.0
   PyQt6-WebEngine-Qt6: 6.8.2
   PyQt6_sip: 13.10.0
   pytest: 8.4.0
   pytest-cov: 6.1.1
   python-dateutil: 2.9.0.post0
   pytz: 2025.2
   pyzmq: 26.4.0
   qtconsole: 5.5.2
   QtPy: 2.4.3
   qtshim: 1.1
   RandomWords: 0.4.0
   requests: 2.32.3
   roman-numerals-py: 3.1.0
   scipy: 1.14.0
   setuptools: 78.1.0
   sfftk-rw: 0.8.1
   six: 1.16.0
   snowballstemmer: 3.0.1
   sortedcontainers: 2.4.0
   soupsieve: 2.7
   Sphinx: 8.2.3
   sphinx-autodoc-typehints: 3.1.0
   sphinxcontrib-applehelp: 2.0.0
   sphinxcontrib-blockdiag: 3.0.0
   sphinxcontrib-devhelp: 2.0.0
   sphinxcontrib-htmlhelp: 2.1.0
   sphinxcontrib-jsmath: 1.0.1
   sphinxcontrib-qthelp: 2.0.0
   sphinxcontrib-serializinghtml: 2.0.0
   stack-data: 0.6.3
   superqt: 0.7.1
   tables: 3.10.2
   tcia_utils: 1.5.1
   tifffile: 2025.3.13
   tinyarray: 1.2.4
   tornado: 6.5.1
   traitlets: 5.14.3
   typing_extensions: 4.14.0
   tzdata: 2025.2
   urllib3: 2.4.0
   wcwidth: 0.2.13
   webcolors: 24.11.1
   wheel: 0.45.1
   wheel-filename: 1.4.2
   widgetsnbextension: 4.0.14
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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

Last modified 9 years ago Last modified on Jan 4, 2017, 10:45:36 AM
Note: See TracWiki for help on using the wiki.