wiki:TracQuery

Version 2 (modified by trac, 9 years ago) ( diff )

--

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 14036)

1 2 3 4 5 6 7 8 9 10 11 →
Ticket Resolution Summary Owner Reporter
#20549 limitation Session restore: Unknown class name 'SceneAnimation' Zach Pearson jguardad@…
#20546 duplicate Crash on Mac waking from sleep Tom Goddard mimi.mayer@…
#20545 not a bug Proofpoint Essentials - Quarantine Digest Eric Pettersen do-not-reply@…
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 14036)

1 2 3 4 5 6 7 8 9 10 11 →
Ticket Resolution Summary Owner Reporter
#20549 limitation Session restore: Unknown class name 'SceneAnimation' Zach Pearson jguardad@…
Description 
The following bug report has been submitted:
Platform:        macOS-12.7.6-x86_64-i386-64bit
ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.11 (2025-12-17)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/johnguardado/Desktop/OhyA/R121_E122.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 847, in restore  
cls = name.class_of(self)  
^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 228, in class_of  
cls = bundle_info.get_class(class_name, session.logger)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 487, in get_class  
return f(class_name)  
^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/animations/__init__.py", line 24, in get_class  
raise ValueError("Unknown class name '%s'" % class_name)  
ValueError: Unknown class name 'SceneAnimation'  
  

> view name session-start

opened ChimeraX session  




OpenGL version: 4.1 INTEL-18.8.16
OpenGL renderer: Intel(R) HD Graphics 6000
OpenGL vendor: Intel Inc.

Python: 3.11.9
Locale: 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: MacBookAir7,1
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 1.6 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 3 MB
      Hyper-Threading Technology: Enabled
      Memory: 4 GB
      System Firmware Version: 489.0.0.0.0
      OS Loader Version: 540.120.3~37
      SMC Version (system): 2.26f2

Software:

    System Software Overview:

      System Version: macOS 12.7.6 (21H1320)
      Kernel Version: Darwin 21.6.0
      Time since boot: 9:53

Graphics/Displays:

    Intel HD Graphics 6000:

      Chipset Model: Intel HD Graphics 6000
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x1626
      Revision ID: 0x0009
      Metal Family: Supported, Metal GPUFamily macOS 1
      Displays:
        Color LCD:
          Display Type: LCD
          Resolution: 1366 x 768 (WSGA - Wide eXtended Graphics Array)
          UI Looks like: 1366 x 768
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          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: 4.12.0
    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
    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: 2.7.11
    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: 7.13.0
    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: 4.25.1
    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: 3.2.5
    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
    pytz: 2025.2
    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: 4.0.0
    roman-numerals-py: 4.0.0
    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
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.2.0
    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
    sse-starlette: 3.0.4
    stack-data: 0.6.3
    starlette: 0.50.0
    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: 2.6.2
    uvicorn: 0.38.0
    wcwidth: 0.2.14
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.15
    yarl: 1.22.0
#20546 duplicate Crash on Mac waking from sleep Tom Goddard mimi.mayer@…
Description 
The following bug report has been submitted:
Platform:        macOS-26.5-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 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 0x00000001f4121e80 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, openmm._openmm, openmm.app.internal.compiled, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, chimerax.atom_search.ast (total: 62)


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===== Log before crash start =====
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/mylanmayer/Library/CloudStorage/OneDrive-
> UCSF/Documents/Integrin/Mg_Apo_Extended_Closed/extended_closed_alpha-
> beta_interactions_labeled_v2.cxs

Opened cryosparc_P6_J300_007_volume_map_sharp_z_flip.mrc as #2, grid size
300,300,300, pixel 0.834, shown at level 0.401, step 1, values float32  
Log from Wed Jan 7 14:11:53 2026 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/mylanmayer/Library/CloudStorage/OneDrive-
> UCSF/Desktop/extended_closed_initial_model_ordered_chainA_goodBGOL_real_space_refined_002_isolde_v3.pdb

Chain information for
extended_closed_initial_model_ordered_chainA_goodBGOL_real_space_refined_002_isolde_v3.pdb
#1  
---  
Chain | Description  
A | No description available  
B | No description available  
G | No description available  
L | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
W | No description available  
X | No description available  
Y | No description available  
c | No description available  
f | No description available  
i | No description available  
  

> style stick

Changed 15637 atom styles  

> open
> /Users/mylanmayer/Downloads/cryosparc_P6_J300_007_volume_map_sharp_z_flip.mrc

Opened cryosparc_P6_J300_007_volume_map_sharp_z_flip.mrc as #2, grid size
300,300,300, pixel 0.834, shown at level 0.183, step 2, values float32  

> volume #2 color #bf9fb5

> volume #2 color #bfae74

> volume #2 color #ffe89b

> volume #2 color #ffe5af

> volume #2 color #ffd1d6

> volume #2 step 1

> volume #2 level 0.3579

> volume #2 color #ffd1d676

> volume #2 color #ffd1d675

> open /Users/mylanmayer/Library/CloudStorage/OneDrive-
> UCSF/Desktop/extended_closed_initial_model_ordered_chainA_goodBGOL_real_space_refined_002_isolde_v3.pdb

Chain information for
extended_closed_initial_model_ordered_chainA_goodBGOL_real_space_refined_002_isolde_v3.pdb
#3  
---  
Chain | Description  
A | No description available  
B | No description available  
G | No description available  
L | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
W | No description available  
X | No description available  
Y | No description available  
c | No description available  
f | No description available  
i | No description available  
  

> hide #!1 models

> show #!1 models

> select add #3

15637 atoms, 15784 bonds, 1 pseudobond, 1031 residues, 2 models selected  

> close #1

> select subtract #3

Nothing selected  

> style stick

Changed 15637 atom styles  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 8 residues in model #3 to IUPAC-IUB
standards.  
Chain information for
extended_closed_initial_model_ordered_chainA_goodBGOL_real_space_refined_002_isolde_v3.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/G | No description available  
1.2/L | No description available  
1.2/O | No description available  
1.2/P | No description available  
1.2/Q | No description available  
1.2/R | No description available  
1.2/S | No description available  
1.2/W | No description available  
1.2/X | No description available  
1.2/Y | No description available  
1.2/c | No description available  
1.2/f | No description available  
1.2/i | No description available  
  

> clipper associate #2 toModel #1

Opened cryosparc_P6_J300_007_volume_map_sharp_z_flip.mrc as #1.1.1.1, grid
size 300,300,300, pixel 0.834, shown at step 1, values float32  

> isolde sim start /A-i

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.6323

> volume #1.1.1.1 level 0.3786

> volume #1.1.1.1 level 0.2676

> volume #1.1.1.1 level 0.2993

> ui mousemode right "isolde tug residue"

> isolde sim pause

> isolde tutorial

> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  

> st first

> isolde shorthand
    
    
    Registered ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  

> st 775

Unrecognised residue argument! If specified, must be either a residue,
"first", "last", "next" or "prev"  

> st 775

Unrecognised residue argument! If specified, must be either a residue,
"first", "last", "next" or "prev"  

> st #1.2/A:775

[Repeated 1 time(s)]

> isolde sim resume

> volume #1.1.1.1 level 0.2517

> isolde pepflip /A:777

> ui tool show "Ramachandran Plot"

> isolde pepflip /A:777

> st prev

[Repeated 1 time(s)]

> st

[Repeated 2 time(s)]

> st prev

> isolde pepflip /A:775

> st

> st prev

> isolde pepflip #!1.2/A:775

[Repeated 1 time(s)]

> st prev

> st

[Repeated 1 time(s)]

> isolde pepflip /A:776

[Repeated 1 time(s)]

> isolde cisflip /A:776

[Repeated 1 time(s)]

> st

[Repeated 2 time(s)]

> st prev

[Repeated 3 time(s)]

> isolde pepflip /A:775

> st prev

> st

[Repeated 1 time(s)]

> volume #1.1.1.1 level 0.3469

> st prev

[Repeated 1 time(s)]

> st

[Repeated 2 time(s)]

> isolde pepflip /A:777

[Repeated 1 time(s)]

> isolde cisflip /A:777

[Repeated 1 time(s)]

> isolde pepflip /A:776

[Repeated 1 time(s)]

> isolde pepflip /A:778

[Repeated 4 time(s)]

> isolde pepflip #!1.2/A:779

[Repeated 1 time(s)]

> isolde pepflip /A:780

> volume #1.1.1.1 level 0.3151

> st

[Repeated 1 time(s)]

> '

incomplete quoted text  

> st

[Repeated 5 time(s)]

> volume #1.1.1.1 level 0.2993

> st

> isolde pepflip /A:786

> st prev

> volume #1.1.1.1 level 0.2834

> st

[Repeated 6 time(s)]

> volume #1.1.1.1 level 0.3469

> st

[Repeated 14 time(s)]

> isolde sim pause

> st

> volume #1.1.1.1 level 0.4103

> st

[Repeated 42 time(s)]

> '

incomplete quoted text  

> st

[Repeated 6 time(s)]

> st prev

> ui mousemode right "isolde tug atom"

> isolde sim resume

> st prev

> st

[Repeated 47 time(s)]

> isolde sim pause

> st

[Repeated 3 time(s)]

> isolde sim resume

> st

[Repeated 2 time(s)]

> ui mousemode right "isolde tug residue"

> st

[Repeated 19 time(s)]

> ui mousemode right "isolde tug residue"

[Repeated 1 time(s)]

> ui mousemode right "isolde tug atom"

> st

[Repeated 2 time(s)]

> isolde sim pause

> st

[Repeated 13 time(s)]

> st #1.2/A:775

> st \

Unrecognised residue argument! If specified, must be either a residue,
"first", "last", "next" or "prev"  

> st

[Repeated 1 time(s)]

> isolde sim resume

> isolde sim pause

> isolde sim resume

> isolde pepflip /A:779

> isolde pepflip /A:778

> isolde cisflip /A:779

> st

> st prev

> volume #1.1.1.1 level 0.3469

> isolde pepflip /A:776

[Repeated 1 time(s)]

> isolde cisflip /A:776

[Repeated 1 time(s)]

> isolde cisflip /A:777

[Repeated 1 time(s)]

> isolde pepflip #!1.2/A:779

[Repeated 1 time(s)]

> st prev

> isolde sim pause

> save /Users/mylanmayer/Library/CloudStorage/OneDrive-
> UCSF/Desktop/extended_closed_initial_model_ordered_chainA_goodBGOL_real_space_refined_002_isolde_v4.pdb

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 5 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> close

> open /Users/mylanmayer/Library/CloudStorage/OneDrive-
> UCSF/Desktop/extended_closed_initial_model_ordered_chainA_goodBGOL_real_space_refined_002_isolde_v4.pdb

Chain information for
extended_closed_initial_model_ordered_chainA_goodBGOL_real_space_refined_002_isolde_v4.pdb
#1  
---  
Chain | Description  
A | No description available  
B | No description available  
G | No description available  
L | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
W | No description available  
X | No description available  
Y | No description available  
c | No description available  
f | No description available  
i | No description available  
  

> style stick

Changed 15637 atom styles  

> open /Users/mylanmayer/Library/CloudStorage/OneDrive-
> UCSF/Desktop/extended_closed_initial_model_ordered_chainA_goodBGOL_real_space_refined_002_isolde_v4.pdb
> format pdb

Chain information for
extended_closed_initial_model_ordered_chainA_goodBGOL_real_space_refined_002_isolde_v4.pdb
#2  
---  
Chain | Description  
A | No description available  
B | No description available  
G | No description available  
L | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
W | No description available  
X | No description available  
Y | No description available  
c | No description available  
f | No description available  
i | No description available  
  

> style stick

Changed 31274 atom styles  

> select add #2

15637 atoms, 15784 bonds, 1 pseudobond, 1031 residues, 2 models selected  

> close #2

> open
> /Users/mylanmayer/Downloads/cryosparc_P6_J300_007_volume_map_sharp_z_flip.mrc

Opened cryosparc_P6_J300_007_volume_map_sharp_z_flip.mrc as #2, grid size
300,300,300, pixel 0.834, shown at level 0.183, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.3676

> label #1-2 attribute name

> ~label #1-2 atoms

> ~label #1-2 residues

> ui tool show "Change Chain IDs"

> select O

1569 atoms, 1031 residues, 1 model selected  

> hide #!2 models

> select clear

> select /L

284 atoms, 286 bonds, 22 residues, 1 model selected  

> select /O

721 atoms, 725 bonds, 46 residues, 1 model selected  

> select /B

4445 atoms, 4490 bonds, 285 residues, 1 model selected  

> select clear

> select /L,O

1005 atoms, 1013 bonds, 68 residues, 1 model selected  

> select /L,O,B

5450 atoms, 5503 bonds, 353 residues, 1 model selected  

> select /L,O,B,G

6585 atoms, 6646 bonds, 427 residues, 1 model selected  

> select /L,O,B,B

5450 atoms, 5503 bonds, 353 residues, 1 model selected  

> select /L,O,B,G

6585 atoms, 6646 bonds, 427 residues, 1 model selected  

> select /L,O,B,G,D

6585 atoms, 6646 bonds, 427 residues, 1 model selected  

> select /L,O,B,G,D,N

6585 atoms, 6646 bonds, 427 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel B

Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (B/4/)  

> select /L,O,B,G,D,N

6585 atoms, 6646 bonds, 427 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> ui tool show "Show Sequence Viewer"

> ui tool show "Change Chain IDs"

> changechains sel z

Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (z/7/)  

> show #!2 models

> color #2 #b2b2b274 models

> color #2 #bf8e7474 models

> color #2 #bf8e7475 models

> set bgColor white

> ui mousemode right zoom

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> volume #2 level 0.2166

> volume #2 level 0.4011

> color sel byhetero

> select H

7723 atoms, 1031 residues, 1 model selected  

> hide sel target a

> ui mousemode right translate

> select /L,O,B,G,D,N

6585 atoms, 6646 bonds, 427 residues, 1 model selected  

> color sel red

> select clear

> select /A

8399 atoms, 8492 bonds, 1 pseudobond, 556 residues, 2 models selected  

> color (#!1 & sel) cornflower blue

> select clear

> hide #!1 models

> show #!1 models

> hide #!2 models

> open /Users/mylanmayer/Library/CloudStorage/OneDrive-
> UCSF/Documents/Integrin/bent_model_9-19-25.pdb

Chain information for bent_model_9-19-25.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
  

> style stick

Changed 27059 atom styles  

> hide #!1 models

> select /L,O,B,G,D,N

10660 atoms, 10783 bonds, 958 residues, 2 models selected  

> color (#!3 & sel) orange

> color (#!3 & sel) orange red

> color (#!3 & sel) orange

> select /F,J,C,A,I,E,K,M,H

14970 atoms, 15187 bonds, 4 pseudobonds, 1415 residues, 4 models selected  

> color (#!3 & sel) cyan

> select clear

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!3 models

> select #1/B:223@CD

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:551@CG

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:217@CB

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:523@CD

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:195@CG

1 atom, 1 residue, 1 model selected  

> select #1/B:195@CD

1 atom, 1 residue, 1 model selected  

> select #1/B:195@CG

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:617@CZ

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:47@CD

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:641@CZ

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:194@CG

1 atom, 1 residue, 1 model selected  

> color sel dim gray

Drag select of 16 atoms, 15 bonds  

> select clear

> select #1/A:50@CZ

1 atom, 1 residue, 1 model selected  
Drag select of 2 bonds  

> select clear

> select #1/A:50@CZ

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:193@CB

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:188@CE

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:212@CZ

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:76@CZ

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:190@C

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:69@CH2

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:191@C

1 atom, 1 residue, 1 model selected  

> color sel dim gray

[Repeated 1 time(s)]

> select #1/B:191@C

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:92@SD

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:378@SD

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:404@CZ2

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:517@SD

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:250@CG

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:487@CG1

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:218@CB

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:219@CA

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:461@CZ

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:181@C

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:490@CZ

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:184@C

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:436@CZ

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:145@CG

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:142@CD

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:96@CB

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:98@CB

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:143@CE2

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:140@C

1 atom, 1 residue, 1 model selected  

> select #1/A:138@CD

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:141@CG

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:101@CE

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:439@CZ

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:185@C

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:383@CE1

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:189@CG

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:399@CB

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:374@CZ

1 atom, 1 residue, 1 model selected  

> select #1/B:144@CG

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:434@CB

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:146@CB

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:553@CZ

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:184@CA

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select /A:76

28 atoms, 26 bonds, 2 residues, 2 models selected  

> select /B:92

25 atoms, 23 bonds, 2 residues, 2 models selected  

> save /Users/mylanmayer/Documents/Integrin/extended_closed_alpha-
> beta_interactions_labeled.cxs

> select clear

> select #1/A:432@C

1 atom, 1 residue, 1 model selected  
Drag select of 2 bonds  

> select clear

> select #1/A:432@C

1 atom, 1 residue, 1 model selected  

> select #1/A:432@CG

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:239@CD

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:521@CE

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/B:250@C

1 atom, 1 residue, 1 model selected  

> color sel dim gray

> select #1/A:486@CD

1 atom, 1 residue, 1 model selected  

> select #1/A:487@CD1

1 atom, 1 residue, 1 model selected  

> select add #1/B:246@OE1

2 atoms, 2 residues, 1 model selected  

> ui tool show Distances

> ui mousemode right zoom

> ui mousemode right clip

[Repeated 1 time(s)]

> ui mousemode right zoom

> save /Users/mylanmayer/Documents/Integrin/extended_closed_alpha-
> beta_interactions_labeled_v2.cxs

——— End of log from Wed Jan 7 14:11:53 2026 ———

opened ChimeraX session  

> ui tool show "Side View"

> ui tool show Contacts

Drag select of 564 atoms, 1 pseudobonds, 579 bonds  
Drag select of 1073 atoms, 1 pseudobonds, 1099 bonds  

> contacts sel restrict both distanceOnly 3.5 resSeparation 5 intraMol false
> ignoreHiddenModels true reveal true

40 distances  

> ui mousemode right zoom

> ui mousemode right translate

> select clear

> ui mousemode right zoom

> ui mousemode right translate

> select add #1

15637 atoms, 15784 bonds, 41 pseudobonds, 1031 residues, 3 models selected  

> color sel byhetero

> select subtract #1

Nothing selected  

> ui mousemode right zoom

> ui mousemode right translate

> ui mousemode right zoom

> ui mousemode right translate

> ui mousemode right zoom

> ui mousemode right translate

> select add #1

15637 atoms, 15784 bonds, 41 pseudobonds, 1031 residues, 3 models selected  

> select subtract #1

Nothing selected  

> select add #1

15637 atoms, 15784 bonds, 41 pseudobonds, 1031 residues, 3 models selected  

> show sel cartoons

> hide sel atoms

> select subtract #1

Nothing selected  


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

Log:
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Volumes/4_IND_EM/southworth_lab/mmayer/processing/mmayer_20260204_TgM83-1_homo/relion/Class3D/selected_singlets_singlet-2_initial_model/run_it050_class003.mrc

Opened run_it050_class003.mrc as #1, grid size 288,288,288, pixel 0.728, shown
at level 0.0034, step 2, values float32  

> open
> /Volumes/4_IND_EM/southworth_lab/mmayer/processing/mmayer_20260204_TgM83-1_homo/relion/Class3D/selected_singlets_singlet-2_initial_model/run_it050_class002.mrc

Opened run_it050_class002.mrc as #2, grid size 288,288,288, pixel 0.728, shown
at level 0.00709, step 2, values float32  

> open
> /Volumes/4_IND_EM/southworth_lab/mmayer/processing/mmayer_20260204_TgM83-1_homo/relion/Class3D/selected_singlets_singlet-2_initial_model/run_it050_class001.mrc

Opened run_it050_class001.mrc as #3, grid size 288,288,288, pixel 0.728, shown
at level 0.00677, step 2, values float32  

> ui tool show Registration




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 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac15,6
      Model Number: MRX73LL/A
      Chip: Apple M3 Pro
      Total Number of Cores: 12 (6 Performance and 6 Efficiency)
      Memory: 18 GB
      System Firmware Version: 18000.120.36
      OS Loader Version: 18000.120.36

Software:

    System Software Overview:

      System Version: macOS 26.5 (25F71)
      Kernel Version: Darwin 25.5.0
      Time since boot: 30 days, 1 hour, 1 minute

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 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: No
          Connection Type: Internal
        DELL P2424HEB:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    autocommand: 2.2.2
    babel: 2.16.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-Clipper: 0.24.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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
    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-ISOLDE: 1.9
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    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
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    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: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    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: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    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: 1.18.1
    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
    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: 1.41
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    importlib_resources: 6.4.0
    inflect: 7.3.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    more-itertools: 10.3.0
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    ordered-set: 4.1.0
    packaging: 23.2
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    platformdirs: 4.2.2
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    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: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4.2
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.12.2
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    zipp: 3.19.2
#20545 not a bug Proofpoint Essentials - Quarantine Digest Eric Pettersen do-not-reply@…
Description 
Proofpoint Essentials - Quarantine Digest

https://us5.proofpointessentials.com/app/digest.php?ts=1782432153&action=hp&a_id=4i728e715ebaa8182fcfa4c831837c7f868932f75dd6724e0f6322ce90124866301630e10829cc982327fbfd56177e24492c88934aa784ba3d6a51867cba74dc63a2f9

https://www.cgl.ucsf.edu
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Quarantine Digest
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chimerax bugs 
chimerax-bugs@cgl.ucsf.edu

2026-06-25
17:02 PDT

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Quarantined (by Score)
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Subject: Security Alert: Update Your Authenticator App Within 48 Hours 26.6.2026 1:55:03
Delivery Date/Time: 25 Jun 26 - 15:58
Contact Administrator to take action on this email


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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

Note: See TracWiki for help on using the wiki.