Trac Ticket Queries

In addition to reports, Trac provides support for custom ticket queries, used to display lists of tickets meeting a specified set of 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 and no name/email 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 of 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.

Once you've edited your filters click the Update button to refresh your results.

Navigating Tickets

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

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

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

Saving Queries

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

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

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

Using TracLinks

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

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

Which is displayed as:

Active tickets against 1.0

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

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

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

Which is displayed as:

Assigned tickets by owner

Using the [[TicketQuery]] Macro

The ​TicketQuery macro lets you display lists of tickets matching certain criteria anywhere you can use WikiFormatting.

Example:

[[TicketQuery(version=0.6|0.7&resolution=duplicate)]]

This is displayed as:

#1317

ChimeraX bug report submission

#1558

Apparent infinite recursion of find_close_points_boxes

#1586

Seq Viewer: unproved enter() call on region browser

Just like the query: wiki links, the parameter of this macro expects a query string formatted according to the rules of the simple ticket query language. This also allows displaying the link and description of a single ticket:

[[TicketQuery(id=123)]]

This is displayed as:

#123

Crash in num_chains for 4v6w.cif

A more compact representation without the ticket summaries is also available:

[[TicketQuery(version=0.6|0.7&resolution=duplicate, compact)]]

This is displayed as:

#1317, #1558, #1586

Finally, if you wish to receive only the number of defects that match the query, use the count parameter.

[[TicketQuery(version=0.6|0.7&resolution=duplicate, count)]]

This is displayed as:

3

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 by placing pipes (|) between the columns like below:

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

This is displayed as:

Results (1 - 3 of 13895)

1 2 3 4 5 6 7 8 9 10 11 →

Ticket	Resolution	Summary	Owner	Reporter
#20396	fixed	msa3d not skipping None residues	Eric Pettersen	Eric Pettersen
#20395	duplicate	Crash in QObject::event in Qt 6.10.1	Tom Goddard	chimerax-bug-report@…
#20393	duplicate	Crash in accessibility routines	Tom Goddard	chimerax-bug-report@…

1 2 3 4 5 6 7 8 9 10 11 →

Full rows

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

[[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 13895)

1 2 3 4 5 6 7 8 9 10 11 →

Ticket	Resolution	Summary	Owner	Reporter
#20396	fixed	msa3d not skipping None residues	Eric Pettersen	Eric Pettersen
Description	The following bug report has been submitted: Platform: macOS-15.7.7-arm64-arm-64bit ChimeraX Version: 1.13.dev202605192122 (2026-05-19 21:22:40 UTC) Description msa3d /A Log: UCSF ChimeraX version: 1.13.dev202605192122 (2026-05-19) © 2016-2026 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 2mnr 1muc 2mnr title: Mechanism of the reaction catalyzed by mandelate racemase. 2. Crystal structure of mandelate racemase At 2.5 angstroms resolution: identification of the active site and possible catalytic residues [more info...] Chain information for 2mnr #1 --- Chain | Description | UniProt A | MANDELATE RACEMASE | MANR_PSEPU 3-359 Non-standard residues in 2mnr #1 --- MN — manganese (II) ion SO4 — sulfate ion 2mnr mmCIF Assemblies --- 1| author_and_software_defined_assembly 1muc title: Structure of muconate lactonizing enzyme At 1.85 angstroms resolution [more info...] Chain information for 1muc #2 --- Chain | Description | UniProt A B | MUCONATE LACTONIZING ENZYME | CATB_PSEPU 1-373 Non-standard residues in 1muc #2 --- MN — manganese (II) ion 1muc mmCIF Assemblies --- 1| author_and_software_defined_assembly > mmaker #1 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 1muc, chain A (#2) with 2mnr, chain A (#1), sequence alignment score = 549.1 RMSD between 202 pruned atom pairs is 1.107 angstroms; (across all 340 pairs: 3.634) > msa3d /A Match→Align cutoff: 5.0, in column if within cutoff of: any 332 residue pairs aligned 357 fully populated columns Traceback (most recent call last): File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/cmd_line/tool.py", line 322, in execute cmd.run(cmd_text) File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/match_align/cmd.py", line 155, in make_alignment coords[seq] = column_atoms(seq, full_cols).scene_coords ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/match_align/cmd.py", line 247, in column_atoms return Atoms([r.principal_atom for r in [residues[i] for i in seq_columns]]) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/match_align/cmd.py", line 247, in <listcomp> return Atoms([r.principal_atom for r in [residues[i] for i in seq_columns]]) ^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'principal_atom' AttributeError: 'NoneType' object has no attribute 'principal_atom' File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/match_align/cmd.py", line 247, in return Atoms([r.principal_atom for r in [residues[i] for i in seq_columns]]) ^^^^^^^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M3 OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.10.2, Qt 6.10.0 Qt runtime version: 6.10.1 Qt platform: cocoa Hardware: Hardware Overview: Model Name: iMac Model Identifier: Mac15,5 Model Number: Z19K0011DLL/A Chip: Apple M3 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: mBoot-18000.120.36 OS Loader Version: 11881.140.96.701.1 Software: System Software Overview: System Version: macOS 15.7.7 (24G720) Kernel Version: Darwin 24.6.0 Time since boot: 3 hours, 48 minutes Graphics/Displays: Apple M3: Chipset Model: Apple M3 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: iMac: Display Type: Built-In Retina LCD Resolution: Retina 4.5K (4480 x 2520) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: accessible-pygments: 0.0.5 aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.1 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.18.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 4.0.0 build: 1.3.0 certifi: 2025.8.3 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: 3.6.2 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.69.1 ChimeraX-AtomicLibrary: 14.4 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4.1 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3.1 ChimeraX-Cluster: 1.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.1 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.13.dev202605192122 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.2 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.8.2 ChimeraX-Label: 1.4 ChimeraX-LightingGUI: 1.0 ChimeraX-ListInfo: 1.3.1 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchAlign: 1.1 ChimeraX-MatchMaker: 2.4 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.2.0 ChimeraX-MDcrds: 2.19 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.8 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.23 ChimeraX-ModelPanel: 1.6.1 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0.1 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.16 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-PhenixUI: 1.6.1 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.8 ChimeraX-ProNA3D: 0.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.8.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.12 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.18 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SNFG: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 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: 1.51.2 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.6.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.4 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.20 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: 7.1.0 ipython: 9.9.0 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: 8.8.0 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: 6.7.1 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 OpenMM: 8.4.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.6 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 pydata-sphinx-theme: 0.16.1 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.5.0 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6: 6.10.2 PyQt6-Qt6: 6.10.1 PyQt6-WebEngine: 6.10.0 PyQt6-WebEngine-Qt6: 6.10.1 PyQt6_sip: 13.10.3 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.22 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2.1 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8.3 Sphinx: 9.0.4 sphinx-autodoc-typehints: 3.6.1 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 sse-starlette: 3.2.0 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 urllib3: 2.6.3 uvicorn: 0.40.0 wcwidth: 0.6.0 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0
#20395	duplicate	Crash in QObject::event in Qt 6.10.1	Tom Goddard	chimerax-bug-report@…
Description	The following bug report has been submitted: Platform: macOS-26.3-arm64-arm-64bit ChimeraX Version: 1.12rc202605192128 (2026-05-19 21:28:39 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x0000000204af7080 (most recent call first): File "/private/var/folders/dt/rckv67dx1pg9t1my06vk_fpm0000gn/T/AppTranslocation/F5732700-B327-4237-9DB2-15CE16DDD4A4/d/ChimeraX-1.12-rc2026.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 424 in event_loop File "/private/var/folders/dt/rckv67dx1pg9t1my06vk_fpm0000gn/T/AppTranslocation/F5732700-B327-4237-9DB2-15CE16DDD4A4/d/ChimeraX-1.12-rc2026.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init File "/private/var/folders/dt/rckv67dx1pg9t1my06vk_fpm0000gn/T/AppTranslocation/F5732700-B327-4237-9DB2-15CE16DDD4A4/d/ChimeraX-1.12-rc2026.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 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.map._map, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb_lib._load_libs, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util (total: 39) {"app_name":"ChimeraX","timestamp":"2026-05-26 17:42:35.00 +0300","app_version":"1.12.0","slice_uuid":"544eb719-b770-3601-b425-1ceb237637ac","build_version":"1.12.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 26.3 (25D125)","roots_installed":0,"name":"ChimeraX","incident_id":"EA736560-23FD-47DA-B30E-E2D2482900AF"} { "uptime" : 1100000, "procRole" : "Foreground", "version" : 2, "userID" : 501, "deployVersion" : 210, "modelCode" : "Mac16,12", "coalitionID" : 68192, "osVersion" : { "train" : "macOS 26.3", "build" : "25D125", "releaseType" : "User" }, "captureTime" : "2026-05-26 17:42:32.2726 +0300", "codeSigningMonitor" : 2, "incident" : "EA736560-23FD-47DA-B30E-E2D2482900AF", "pid" : 14227, "translated" : false, "cpuType" : "ARM-64", "procLaunch" : "2026-05-26 17:42:18.0301 +0300", "procStartAbsTime" : 26405503014828, "procExitAbsTime" : 26405844632130, "procName" : "ChimeraX", "procPath" : "\/private\/var\/folders\/*\/ChimeraX-1.12-rc2026.05.20.app\/Contents\/MacOS\/ChimeraX", "bundleInfo" : {"CFBundleShortVersionString":"1.12.0","CFBundleVersion":"1.12.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"}, "storeInfo" : {"deviceIdentifierForVendor":"61AC08BF-03F2-5807-862F-52CA2E20AA25","thirdParty":true}, "parentProc" : "launchd", "parentPid" : 1, "coalitionName" : "edu.ucsf.cgl.ChimeraX", "crashReporterKey" : "421F22A6-197C-9B0F-F19F-CC565D8A5731", "lowPowerMode" : 1, "appleIntelligenceStatus" : {"state":"unavailable","reasons":["assetIsNotReady","notOptedIn"]}, "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" : "C2F858DB-6D87-4040-A34B-7CAD7CB36732", "wakeTime" : 8145, "sleepWakeUUID" : "1909E0C4-691F-4B69-8461-9E3EF008E236", "sip" : "enabled", "vmRegionInfo" : "0x2ac is not in any region. 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All rights reserved. How to cite UCSF ChimeraX ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.12rc202605192128 (2026-05-19) © 2016-2026 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/prensesnisanur/Desktop/darunavir.pdbqt Summary of feedback from opening /Users/prensesnisanur/Desktop/darunavir.pdbqt --- warnings | Ignored bad PDB record found on line 1 REMARK Name = darunavir.pdb Ignored bad PDB record found on line 2 REMARK 2 active torsions: Ignored bad PDB record found on line 3 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 4 REMARK 1 A between atoms: C_1 and C_3 Ignored bad PDB record found on line 5 REMARK 2 A between atoms: C_1 and O_4 5 messages similar to the above omitted Opened darunavir.pdbqt containing 1 structures (5 atoms, 4 bonds) > open /Users/prensesnisanur/Desktop/protein.pdbqt Summary of feedback from opening /Users/prensesnisanur/Desktop/protein.pdbqt --- warnings | Ignored bad PDB record found on line 1 REMARK Name = protein.pdb Ignored bad PDB record found on line 2 REMARK 350 active torsions: Ignored bad PDB record found on line 3 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 4 REMARK 1 A between atoms: CA_2 and C_3 Ignored bad PDB record found on line 5 REMARK 2 A between atoms: N_8 and CA_9 843 messages similar to the above omitted Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Ignored bad PDB record found on line 1009 ENDROOT Ignored bad PDB record found on line 1010 BRANCH 4 5 Duplicate atom serial number found: 5 Duplicate atom serial number found: 6 Ignored bad PDB record found on line 1013 ENDBRANCH 4 5 Ignored bad PDB record found on line 1014 BRANCH 3 7 Duplicate atom serial number found: 7 Ignored bad PDB record found on line 1016 BRANCH 7 8 Duplicate atom serial number found: 8 Duplicate atom serial number found: 9 Ignored bad PDB record found on line 1019 ENDBRANCH 7 8 Ignored bad PDB record found on line 1020 ENDBRANCH 3 7 Ignored bad PDB record found on line 1021 TORSDOF 3 Ignored bad PDB record found on line 1022 REMARK Name = protein.pdb Ignored bad PDB record found on line 1023 REMARK 350 active torsions: 352 messages similar to the above omitted Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Ignored bad PDB record found on line 1380 ENDROOT Ignored bad PDB record found on line 1381 TORSDOF 0 Ignored bad PDB record found on line 1382 REMARK Name = protein.pdb Ignored bad PDB record found on line 1383 REMARK 350 active torsions: Ignored bad PDB record found on line 1384 REMARK status: ('A' for Active; 'I' for Inactive) 351 messages similar to the above omitted Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 6 messages similar to the above omitted Ignored bad PDB record found on line 1749 ENDROOT Ignored bad PDB record found on line 1750 TORSDOF 0 Ignored bad PDB record found on line 1751 REMARK Name = protein.pdb Ignored bad PDB record found on line 1752 REMARK 350 active torsions: Ignored bad PDB record found on line 1753 REMARK status: ('A' for Active; 'I' for Inactive) 351 messages similar to the above omitted Duplicate atom serial number found: 1 Ignored bad PDB record found on line 2108 ENDROOT Ignored bad PDB record found on line 2109 TORSDOF 0 Ignored bad PDB record found on line 2110 REMARK Name = protein.pdb Ignored bad PDB record found on line 2111 REMARK 350 active torsions: Ignored bad PDB record found on line 2112 REMARK status: ('A' for Active; 'I' for Inactive) 351 messages similar to the above omitted Duplicate atom serial number found: 1 Ignored bad PDB record found on line 2467 ENDROOT Ignored bad PDB record found on line 2468 BRANCH 1 2 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Ignored bad PDB record found on line 2471 ENDBRANCH 1 2 Ignored bad PDB record found on line 2472 BRANCH 1 4 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 Ignored bad PDB record found on line 2475 ENDBRANCH 1 4 Ignored bad PDB record found on line 2476 TORSDOF 2 Ignored bad PDB record found on line 2477 REMARK Name = protein.pdb Ignored bad PDB record found on line 2478 REMARK 350 active torsions: Ignored bad PDB record found on line 2479 REMARK status: ('A' for Active; 'I' for Inactive) 351 messages similar to the above omitted Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Ignored bad PDB record found on line 2836 ENDROOT Ignored bad PDB record found on line 2837 BRANCH 3 4 Duplicate atom serial number found: 4 Ignored bad PDB record found on line 2839 BRANCH 4 5 Duplicate atom serial number found: 5 Duplicate atom serial number found: 6 Duplicate atom serial number found: 7 Ignored bad PDB record found on line 2843 BRANCH 7 8 Duplicate atom serial number found: 8 Ignored bad PDB record found on line 2845 BRANCH 8 9 Duplicate atom serial number found: 9 Duplicate atom serial number found: 10 Duplicate atom serial number found: 11 Ignored bad PDB record found on line 2849 BRANCH 11 12 Duplicate atom serial number found: 12 Duplicate atom serial number found: 13 Ignored bad PDB record found on line 2852 BRANCH 12 14 Duplicate atom serial number found: 14 Duplicate atom serial number found: 15 Duplicate atom serial number found: 16 Ignored bad PDB record found on line 2856 BRANCH 16 17 Duplicate atom serial number found: 17 Ignored bad PDB record found on line 2858 BRANCH 17 18 Duplicate atom serial number found: 18 Duplicate atom serial number found: 19 Duplicate atom serial number found: 20 Ignored bad PDB record found on line 2862 BRANCH 20 21 Duplicate atom serial number found: 21 Duplicate atom serial number found: 22 Ignored bad PDB record found on line 2865 BRANCH 22 23 Duplicate atom serial number found: 23 Duplicate atom serial number found: 24 Ignored bad PDB record found on line 2868 BRANCH 23 25 Duplicate atom serial number found: 25 Ignored bad PDB record found on line 2870 BRANCH 25 26 Duplicate atom serial number found: 26 Ignored bad PDB record found on line 2872 BRANCH 26 27 Duplicate atom serial number found: 27 Duplicate atom serial number found: 28 Ignored bad PDB record found on line 2875 ENDBRANCH 26 27 Ignored bad PDB record found on line 2876 ENDBRANCH 25 26 Ignored bad PDB record found on line 2877 ENDBRANCH 23 25 Ignored bad PDB record found on line 2878 ENDBRANCH 22 23 Ignored bad PDB record found on line 2879 ENDBRANCH 20 21 2 messages similar to the above omitted Duplicate atom serial number found: 29 Ignored bad PDB record found on line 2883 BRANCH 29 30 Duplicate atom serial number found: 30 Duplicate atom serial number found: 31 Duplicate atom serial number found: 32 Ignored bad PDB record found on line 2887 ENDBRANCH 29 30 Ignored bad PDB record found on line 2888 ENDBRANCH 17 29 Ignored bad PDB record found on line 2889 ENDBRANCH 16 17 Ignored bad PDB record found on line 2890 ENDBRANCH 12 14 Ignored bad PDB record found on line 2891 ENDBRANCH 11 12 4 messages similar to the above omitted Duplicate atom serial number found: 33 Duplicate atom serial number found: 34 Duplicate atom serial number found: 35 Ignored bad PDB record found on line 2899 ENDBRANCH 4 33 Ignored bad PDB record found on line 2900 ENDBRANCH 3 4 Ignored bad PDB record found on line 2901 BRANCH 1 36 Duplicate atom serial number found: 36 Ignored bad PDB record found on line 2903 BRANCH 36 39 Duplicate atom serial number found: 37 Duplicate atom serial number found: 38 Duplicate atom serial number found: 39 Ignored bad PDB record found on line 2907 BRANCH 37 40 Duplicate atom serial number found: 40 Ignored bad PDB record found on line 2909 BRANCH 40 43 Duplicate atom serial number found: 41 Duplicate atom serial number found: 42 Duplicate atom serial number found: 43 Ignored bad PDB record found on line 2913 BRANCH 41 44 Duplicate atom serial number found: 44 Ignored bad PDB record found on line 2915 BRANCH 44 47 Duplicate atom serial number found: 45 Duplicate atom serial number found: 46 Duplicate atom serial number found: 47 Ignored bad PDB record found on line 2919 BRANCH 45 48 Duplicate atom serial number found: 48 Duplicate atom serial number found: 49 Ignored bad PDB record found on line 2922 BRANCH 48 52 Duplicate atom serial number found: 50 Duplicate atom serial number found: 51 Duplicate atom serial number found: 52 Ignored bad PDB record found on line 2926 ENDBRANCH 48 52 Ignored bad PDB record found on line 2927 ENDBRANCH 45 48 Ignored bad PDB record found on line 2928 ENDBRANCH 44 47 Ignored bad PDB record found on line 2929 BRANCH 44 53 Duplicate atom serial number found: 53 Ignored bad PDB record found on line 2931 BRANCH 53 54 Duplicate atom serial number found: 54 Duplicate atom serial number found: 55 Duplicate atom serial number found: 56 Ignored bad PDB record found on line 2935 ENDBRANCH 53 54 Ignored bad PDB record found on line 2936 ENDBRANCH 44 53 Ignored bad PDB record found on line 2937 ENDBRANCH 41 44 Ignored bad PDB record found on line 2938 ENDBRANCH 40 43 Ignored bad PDB record found on line 2939 BRANCH 40 57 Duplicate atom serial number found: 57 Ignored bad PDB record found on line 2941 BRANCH 57 58 Duplicate atom serial number found: 58 Duplicate atom serial number found: 59 Duplicate atom serial number found: 60 Ignored bad PDB record found on line 2945 ENDBRANCH 57 58 Ignored bad PDB record found on line 2946 ENDBRANCH 40 57 Ignored bad PDB record found on line 2947 ENDBRANCH 37 40 Ignored bad PDB record found on line 2948 ENDBRANCH 36 39 Ignored bad PDB record found on line 2949 BRANCH 36 61 Duplicate atom serial number found: 61 Ignored bad PDB record found on line 2951 BRANCH 61 62 Duplicate atom serial number found: 62 Duplicate atom serial number found: 63 Duplicate atom serial number found: 64 Ignored bad PDB record found on line 2955 ENDBRANCH 61 62 Ignored bad PDB record found on line 2956 ENDBRANCH 36 61 Ignored bad PDB record found on line 2957 ENDBRANCH 1 36 Ignored bad PDB record found on line 2958 TORSDOF 30 Ignored bad PDB record found on line 2959 REMARK Name = protein.pdb 353 messages similar to the above omitted Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Ignored bad PDB record found on line 3317 ENDROOT Ignored bad PDB record found on line 3318 TORSDOF 0 Ignored bad PDB record found on line 3319 REMARK Name = protein.pdb Ignored bad PDB record found on line 3320 REMARK 350 active torsions: Ignored bad PDB record found on line 3321 REMARK status: ('A' for Active; 'I' for Inactive) 351 messages similar to the above omitted Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Ignored bad PDB record found on line 3678 ENDROOT Ignored bad PDB record found on line 3679 TORSDOF 0 Ignored bad PDB record found on line 3680 REMARK Name = protein.pdb Ignored bad PDB record found on line 3681 REMARK 350 active torsions: Ignored bad PDB record found on line 3682 REMARK status: ('A' for Active; 'I' for Inactive) 351 messages similar to the above omitted Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Ignored bad PDB record found on line 4039 ENDROOT Ignored bad PDB record found on line 4040 TORSDOF 0 Ignored bad PDB record found on line 4041 REMARK Name = protein.pdb Ignored bad PDB record found on line 4042 REMARK 350 active torsions: Ignored bad PDB record found on line 4043 REMARK status: ('A' for Active; 'I' for Inactive) 351 messages similar to the above omitted Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 2 messages similar to the above omitted Ignored bad PDB record found on line 4404 ENDROOT Ignored bad PDB record found on line 4405 BRANCH 4 8 Duplicate atom serial number found: 8 Duplicate atom serial number found: 9 Duplicate atom serial number found: 10 Ignored bad PDB record found on line 4409 BRANCH 10 11 Duplicate atom serial number found: 11 Ignored bad PDB record found on line 4411 BRANCH 11 12 Duplicate atom serial number found: 12 Duplicate atom serial number found: 13 Duplicate atom serial number found: 14 Ignored bad PDB record found on line 4415 BRANCH 14 15 Duplicate atom serial number found: 15 Ignored bad PDB record found on line 4417 BRANCH 15 16 Duplicate atom serial number found: 16 Duplicate atom serial number found: 17 Duplicate atom serial number found: 18 Ignored bad PDB record found on line 4421 BRANCH 18 19 Duplicate atom serial number found: 19 Ignored bad PDB record found on line 4423 BRANCH 19 20 Duplicate atom serial number found: 20 Duplicate atom serial number found: 21 Duplicate atom serial number found: 22 Ignored bad PDB record found on line 4427 BRANCH 22 23 Duplicate atom serial number found: 23 Ignored bad PDB record found on line 4429 BRANCH 23 24 Duplicate atom serial number found: 24 Duplicate atom serial number found: 25 Duplicate atom serial number found: 26 Duplicate atom serial number found: 27 Duplicate atom serial number found: 28 2 messages similar to the above omitted Ignored bad PDB record found on line 4437 BRANCH 27 31 Duplicate atom serial number found: 31 Duplicate atom serial number found: 32 Duplicate atom serial number found: 33 Ignored bad PDB record found on line 4441 BRANCH 33 34 Duplicate atom serial number found: 34 Ignored bad PDB record found on line 4443 BRANCH 34 35 Duplicate atom serial number found: 35 Duplicate atom serial number found: 36 Duplicate atom serial number found: 37 Ignored bad PDB record found on line 4447 BRANCH 37 38 Duplicate atom serial number found: 38 Duplicate atom serial number found: 39 Ignored bad PDB record found on line 4450 ENDBRANCH 37 38 Ignored bad PDB record found on line 4451 ENDBRANCH 34 35 Ignored bad PDB record found on line 4452 BRANCH 34 40 Duplicate atom serial number found: 40 Ignored bad PDB record found on line 4454 BRANCH 40 41 Duplicate atom serial number found: 41 Ignored bad PDB record found on line 4456 BRANCH 41 42 Duplicate atom serial number found: 42 Ignored bad PDB record found on line 4458 BRANCH 42 43 Duplicate atom serial number found: 43 Duplicate atom serial number found: 44 Ignored bad PDB record found on line 4461 ENDBRANCH 42 43 Ignored bad PDB record found on line 4462 ENDBRANCH 41 42 Ignored bad PDB record found on line 4463 ENDBRANCH 40 41 Ignored bad PDB record found on line 4464 ENDBRANCH 34 40 Ignored bad PDB record found on line 4465 ENDBRANCH 33 34 3 messages similar to the above omitted Duplicate atom serial number found: 45 Ignored bad PDB record found on line 4470 BRANCH 45 46 Duplicate atom serial number found: 46 Ignored bad PDB record found on line 4472 BRANCH 46 47 Duplicate atom serial number found: 47 Ignored bad PDB record found on line 4474 BRANCH 47 48 Duplicate atom serial number found: 48 Duplicate atom serial number found: 49 Ignored bad PDB record found on line 4477 ENDBRANCH 47 48 Ignored bad PDB record found on line 4478 ENDBRANCH 46 47 Ignored bad PDB record found on line 4479 ENDBRANCH 45 46 Ignored bad PDB record found on line 4480 ENDBRANCH 23 45 Ignored bad PDB record found on line 4481 ENDBRANCH 22 23 2 messages similar to the above omitted Duplicate atom serial number found: 50 Ignored bad PDB record found on line 4485 BRANCH 50 51 Duplicate atom serial number found: 51 Duplicate atom serial number found: 52 Duplicate atom serial number found: 53 Duplicate atom serial number found: 54 Duplicate atom serial number found: 55 4 messages similar to the above omitted Ignored bad PDB record found on line 4495 ENDBRANCH 50 51 Ignored bad PDB record found on line 4496 ENDBRANCH 19 50 Ignored bad PDB record found on line 4497 ENDBRANCH 18 19 Ignored bad PDB record found on line 4498 ENDBRANCH 15 16 Ignored bad PDB record found on line 4499 BRANCH 15 60 Duplicate atom serial number found: 60 Ignored bad PDB record found on line 4501 BRANCH 60 61 Duplicate atom serial number found: 61 Ignored bad PDB record found on line 4503 BRANCH 61 62 Duplicate atom serial number found: 62 Ignored bad PDB record found on line 4505 BRANCH 62 63 Duplicate atom serial number found: 63 Duplicate atom serial number found: 64 Duplicate atom serial number found: 65 Duplicate atom serial number found: 66 Ignored bad PDB record found on line 4510 ENDBRANCH 62 63 Ignored bad PDB record found on line 4511 ENDBRANCH 61 62 Ignored bad PDB record found on line 4512 ENDBRANCH 60 61 Ignored bad PDB record found on line 4513 ENDBRANCH 15 60 Ignored bad PDB record found on line 4514 ENDBRANCH 14 15 4 messages similar to the above omitted Duplicate atom serial number found: 67 Ignored bad PDB record found on line 4520 BRANCH 67 70 Duplicate atom serial number found: 68 Duplicate atom serial number found: 69 Duplicate atom serial number found: 70 Ignored bad PDB record found on line 4524 BRANCH 68 71 Duplicate atom serial number found: 71 Ignored bad PDB record found on line 4526 BRANCH 71 74 Duplicate atom serial number found: 72 Duplicate atom serial number found: 73 Duplicate atom serial number found: 74 Ignored bad PDB record found on line 4530 BRANCH 72 75 Duplicate atom serial number found: 75 Ignored bad PDB record found on line 4532 BRANCH 75 78 Duplicate atom serial number found: 76 Duplicate atom serial number found: 77 Duplicate atom serial number found: 78 Ignored bad PDB record found on line 4536 BRANCH 76 79 Duplicate atom serial number found: 79 Ignored bad PDB record found on line 4538 BRANCH 79 82 Duplicate atom serial number found: 80 Duplicate atom serial number found: 81 Duplicate atom serial number found: 82 Ignored bad PDB record found on line 4542 BRANCH 80 83 Duplicate atom serial number found: 83 Ignored bad PDB record found on line 4544 BRANCH 83 86 Duplicate atom serial number found: 84 Duplicate atom serial number found: 85 Duplicate atom serial number found: 86 Ignored bad PDB record found on line 4548 BRANCH 84 87 Duplicate atom serial number found: 87 Ignored bad PDB record found on line 4550 BRANCH 87 90 Duplicate atom serial number found: 88 Duplicate atom serial number found: 89 Duplicate atom serial number found: 90 Ignored bad PDB record found on line 4554 BRANCH 88 91 Duplicate atom serial number found: 91 Ignored bad PDB record found on line 4556 BRANCH 91 92 Duplicate atom serial number found: 92 Duplicate atom serial number found: 93 Duplicate atom serial number found: 94 Ignored bad PDB record found on line 4560 ENDBRANCH 91 92 Ignored bad PDB record found on line 4561 BRANCH 91 97 Duplicate atom serial number found: 95 Duplicate atom serial number found: 96 Duplicate atom serial number found: 97 Ignored bad PDB record found on line 4565 BRANCH 95 98 Duplicate atom serial number found: 98 Ignored bad PDB record found on line 4567 BRANCH 98 101 Duplicate atom serial number found: 99 Duplicate atom serial number found: 100 Duplicate atom serial number found: 101 Ignored bad PDB record found on line 4571 ENDBRANCH 98 101 Ignored bad PDB record found on line 4572 BRANCH 98 102 Duplicate atom serial number found: 102 Duplicate atom serial number found: 103 Duplicate atom serial number found: 104 Ignored bad PDB record found on line 4576 ENDBRANCH 98 102 Ignored bad PDB record found on line 4577 ENDBRANCH 95 98 Ignored bad PDB record found on line 4578 ENDBRANCH 91 97 Ignored bad PDB record found on line 4579 ENDBRANCH 88 91 Ignored bad PDB record found on line 4580 ENDBRANCH 87 90 1 messages similar to the above omitted Duplicate atom serial number found: 105 Duplicate atom serial number found: 106 Ignored bad PDB record found on line 4584 BRANCH 105 107 Duplicate atom serial number found: 107 Duplicate atom serial number found: 108 Ignored bad PDB record found on line 4587 ENDBRANCH 105 107 Ignored bad PDB record found on line 4588 ENDBRANCH 87 105 Ignored bad PDB record found on line 4589 ENDBRANCH 84 87 Ignored bad PDB record found on line 4590 ENDBRANCH 83 86 Ignored bad PDB record found on line 4591 BRANCH 83 109 Duplicate atom serial number found: 109 Ignored bad PDB record found on line 4593 BRANCH 109 110 Duplicate atom serial number found: 110 Ignored bad PDB record found on line 4595 BRANCH 110 111 Duplicate atom serial number found: 111 Duplicate atom serial number found: 112 Duplicate atom serial number found: 113 Ignored bad PDB record found on line 4599 ENDBRANCH 110 111 Ignored bad PDB record found on line 4600 ENDBRANCH 109 110 Ignored bad PDB record found on line 4601 ENDBRANCH 83 109 Ignored bad PDB record found on line 4602 ENDBRANCH 80 83 Ignored bad PDB record found on line 4603 ENDBRANCH 79 82 1 messages similar to the above omitted Duplicate atom serial number found: 114 Ignored bad PDB record found on line 4606 BRANCH 114 115 Duplicate atom serial number found: 115 Ignored bad PDB record found on line 4608 BRANCH 115 116 Duplicate atom serial number found: 116 Duplicate atom serial number found: 117 Duplicate atom serial number found: 118 Ignored bad PDB record found on line 4612 ENDBRANCH 115 116 Ignored bad PDB record found on line 4613 ENDBRANCH 114 115 Ignored bad PDB record found on line 4614 ENDBRANCH 79 114 Ignored bad PDB record found on line 4615 ENDBRANCH 76 79 Ignored bad PDB record found on line 4616 ENDBRANCH 75 78 1 messages similar to the above omitted Duplicate atom serial number found: 119 Ignored bad PDB record found on line 4619 BRANCH 119 120 Duplicate atom serial number found: 120 Ignored bad PDB record found on line 4621 BRANCH 120 121 Duplicate atom serial number found: 121 Duplicate atom serial number found: 122 Ignored bad PDB record found on line 4624 ENDBRANCH 120 121 Ignored bad PDB record found on line 4625 ENDBRANCH 119 120 Ignored bad PDB record found on line 4626 ENDBRANCH 75 119 Ignored bad PDB record found on line 4627 ENDBRANCH 72 75 Ignored bad PDB record found on line 4628 ENDBRANCH 71 74 1 messages similar to the above omitted Duplicate atom serial number found: 123 Duplicate atom serial number found: 124 Ignored bad PDB record found on line 4632 ENDBRANCH 71 123 Ignored bad PDB record found on line 4633 ENDBRANCH 68 71 Ignored bad PDB record found on line 4634 ENDBRANCH 67 70 Ignored bad PDB record found on line 4635 BRANCH 67 125 Duplicate atom serial number found: 125 Ignored bad PDB record found on line 4637 BRANCH 125 126 Duplicate atom serial number found: 126 Duplicate atom serial number found: 127 Duplicate atom serial number found: 128 Ignored bad PDB record found on line 4641 ENDBRANCH 125 126 Ignored bad PDB record found on line 4642 ENDBRANCH 67 125 Ignored bad PDB record found on line 4643 ENDBRANCH 1 67 Ignored bad PDB record found on line 4644 TORSDOF 59 Ignored bad PDB record found on line 4645 REMARK Name = protein.pdb 353 messages similar to the above omitted Duplicate atom serial number found: 1 Ignored bad PDB record found on line 5002 ENDROOT Ignored bad PDB record found on line 5003 TORSDOF 0 Ignored bad PDB record found on line 5004 REMARK Name = protein.pdb Ignored bad PDB record found on line 5005 REMARK 350 active torsions: Ignored bad PDB record found on line 5006 REMARK status: ('A' for Active; 'I' for Inactive) 351 messages similar to the above omitted Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Ignored bad PDB record found on line 5362 ENDROOT Ignored bad PDB record found on line 5363 TORSDOF 0 Ignored bad PDB record found on line 5364 REMARK Name = protein.pdb Ignored bad PDB record found on line 5365 REMARK 350 active torsions: Ignored bad PDB record found on line 5366 REMARK status: ('A' for Active; 'I' for Inactive) 351 messages similar to the above omitted Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Ignored bad PDB record found on line 5724 ENDROOT Ignored bad PDB record found on line 5725 BRANCH 1 5 Duplicate atom serial number found: 5 Ignored bad PDB record found on line 5727 BRANCH 5 7 Duplicate atom serial number found: 6 Duplicate atom serial number found: 7 Ignored bad PDB record found on line 5730 ENDBRANCH 5 7 Ignored bad PDB record found on line 5731 ENDBRANCH 1 5 Ignored bad PDB record found on line 5732 TORSDOF 2 Ignored bad PDB record found on line 5733 REMARK Name = protein.pdb Ignored bad PDB record found on line 5734 REMARK 350 active torsions: 352 messages similar to the above omitted Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Ignored bad PDB record found on line 6092 ENDROOT Ignored bad PDB record found on line 6093 BRANCH 1 4 Duplicate atom serial number found: 4 Ignored bad PDB record found on line 6095 BRANCH 4 7 Duplicate atom serial number found: 5 Duplicate atom serial number found: 6 Duplicate atom serial number found: 7 Ignored bad PDB record found on line 6099 ENDBRANCH 4 7 Ignored bad PDB record found on line 6100 BRANCH 4 8 Duplicate atom serial number found: 8 Duplicate atom serial number found: 9 Ignored bad PDB record found on line 6103 BRANCH 8 10 Duplicate atom serial number found: 10 Duplicate atom serial number found: 11 Ignored bad PDB record found on line 6106 ENDBRANCH 8 10 Ignored bad PDB record found on line 6107 ENDBRANCH 4 8 Ignored bad PDB record found on line 6108 ENDBRANCH 1 4 Ignored bad PDB record found on line 6109 BRANCH 3 12 Duplicate atom serial number found: 12 Ignored bad PDB record found on line 6111 BRANCH 12 13 Duplicate atom serial number found: 13 Duplicate atom serial number found: 14 Duplicate atom serial number found: 15 Ignored bad PDB record found on line 6115 BRANCH 15 16 Duplicate atom serial number found: 16 Ignored bad PDB record found on line 6117 BRANCH 16 17 Duplicate atom serial number found: 17 Duplicate atom serial number found: 18 Duplicate atom serial number found: 19 Duplicate atom serial number found: 20 Ignored bad PDB record found on line 6122 ENDBRANCH 16 17 Ignored bad PDB record found on line 6123 ENDBRANCH 15 16 Ignored bad PDB record found on line 6124 ENDBRANCH 12 13 Ignored bad PDB record found on line 6125 ENDBRANCH 3 12 Ignored bad PDB record found on line 6126 TORSDOF 8 354 messages similar to the above omitted Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 Ignored bad PDB record found on line 6488 ENDROOT Ignored bad PDB record found on line 6489 BRANCH 1 7 Duplicate atom serial number found: 6 Duplicate atom serial number found: 7 Ignored bad PDB record found on line 6492 ENDBRANCH 1 7 Ignored bad PDB record found on line 6493 TORSDOF 1 Ignored bad PDB record found on line 6494 REMARK Name = protein.pdb Ignored bad PDB record found on line 6495 REMARK 350 active torsions: Ignored bad PDB record found on line 6496 REMARK status: ('A' for Active; 'I' for Inactive) 351 messages similar to the above omitted Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 2 messages similar to the above omitted Ignored bad PDB record found on line 6857 ENDROOT Ignored bad PDB record found on line 6858 TORSDOF 0 Ignored bad PDB record found on line 6859 REMARK Name = protein.pdb Ignored bad PDB record found on line 6860 REMARK 350 active torsions: Ignored bad PDB record found on line 6861 REMARK status: ('A' for Active; 'I' for Inactive) 351 messages similar to the above omitted Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Ignored bad PDB record found on line 7217 ENDROOT Ignored bad PDB record found on line 7218 BRANCH 1 3 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Ignored bad PDB record found on line 7221 ENDBRANCH 1 3 Ignored bad PDB record found on line 7222 TORSDOF 1 Ignored bad PDB record found on line 7223 REMARK Name = protein.pdb Ignored bad PDB record found on line 7224 REMARK 350 active torsions: Ignored bad PDB record found on line 7225 REMARK status: ('A' for Active; 'I' for Inactive) 351 messages similar to the above omitted Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Ignored bad PDB record found on line 7582 ENDROOT Ignored bad PDB record found on line 7583 BRANCH 3 4 Duplicate atom serial number found: 4 Ignored bad PDB record found on line 7585 BRANCH 4 5 Duplicate atom serial number found: 5 Duplicate atom serial number found: 6 Duplicate atom serial number found: 7 Ignored bad PDB record found on line 7589 BRANCH 7 8 Duplicate atom serial number found: 8 Ignored bad PDB record found on line 7591 BRANCH 8 9 Duplicate atom serial number found: 9 Duplicate atom serial number found: 10 Duplicate atom serial number found: 11 Ignored bad PDB record found on line 7595 BRANCH 11 12 Duplicate atom serial number found: 12 Ignored bad PDB record found on line 7597 BRANCH 12 13 Duplicate atom serial number found: 13 Duplicate atom serial number found: 14 Duplicate atom serial number found: 15 Ignored bad PDB record found on line 7601 ENDBRANCH 12 13 Ignored bad PDB record found on line 7602 BRANCH 12 16 Duplicate atom serial number found: 16 Duplicate atom serial number found: 17 Duplicate atom serial number found: 18 Ignored bad PDB record found on line 7606 BRANCH 18 19 Duplicate atom serial number found: 19 Ignored bad PDB record found on line 7608 BRANCH 19 20 Duplicate atom serial number found: 20 Duplicate atom serial number found: 21 Duplicate atom serial number found: 22 Duplicate atom serial number found: 23 Duplicate atom serial number found: 24 2 messages similar to the above omitted Ignored bad PDB record found on line 7616 BRANCH 23 27 Duplicate atom serial number found: 27 Duplicate atom serial number found: 28 Duplicate atom serial number found: 29 Ignored bad PDB record found on line 7620 BRANCH 29 30 Duplicate atom serial number found: 30 Ignored bad PDB record found on line 7622 BRANCH 30 31 Duplicate atom serial number found: 31 Duplicate atom serial number found: 32 Duplicate atom serial number found: 33 Duplicate atom serial number found: 34 Duplicate atom serial number found: 35 2 messages similar to the above omitted Ignored bad PDB record found on line 7630 BRANCH 34 38 Duplicate atom serial number found: 38 Duplicate atom serial number found: 39 Duplicate atom serial number found: 40 Ignored bad PDB record found on line 7634 BRANCH 40 41 Duplicate atom serial number found: 41 Ignored bad PDB record found on line 7636 BRANCH 41 42 Duplicate atom serial number found: 42 Duplicate atom serial number found: 43 Duplicate atom serial number found: 44 Ignored bad PDB record found on line 7640 BRANCH 44 45 Duplicate atom serial number found: 45 Ignored bad PDB record found on line 7642 BRANCH 45 46 Duplicate atom serial number found: 46 Duplicate atom serial number found: 47 Duplicate atom serial number found: 48 Ignored bad PDB record found on line 7646 BRANCH 48 49 Duplicate atom serial number found: 49 Ignored bad PDB record found on line 7648 BRANCH 49 50 Duplicate atom serial number found: 50 Duplicate atom serial number found: 51 Duplicate atom serial number found: 52 Ignored bad PDB record found on line 7652 BRANCH 52 53 Duplicate atom serial number found: 53 Ignored bad PDB record found on line 7654 BRANCH 53 54 Duplicate atom serial number found: 54 Duplicate atom serial number found: 55 Duplicate atom serial number found: 56 Ignored bad PDB record found on line 7658 BRANCH 56 57 Duplicate atom serial number found: 57 Ignored bad PDB record found on line 7660 BRANCH 57 58 Duplicate atom serial number found: 58 Duplicate atom serial number found: 59 Duplicate atom serial number found: 60 Ignored bad PDB record found on line 7664 BRANCH 60 61 Duplicate atom serial number found: 61 Ignored bad PDB record found on line 7666 BRANCH 61 62 Duplicate atom serial number found: 62 Duplicate atom serial number found: 63 Duplicate atom serial number found: 64 Ignored bad PDB record found on line 7670 BRANCH 64 65 Duplicate atom serial number found: 65 Ignored bad PDB record found on line 7672 BRANCH 65 66 Duplicate atom serial number found: 66 Duplicate atom serial number found: 67 Duplicate atom serial number found: 68 Ignored bad PDB record found on line 7676 BRANCH 68 69 Duplicate atom serial number found: 69 Ignored bad PDB record found on line 7678 BRANCH 69 70 Duplicate atom serial number found: 70 Duplicate atom serial number found: 71 Duplicate atom serial number found: 72 Ignored bad PDB record found on line 7682 BRANCH 72 73 Duplicate atom serial number found: 73 Ignored bad PDB record found on line 7684 BRANCH 73 74 Duplicate atom serial number found: 74 Duplicate atom serial number found: 75 Duplicate atom serial number found: 76 Ignored bad PDB record found on line 7688 BRANCH 76 77 Duplicate atom serial number found: 77 Ignored bad PDB record found on line 7690 BRANCH 77 78 Duplicate atom serial number found: 78 Duplicate atom serial number found: 79 Duplicate atom serial number found: 80 Ignored bad PDB record found on line 7694 ENDBRANCH 77 78 Ignored bad PDB record found on line 7695 BRANCH 77 81 Duplicate atom serial number found: 81 Duplicate atom serial number found: 82 Duplicate atom serial number found: 83 Ignored bad PDB record found on line 7699 BRANCH 83 84 Duplicate atom serial number found: 84 Ignored bad PDB record found on line 7701 BRANCH 84 85 Duplicate atom serial number found: 85 Duplicate atom serial number found: 86 Duplicate atom serial number found: 87 Ignored bad PDB record found on line 7705 BRANCH 87 88 Duplicate atom serial number found: 88 Ignored bad PDB record found on line 7707 BRANCH 88 89 Duplicate atom serial number found: 89 Duplicate atom serial number found: 90 Duplicate atom serial number found: 91 Ignored bad PDB record found on line 7711 BRANCH 91 92 Duplicate atom serial number found: 92 Ignored bad PDB record found on line 7713 BRANCH 92 93 Duplicate atom serial number found: 93 Duplicate atom serial number found: 94 Duplicate atom serial number found: 95 Ignored bad PDB record found on line 7717 BRANCH 95 96 Duplicate atom serial number found: 96 Duplicate atom serial number found: 97 Ignored bad PDB record found on line 7720 BRANCH 96 98 Duplicate atom serial number found: 98 Duplicate atom serial number found: 99 Duplicate atom serial number found: 100 Ignored bad PDB record found on line 7724 BRANCH 100 101 Duplicate atom serial number found: 101 Ignored bad PDB record found on line 7726 BRANCH 101 102 Duplicate atom serial number found: 102 Duplicate atom serial number found: 103 Duplicate atom serial number found: 104 Ignored bad PDB record found on line 7730 ENDBRANCH 101 102 Ignored bad PDB record found on line 7731 BRANCH 101 105 Duplicate atom serial number found: 105 Duplicate atom serial number found: 106 Duplicate atom serial number found: 107 Ignored bad PDB record found on line 7735 BRANCH 107 108 Duplicate atom serial number found: 108 Ignored bad PDB record found on line 7737 BRANCH 108 109 Duplicate atom serial number found: 109 Duplicate atom serial number found: 110 Duplicate atom serial number found: 111 Ignored bad PDB record found on line 7741 BRANCH 111 112 Duplicate atom serial number found: 112 Ignored bad PDB record found on line 7743 BRANCH 112 113 Duplicate atom serial number found: 113 Duplicate atom serial number found: 114 Duplicate atom serial number found: 115 Ignored bad PDB record found on line 7747 BRANCH 115 116 Duplicate atom serial number found: 116 Ignored bad PDB record found on line 7749 BRANCH 116 117 Duplicate atom serial number found: 117 Duplicate atom serial number found: 118 Duplicate atom serial number found: 119 Ignored bad PDB record found on line 7753 ENDBRANCH 116 117 Ignored bad PDB record found on line 7754 BRANCH 116 120 Duplicate atom serial number found: 120 Ignored bad PDB record found on line 7756 BRANCH 120 121 Duplicate atom serial number found: 121 Duplicate atom serial number found: 122 Duplicate atom serial number found: 123 Duplicate atom serial number found: 124 Duplicate atom serial number found: 125 1 messages similar to the above omitted Ignored bad PDB record found on line 7763 ENDBRANCH 120 121 Ignored bad PDB record found on line 7764 ENDBRANCH 116 120 Ignored bad PDB record found on line 7765 ENDBRANCH 115 116 Ignored bad PDB record found on line 7766 ENDBRANCH 112 113 Ignored bad PDB record found on line 7767 BRANCH 112 127 Duplicate atom serial number found: 127 Ignored bad PDB record found on line 7769 BRANCH 127 128 Duplicate atom serial number found: 128 Duplicate atom serial number found: 129 Duplicate atom serial number found: 130 Ignored bad PDB record found on line 7773 ENDBRANCH 127 128 Ignored bad PDB record found on line 7774 ENDBRANCH 112 127 Ignored bad PDB record found on line 7775 ENDBRANCH 111 112 Ignored bad PDB record found on line 7776 ENDBRANCH 108 109 Ignored bad PDB record found on line 7777 BRANCH 108 132 Duplicate atom serial number found: 131 Duplicate atom serial number found: 132 Ignored bad PDB record found on line 7780 BRANCH 132 133 Duplicate atom serial number found: 133 Duplicate atom serial number found: 134 Duplicate atom serial number found: 135 Duplicate atom serial number found: 136 Ignored bad PDB record found on line 7785 BRANCH 133 137 Duplicate atom serial number found: 137 Duplicate atom serial number found: 138 Ignored bad PDB record found on line 7788 ENDBRANCH 133 137 Ignored bad PDB record found on line 7789 ENDBRANCH 132 133 Ignored bad PDB record found on line 7790 ENDBRANCH 108 132 Ignored bad PDB record found on line 7791 ENDBRANCH 107 108 Ignored bad PDB record found on line 7792 ENDBRANCH 101 105 7 messages similar to the above omitted Duplicate atom serial number found: 139 Duplicate atom serial number found: 140 Ignored bad PDB record found on line 7802 BRANCH 139 141 Duplicate atom serial number found: 141 Duplicate atom serial number found: 142 Ignored bad PDB record found on line 7805 ENDBRANCH 139 141 Ignored bad PDB record found on line 7806 ENDBRANCH 88 139 Ignored bad PDB record found on line 7807 ENDBRANCH 87 88 Ignored bad PDB record found on line 7808 ENDBRANCH 84 85 Ignored bad PDB record found on line 7809 BRANCH 84 143 Duplicate atom serial number found: 143 Ignored bad PDB record found on line 7811 BRANCH 143 144 Duplicate atom serial number found: 144 Ignored bad PDB record found on line 7813 BRANCH 144 145 Duplicate atom serial number found: 145 Duplicate atom serial number found: 146 Duplicate atom serial number found: 147 Ignored bad PDB record found on line 7817 ENDBRANCH 144 145 Ignored bad PDB record found on line 7818 ENDBRANCH 143 144 Ignored bad PDB record found on line 7819 ENDBRANCH 84 143 Ignored bad PDB record found on line 7820 ENDBRANCH 83 84 Ignored bad PDB record found on line 7821 ENDBRANCH 77 81 3 messages similar to the above omitted Duplicate atom serial number found: 148 Ignored bad PDB record found on line 7826 BRANCH 148 149 Duplicate atom serial number found: 149 Duplicate atom serial number found: 150 Duplicate atom serial number found: 151 Ignored bad PDB record found on line 7830 ENDBRANCH 148 149 Ignored bad PDB record found on line 7831 ENDBRANCH 73 148 Ignored bad PDB record found on line 7832 ENDBRANCH 72 73 Ignored bad PDB record found on line 7833 ENDBRANCH 69 70 Ignored bad PDB record found on line 7834 BRANCH 69 152 Duplicate atom serial number found: 152 Ignored bad PDB record found on line 7836 BRANCH 152 153 Ignored bad PDB record found on line 7840 ENDBRANCH 152 153 Ignored bad PDB record found on line 7841 ENDBRANCH 69 152 Ignored bad PDB record found on line 7842 ENDBRANCH 68 69 Ignored bad PDB record found on line 7843 ENDBRANCH 65 66 584 messages similar to the above omitted Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Ignored bad PDB record found on line 8643 ENDROOT Ignored bad PDB record found on line 8644 BRANCH 3 4 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 Ignored bad PDB record found on line 8647 ENDBRANCH 3 4 Ignored bad PDB record found on line 8648 TORSDOF 1 Ignored bad PDB record found on line 8649 REMARK Name = protein.pdb Ignored bad PDB record found on line 8650 REMARK 350 active torsions: Ignored bad PDB record found on line 8651 REMARK status: ('A' for Active; 'I' for Inactive) 351 messages similar to the above omitted Duplicate atom serial number found: 1 Ignored bad PDB record found on line 9006 ENDROOT Ignored bad PDB record found on line 9007 TORSDOF 0 Ignored bad PDB record found on line 9008 REMARK Name = protein.pdb Ignored bad PDB record found on line 9009 REMARK 350 active torsions: Ignored bad PDB record found on line 9010 REMARK status: ('A' for Active; 'I' for Inactive) 351 messages similar to the above omitted Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Ignored bad PDB record found on line 9367 ENDROOT Ignored bad PDB record found on line 9368 TORSDOF 0 Ignored bad PDB record found on line 9369 REMARK Name = protein.pdb Ignored bad PDB record found on line 9370 REMARK 350 active torsions: Ignored bad PDB record found on line 9371 REMARK status: ('A' for Active; 'I' for Inactive) 351 messages similar to the above omitted Duplicate atom serial number found: 1 Ignored bad PDB record found on line 9726 ENDROOT Ignored bad PDB record found on line 9727 BRANCH 1 3 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Ignored bad PDB record found on line 9730 ENDBRANCH 1 3 Ignored bad PDB record found on line 9731 BRANCH 1 4 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 Ignored bad PDB record found on line 9734 ENDBRANCH 1 4 Ignored bad PDB record found on line 9735 TORSDOF 2 Ignored bad PDB record found on line 9736 REMARK Name = protein.pdb Ignored bad PDB record found on line 9737 REMARK 350 active torsions: Ignored bad PDB record found on line 9738 REMARK status: ('A' for Active; 'I' for Inactive) 351 messages similar to the above omitted Duplicate atom serial number found: 1 Ignored bad PDB record found on line 10093 ENDROOT Ignored bad PDB record found on line 10094 BRANCH 1 2 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Ignored bad PDB record found on line 10097 ENDBRANCH 1 2 Ignored bad PDB record found on line 10098 BRANCH 1 4 Duplicate atom serial number found: 4 Ignored bad PDB record found on line 10100 BRANCH 4 5 Duplicate atom serial number found: 5 Duplicate atom serial number found: 6 Ignored bad PDB record found on line 10103 ENDBRANCH 4 5 Ignored bad PDB record found on line 10104 ENDBRANCH 1 4 Ignored bad PDB record found on line 10105 TORSDOF 3 Ignored bad PDB record found on line 10106 REMARK Name = protein.pdb Ignored bad PDB record found on line 10107 REMARK 350 active torsions: 352 messages similar to the above omitted Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 3 messages similar to the above omitted Ignored bad PDB record found on line 10470 ENDROOT Ignored bad PDB record found on line 10471 TORSDOF 0 Chain information for protein.pdb #2 --- Chain | Description A | No description available Opened protein.pdbqt containing 1 structures (821 atoms, 692 bonds) Computing secondary structure OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M4 OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.10.2, Qt 6.10.0 Qt runtime version: 6.10.1 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac16,12 Model Number: MW0Y3TU/A Chip: Apple M4 Total Number of Cores: 10 (4 Performance and 6 Efficiency) Memory: 16 GB System Firmware Version: 13822.81.10 OS Loader Version: 13822.81.10 Software: System Software Overview: System Version: macOS 26.3 (25D125) Kernel Version: Darwin 25.3.0 Time since boot: 95 gün 6 saat 7 dakika Graphics/Displays: Apple M4: Chipset Model: Apple M4 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: accessible-pygments: 0.0.5 aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.13.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 26.1.0 babel: 2.18.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 4.3.1 bs4: 0.0.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.7 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.2 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.67.1 ChimeraX-AtomicLibrary: 14.4 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4.1 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.4 ChimeraX-Cluster: 1.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.1 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.12rc202605192128 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.2.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.8.2 ChimeraX-Label: 1.5 ChimeraX-LightingGUI: 1.0 ChimeraX-ListInfo: 1.3.1 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.3 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchAlign: 1.1 ChimeraX-MatchMaker: 2.4 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.2.0 ChimeraX-MDcrds: 2.19 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.8 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.23 ChimeraX-ModelPanel: 1.6.1 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0.1 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.15.4 ChimeraX-OpenFold: 1.0 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.13 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.6 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.8.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.12 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.18 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SNFG: 1.0 ChimeraX-SpaceNavigator: 1.0 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#20393	duplicate	Crash in accessibility routines	Tom Goddard	chimerax-bug-report@…
Description	The following bug report has been submitted: Platform: macOS-26.5-arm64-arm-64bit ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x00000001f0c91e80 (most recent call first): 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 414 in event_loop File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 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, psutil._psutil_osx, psutil._psutil_posix, PIL._imaging, chimerax.map._map, chimerax.surface._surface, chimerax.pdb_lib._load_libs, 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, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 53) {"app_name":"ChimeraX","timestamp":"2026-05-26 20:44:53.00 +0800","app_version":"1.11.1","slice_uuid":"c20e09a8-923e-3fb3-856b-3e765bcb267b","build_version":"1.11.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 26.5 (25F71)","roots_installed":0,"name":"ChimeraX","incident_id":"DDFD8DE7-3ACB-418B-9154-EF861E2002DC"} { "uptime" : 16000, "procRole" : "Background", "version" : 2, "userID" : 501, "deployVersion" : 210, "modelCode" : "Mac16,8", "coalitionID" : 2429, "osVersion" : { "train" : "macOS 26.5", "build" : "25F71", "releaseType" : "User" }, "captureTime" : "2026-05-26 20:44:50.2601 +0800", "codeSigningMonitor" : 2, "incident" : "DDFD8DE7-3ACB-418B-9154-EF861E2002DC", "pid" : 22911, "translated" : false, "cpuType" : "ARM-64", "procLaunch" : "2026-05-26 20:15:39.6507 +0800", "procStartAbsTime" : 342886811054, "procExitAbsTime" : 384901406276, "procName" : "ChimeraX", "procPath" : "\/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX", "bundleInfo" : {"CFBundleShortVersionString":"1.11.1","CFBundleVersion":"1.11.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"}, "storeInfo" : {"deviceIdentifierForVendor":"4E0236E9-BE6A-50EE-89FE-0B03FAF837C5","thirdParty":true}, "parentProc" : "launchd", "parentPid" : 1, "coalitionName" : "edu.ucsf.cgl.ChimeraX", "crashReporterKey" : "3CBD6CDB-C595-E374-3DEC-118C93359FF2", "appleIntelligenceStatus" : {"reasons":["regionIneligible"],"state":"unavailable"}, "developerMode" : 1, "codeSigningID" : "edu.ucsf.cgl.ChimeraX", "codeSigningTeamID" : "LWV8X224YF", "codeSigningFlags" : 570491649, "codeSigningValidationCategory" : 6, "codeSigningTrustLevel" : 4294967295, "codeSigningAuxiliaryInfo" : 0, "instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRCuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkf\/f\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="}, "bootSessionUUID" : "C6F48A00-3E13-41FA-AD41-34B5A2BDD513", "sip" : "enabled", "vmRegionInfo" : "0x6171bbbc0776 is not in any region. 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REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 128K 1 Activity Tracing 256K 1 AttributeGraph Data 1024K 1 ColorSync 128K 6 CoreAnimation 1584K 94 CoreGraphics 48K 3 CoreUI image data 2848K 19 Foundation 80K 2 Kernel Alloc Once 32K 1 MALLOC 288.3M 83 MALLOC guard page 3728K 4 Mach message 64K 3 Memory Tag 22 64.0M 1 OpenGL GLSL 256K 3 PROTECTED_MEMORY 16K 1 STACK GUARD 624K 39 Stack 193.4M 40 Stack Guard 56.0M 1 VM_ALLOCATE 183.3M 147 VM_ALLOCATE (reserved) 288.0M 1 reserved VM address space (unallocated) __AUTH 6144K 646 __AUTH_CONST 91.3M 1042 __CTF 824 1 __DATA 42.5M 1130 __DATA_CONST 61.3M 1178 __DATA_DIRTY 8458K 896 __FONT_DATA 2352 1 __GLSLBUILTINS 5176K 1 __LINKEDIT 604.3M 133 __OBJC_RO 79.1M 1 __OBJC_RW 2599K 1 __TEXT 1.5G 1200 __TPRO_CONST 128K 2 dyld private memory 304K 5 mapped file 327.6M 57 page table in kernel 1234K 1 shared memory 3712K 26 =========== ======= ======= TOTAL 3.7G 6772 TOTAL, minus reserved VM space 3.5G 6772 ", "legacyInfo" : { "threadTriggered" : { "name" : "CrBrowserMain", "queue" : "com.apple.main-thread" } }, "logWritingSignature" : "f5e14e193fc5ff30984282cc5492eaaf55c16cd7", "bug_type" : "309", "roots_installed" : 0, "trmStatus" : 1, "voucherInfos" : [{"originatorName":"SkyComputerUseClient","proximateName":"SkyComputerUseService","thread_id":215895}], "trialInfo" : { "rollouts" : [ { "rolloutId" : "644114de41e7236e6177f9bd", "factorPackIds" : [ ], "deploymentId" : 240000013 }, { "rolloutId" : "6425c75e4327780c10cc4252", "factorPackIds" : [ "642600a457e7664b1698eb32" ], "deploymentId" : 240000004 } ], "experiments" : [ ] } } ===== Log before crash start ===== 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/jin/Downloads/1BF5-assembly1.cif 1BF5-assembly1.cif title: Tyrosine phosphorylated stat-1/DNA complex [more info...] Chain information for 1BF5-assembly1.cif #1 --- Chain | Description A A-2 | SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 1-ALPHA/BETA B-2 | DNA (5'-D(*AP*CP*AP*GP*TP*TP*TP*CP*CP*CP*GP*TP*AP*AP*AP*TP*G P*C)-3') C-2 | DNA (5'-D(*TP*GP*CP*AP*TP*TP*TP*AP*CP*GP*GP*GP*AP*AP*AP*CP*T P*G)-3') > save /Users/jin/Downloads/1BF5_assembly.pdb models #1 Chain IDs longer than 2 characters; truncating > split #2 atoms #2//chain_id==A atoms #2//chain_id=="A-2" atoms (#2//chain_id=="B-2" | #2//chain_id=="C-2") > split #1 atoms #1//chain_id==A atoms #1//chain_id=="A-2" atoms (#1//chain_id=="B-2" | #1//chain_id=="C-2") Split 1BF5-assembly1.cif (#1) into 3 models Chain information for 1BF5-assembly1.cif 1 #1.1 --- Chain | Description A | No description available Chain information for 1BF5-assembly1.cif 2 #1.2 --- Chain | Description A-2 | No description available Chain information for 1BF5-assembly1.cif 3 #1.3 --- Chain | Description B-2 | No description available C-2 | No description available > hide #!1 models > show #!1 models > hide #!1.1 models > show #!1.1 models > hide #!1.2 models > show #!1.2 models > hide #1.3 models > show #1.3 models > hide #1.3 models > hide #!1.2 models > show #!1.2 models > hide #!1.2 models > show #!1.2 models > hide #!1.2 models > show #!1.2 models > open > /Users/jin/Downloads/fold_stat5b_human_2026_05_13_14_48/fold_stat5b_human_2026_05_13_14_48_model_0.cif Chain information for fold_stat5b_human_2026_05_13_14_48_model_0.cif #2 --- Chain | Description A | . Computing secondary structure Called accessibilityLabel on invalid object: 2147489986 Called accessibilityLabel on invalid object: 2147489999 Called accessibilityLabel on invalid object: 2147489955 Called accessibilityLabel on invalid object: 2147490062 Called accessibilityLabel on invalid object: 2147490012 > matchmaker #2 to #1.1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 1BF5-assembly1.cif 1, chain A (#1.1) with fold_stat5b_human_2026_05_13_14_48_model_0.cif, chain A (#2), sequence alignment score = 1017.1 RMSD between 297 pruned atom pairs is 1.162 angstroms; (across all 513 pairs: 11.341) > show #1.3 models > hide #1.3 models > hide #!1.2 models > select #1.1:699 Nothing selected ===== Log before crash end ===== 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 OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M4 Pro 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 Pro Model Identifier: Mac16,8 Model Number: MX2H3CH/A Chip: Apple M4 Pro Total Number of Cores: 12 (8 Performance and 4 Efficiency) Memory: 24 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: 4小时27分钟 Graphics/Displays: Apple M4 Pro: Chipset Model: Apple M4 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Mi Monitor: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina 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 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Query Language

query: TracLinks and the [[TicketQuery]] macro both use a mini “query language” for specifying query filters. Basically, the filters are separated by ampersands (&). Each filter then 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 left out 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

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See also: TracTickets, TracReports, TracGuide