![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
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.
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:
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:
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 13761)
| Ticket | Resolution | Summary | Owner | Reporter |
|---|---|---|---|---|
| #20245 | duplicate | Crash in QAccessible::uniqueId | ||
| #20243 | duplicate | Crash in QDockWidget::event() in Qt 6.9.2 | ||
| #20242 | can't reproduce | Error in atom spec evaluation |
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 13761)
| Ticket | Resolution | Summary | Owner | Reporter |
|---|---|---|---|---|
| #20245 | duplicate | Crash in QAccessible::uniqueId | ||
| Description |
The following bug report has been submitted:
Platform: macOS-14.1.1-arm64-arm-64bit
ChimeraX Version: 1.12.dev202604290127 (2026-04-29 01:27:48 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 0x00000001d9891ec0 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 424 in event_loop
File "/Applications/ChimeraX_Daily.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_Daily.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, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, 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, charset_normalizer.md, charset_normalizer.cd, requests.packages.charset_normalizer.md, requests.packages.chardet.md, requests.packages.charset_normalizer.cd, requests.packages.chardet.cd (total: 47)
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"procLaunch" : "2026-04-29 18:43:26.4881 +0100",
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"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4334567424
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 1025c4000-1025c8000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":67681},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4334567424
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 1025c4000-1025c8000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
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"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 2883584,
"uuid" : "4dffb7eb-bbcd-3ff6-a203-5a0b97358ee8",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6559223808,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 20008960,
"uuid" : "b475e541-691d-39c6-8ca4-e414b0d3dd88",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2487.20.107"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6496317440,
"size" : 607000,
"uuid" : "ec7a3ba0-f9bf-3ab8-a0f4-8622e5606b20",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6518382592,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.Foundation",
"size" : 12902400,
"uuid" : "2126fd9a-52ce-3eb2-8640-b57535e073b8",
"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
"name" : "Foundation",
"CFBundleVersion" : "2106"
}
],
"sharedCache" : {
"base" : 6495567872,
"size" : 4018896896,
"uuid" : "80dd42b3-8a52-3caf-9848-54a1c2732864"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=2.0G resident=0K(0%) swapped_out_or_unallocated=2.0G(100%)
Writable regions: Total=2.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.3G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 128K 1
Activity Tracing 256K 1
CG image 5568K 24
CG raster data 3328K 4
ColorSync 640K 30
CoreAnimation 832K 52
CoreGraphics 32K 2
CoreServices 624K 2
CoreUI image data 3472K 24
Foundation 48K 2
Kernel Alloc Once 32K 1
MALLOC 1.7G 86
MALLOC guard page 192K 12
Mach message 96K 3
OpenGL GLSL 256K 3
PROTECTED_MEMORY 16K 1
STACK GUARD 672K 42
Stack 239.9M 43
Stack Guard 56.0M 1
VM_ALLOCATE 159.3M 136
VM_ALLOCATE (reserved) 160.0M 4 reserved VM address space (unallocated)
__AUTH 3254K 551
__AUTH_CONST 40.2M 810
__CTF 824 1
__DATA 25.1M 925
__DATA_CONST 67.3M 938
__DATA_DIRTY 2888K 320
__FONT_DATA 4K 1
__GLSLBUILTINS 5174K 1
__INFO_FILTER 8 1
__LINKEDIT 913.7M 122
__OBJC_RO 70.8M 1
__OBJC_RW 2156K 1
__TEXT 1.1G 956
dyld private memory 320K 4
mapped file 226.2M 108
shared memory 3168K 23
=========== ======= =======
TOTAL 4.7G 5237
TOTAL, minus reserved VM space 4.6G 5237
",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "cea5a0272b6af480487960391e53923d52e9e689",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "645197bf528fbf3c3af54105",
"factorPackIds" : {
"SIRI_VALUE_INFERENCE_PERVASIVE_ENTITY_RESOLUTION" : "663e65b4a1526e1ca0e288a1"
},
"deploymentId" : 240000002
},
{
"rolloutId" : "644114de41e7236e6177f9bd",
"factorPackIds" : {
},
"deploymentId" : 240000013
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.12.dev202604290127 (2026-04-29)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show AlphaFold
QTextCursor::setPosition: Position '1' out of range
> alphafold predict
> MHSLATAAPVPTTLAQVDREKIYQWINELSSPETRENALLELSKKRESVPDLAPMLWHSFGTIAALLQEIVNIYPSINPPTLTAHQSNRVCNALALLQCVASHPETRSAFLAAHIPLFLYPFLHTVSKTRPFEYLRLTSLGVIGALVKTDEQEVINFLLTTEIIPLCLRIMESGSELSKTVATFILQKILLDDTGLAYICQTYERFSHVAMILGKMVLQLSKEPSARLLKHVVRCYLRLSDNPRAREALRQCLPDQLKDTTFAQVLKDDTTTKRWLAQLVKNLQEGQVTDPRGIPLPPQ,MLTMLTDRIDSQLVLSRLPRSRFQRFWETPTLIMKEESAPSSGSIILAEKSVNMRYCVRFASDSDFQTTFTLPQSTEEKYDKEQHPGEDEASSPLPSPLKVPYKWMPSSFIVKQCHTQLAFYNKHIIWLSRERKVPTSLGVSLYIPEGFFGITFYKCLDAQFVCMPELLESGLQVPQLDVVNLNDTFQSIFPGTIEGDIGVFPCFVPEPWQLMNLPPPNEHRFFSLRTRQTLVIGPGHTQTVYFDAAYVHAPGICALIVGVRQFSQSDLIIRPTIWLPGTAAGVTVVNTSHTTVCISPHTTVAKAVFTTHRFTYLPVGSHPLGQMIVPPTPDIGFTHTPEHALLQRTPSPVDDDVDETEEDEKSSDAESPVNTSDVIFDVGPKPPRHP
Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.
Running AlphaFold prediction
QTextCursor::setPosition: Position '1' out of range
QTextCursor::setPosition: Position '689' out of range
QTextCursor::setPosition: Position '690' out of range
QTextCursor::setPosition: Position '1' out of range
> help help:user/tools/alphafold.html
QTextCursor::setPosition: Position '1' out of range
> alphafold predict
> MHSLATAAPVPTTLAQVDREKIYQWINELSSPETRENALLELSKKRESVPDLAPMLWHSFGTIAALLQEIVNIYPSINPPTLTAHQSNRVCNALALLQCVASHPETRSAFLAAHIPLFLYPFLHTVSKTRPFEYLRLTSLGVIGALVKTDEQEVINFLLTTEIIPLCLRIMESGSELSKTVATFILQKILLDDTGLAYICQTYERFSHVAMILGKMVLQLSKEPSARLLKHVVRCYLRLSDNPRAREALRQCLPDQLKDTTFAQVLKDDTTTKRWLAQLVKNLQEGQVTDPRGIPLPPQ
Running AlphaFold prediction
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.12.dev202604290127 (2026-04-29)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.9
Locale: UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.1
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Model Number: MYD92RU/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 10151.41.12
OS Loader Version: 10151.41.12
Software:
System Software Overview:
System Version: macOS 14.1.1 (23B81)
Kernel Version: Darwin 23.1.0
Time since boot: 5 days, 1 hour, 53 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
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: 4.1.2
bs4: 0.0.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.7
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.67.1
ChimeraX-AtomicLibrary: 14.4
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4.1
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.4
ChimeraX-Cluster: 1.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12.dev202604290127
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.2.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.8.2
ChimeraX-Label: 1.4
ChimeraX-LightingGUI: 1.0
ChimeraX-ListInfo: 1.3.1
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchAlign: 1.1
ChimeraX-MatchMaker: 2.4
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.19
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.8
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.23
ChimeraX-ModelPanel: 1.6.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.4
ChimeraX-OpenFold: 1.0
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.13
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.6
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.12
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.18
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.4
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.50.5
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.3
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.5
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
debugpy: 1.8.20
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.62.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.16.0
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.13
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 2.0.0
iniconfig: 2.3.0
ipykernel: 7.1.0
ipython: 9.9.0
ipython_pygments_lexers: 1.1.1
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.8.0
jupyter_core: 5.9.1
kiwisolver: 1.5.0
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.1
narwhals: 2.20.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
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: 4.9.6
plotly: 6.7.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.13.3
pydantic-settings: 2.14.0
pydantic_core: 2.46.3
pydata-sphinx-theme: 0.17.1
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.5.1
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.10.2
PyQt6-Qt6: 6.10.1
PyQt6-WebEngine-commercial: 6.10.0
PyQt6-WebEngine-Qt6: 6.10.1
PyQt6_sip: 13.10.3
pytest: 9.0.3
pytest-cov: 7.1.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.27
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 9.0.4
sphinx-autodoc-typehints: 3.6.1
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.4.1
stack-data: 0.6.3
starlette: 1.0.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 3.2.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.5
tqdm: 4.67.3
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
Unidecode: 1.4.0
urllib3: 2.6.3
uvicorn: 0.46.0
wcwidth: 0.6.0
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
yarl: 1.23.0
|
|||
| #20243 | duplicate | Crash in QDockWidget::event() in Qt 6.9.2 | ||
| Description |
The following bug report has been submitted:
Platform: macOS-26.3.1-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.
{"app_name":"ChimeraX","timestamp":"2026-04-28 23:12:48.00 -0700","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 26.3.1 (25D771280a)","roots_installed":0,"name":"ChimeraX","incident_id":"622683A9-CAA4-4B32-AEA3-12C50DEF63E7"}
{
"uptime" : 38000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac14,5",
"coalitionID" : 8643,
"osVersion" : {
"train" : "macOS 26.3.1",
"build" : "25D771280a",
"releaseType" : "User"
},
"captureTime" : "2026-04-28 23:12:37.3218 -0700",
"codeSigningMonitor" : 2,
"incident" : "622683A9-CAA4-4B32-AEA3-12C50DEF63E7",
"pid" : 83281,
"translated" : false,
"cpuType" : "ARM-64",
"procLaunch" : "2026-04-28 22:21:59.3604 -0700",
"procStartAbsTime" : 854598862732,
"procExitAbsTime" : 927509538556,
"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":"5922596A-238F-57CD-BA55-0E4530670318","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "EC79E13B-C433-BC40-C5F9-15228F381DA6",
"appleIntelligenceStatus" : {"state":"available"},
"developerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
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Log:
> ui tool hide "command line interface"
> ui tool show clix
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 M2 Max
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: Mac14,5
Model Number: MPHG3LL/A
Chip: Apple M2 Max
Total Number of Cores: 12 (8 Performance and 4 Efficiency)
Memory: 32 GB
System Firmware Version: 13822.81.10
OS Loader Version: 13822.81.10
Software:
System Software Overview:
System Version: macOS 26.3.1 (a) (25D771280a)
Kernel Version: Darwin 25.3.0
Time since boot: 43 minutes, 12 seconds
Graphics/Displays:
Apple M2 Max:
Chipset Model: Apple M2 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 30
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
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-Clipper: 0.26.1
ChimeraX-clix: 0.2.6
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-DAQplugin: 0.13.60
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-ISOLDE: 1.11.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.5.4
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
flatbuffers: 25.12.19
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
mrcfile: 1.5.4
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
onnxruntime: 1.25.1
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
protobuf: 7.34.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
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: 3.2.0
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: 0.3.2
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
|
|||
| #20242 | can't reproduce | Error in atom spec evaluation | ||
| Description |
The following bug report has been submitted:
Platform: Windows-10-10.0.26100
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Tried to make electrostatic surface of the protein
Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> D:/Projects/HERC5/data_sorted/80S-HERC5-dimer-1/80S_HERC5-dimer1-517-coot-4.pdb
Summary of feedback from opening
D:/Projects/HERC5/data_sorted/80S-HERC5-dimer-1/80S_HERC5-dimer1-517-coot-4.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LEU D 5 PHE D 9 1 5
Start residue of secondary structure not found: HELIX 2 2 PHE D 17 PHE D 21 1
5
Start residue of secondary structure not found: HELIX 3 3 ASP D 26 LYS D 37 1
12
Start residue of secondary structure not found: HELIX 4 4 ASN I 51 ARG I 63 1
13
Start residue of secondary structure not found: HELIX 5 5 ASP A 33 GLY A 39 1
7
195 messages similar to the above omitted
End residue of secondary structure not found: HELIX 201 201 GLY b 105 LEU b
118 1 14
Start residue of secondary structure not found: HELIX 202 202 SER c 10 MET c
22 1 13
Start residue of secondary structure not found: HELIX 203 203 GLY c 30 GLN c
40 1 11
Start residue of secondary structure not found: HELIX 204 204 PRO c 53 LYS c
68 1 16
Start residue of secondary structure not found: HELIX 205 205 ASN c 77 CYS c
85 1 9
Start residue of secondary structure not found: HELIX 206 206 ILE d 29 HIS d
34 1 6
648 messages similar to the above omitted
Cannot find LINK/SSBOND residue K (5360 )
Cannot find LINK/SSBOND residue A (2529 )
Cannot find LINK/SSBOND residue G (2584 )
Cannot find LINK/SSBOND residue G (2331 )
Cannot find LINK/SSBOND residue C (2411 )
1015 messages similar to the above omitted
Chain information for 80S_HERC5-dimer1-517-coot-4.pdb #1
---
Chain | Description
8 | No description available
CD | No description available
CI | No description available
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LU | No description available
LV | No description available
LW | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
Lp | No description available
Lr | No description available
Ls | No description available
Lt | No description available
Pt | No description available
S2 | No description available
SA | No description available
SB | No description available
SC | No description available
SD | No description available
SE | No description available
SF | No description available
SG | No description available
SH | No description available
SI | No description available
SJ | No description available
SK | No description available
SL | No description available
SM | No description available
SN | No description available
SO | No description available
SP | No description available
SQ | No description available
SR | No description available
SS | No description available
ST | No description available
SU | No description available
SV | No description available
SW | No description available
SX | No description available
SY | No description available
SZ | No description available
Sa | No description available
Sb | No description available
Sc | No description available
Sd | No description available
Se | No description available
Sf | No description available
Sg | No description available
a b | No description available
23 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> show cartoons
Computing secondary structure
> hide atoms
> select /a
8006 atoms, 8189 bonds, 999 residues, 1 model selected
> save D:/Projects/HERC5/data_sorted/80S-HERC5-dimer-1/mono1.pdb selectedOnly
> true
> select /b
8004 atoms, 8188 bonds, 997 residues, 1 model selected
> save D:/Projects/HERC5/data_sorted/80S-HERC5-dimer-1/mono2.pdb selectedOnly
> true relModel #1
> open D:/Projects/HERC5/data_sorted/80S-HERC5-dimer-1/mono1.pdb
> D:/Projects/HERC5/data_sorted/80S-HERC5-dimer-1/mono2.pdb
Summary of feedback from opening
D:/Projects/HERC5/data_sorted/80S-HERC5-dimer-1/mono1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLNCD 6 GLYCD 8 1 3
Start residue of secondary structure not found: HELIX 2 2 ASPCD 18 LEUCD 20 1
3
Start residue of secondary structure not found: HELIX 3 3 PROCD 27 ASNCD 36 1
10
Start residue of secondary structure not found: HELIX 4 4 GLNCI 52 VALCI 62 1
11
Start residue of secondary structure not found: HELIX 5 5 PHELA 34 HISLA 38 1
5
901 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYSS (121 )
Cannot find LINK/SSBOND residue CYSS (121 )
Cannot find LINK/SSBOND residue CYSS (121 )
Cannot find LINK/SSBOND residue CYSS (126 )
Cannot find LINK/SSBOND residue CYSS (126 )
2 messages similar to the above omitted
Summary of feedback from opening
D:/Projects/HERC5/data_sorted/80S-HERC5-dimer-1/mono2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLNCD 6 GLYCD 8 1 3
Start residue of secondary structure not found: HELIX 2 2 ASPCD 18 LEUCD 20 1
3
Start residue of secondary structure not found: HELIX 3 3 PROCD 27 ASNCD 36 1
10
Start residue of secondary structure not found: HELIX 4 4 GLNCI 52 VALCI 62 1
11
Start residue of secondary structure not found: HELIX 5 5 PHELA 34 HISLA 38 1
5
897 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYSS (121 )
Cannot find LINK/SSBOND residue CYSS (121 )
Cannot find LINK/SSBOND residue CYSS (121 )
Cannot find LINK/SSBOND residue CYSS (126 )
Cannot find LINK/SSBOND residue CYSS (126 )
2 messages similar to the above omitted
Chain information for mono1.pdb #2
---
Chain | Description
a | No description available
Chain information for mono2.pdb #3
---
Chain | Description
b | No description available
> hide #!1 models
> select #2/a:774
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #2
8006 atoms, 8189 bonds, 999 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen copy of mono1.pdb #/a ALA 365 H bonded to atom that should not have
hydrogens (copy of mono1.pdb #/a ALA 365 C)
> select H
Nothing selected
> select 365
Expected an objects specifier or a keyword
> select :365
75 atoms, 70 bonds, 9 residues, 3 models selected
> close #1
> select :365
10 atoms, 8 bonds, 2 residues, 2 models selected
> delete sel
> select add #2
8001 atoms, 8184 bonds, 998 residues, 1 model selected
> coulombic sel
Traceback (most recent call last):
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\std_commands\defattr.py", line 185, in defattr
objects = atom_spec.evaluate(session, models=restriction)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\atomspec.py", line 1157, in evaluate
results = self._left_spec.evaluate(
^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\atomspec.py", line 1067, in evaluate
return self.find_matches(session, models, results, ordered,
add_implied=add_implied)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\atomspec.py", line 1070, in find_matches
self._specifier.find_matches(session, models, results, ordered,
add_implied=add_implied)
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\atomspec.py", line 511, in find_matches
model_spec.find_matches(session, model_list, results, ordered,
add_implied=add_implied)
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\atomspec.py", line 673, in find_matches
_add_model_parts(session, model, self.sub_parts, results, ordered)
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\atomspec.py", line 693, in _add_model_parts
chain_spec.find_selected_parts(model, atoms, num_atoms, my_results)
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\atomspec.py", line 628, in find_selected_parts
subpart.find_selected_parts(model, atoms, num_atoms, sub_results)
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\atomspec.py", line 617, in find_selected_parts
atoms = self._filter_parts(model, atoms, num_atoms)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\atomspec.py", line 635, in _filter_parts
mask = model.atomspec_filter(self.Symbol, atoms, num_atoms,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1024, in atomspec_filter
return self._atomspec_filter_residue(atoms, num_atoms, parts, attrs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1089, in _atomspec_filter_residue
selected = self._atomspec_attr_filter(atoms.residues, selected, attrs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1061, in _atomspec_attr_filter
selected = [(selected[i] and choose(obj)) for i, obj in enumerate(objects)]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1061, in <listcomp>
selected = [(selected[i] and choose(obj)) for i, obj in enumerate(objects)]
~~~~~~~~^^^
IndexError: tuple index out of range
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 230, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1420, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\shortcuts\\__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1393, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 403, in try_shortcut
self.run_shortcut(keys)
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 421, in run_shortcut
sc.run(self.session, status = self._enabled)
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 340, in run
f(s)
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 72, in func_plus_tip
func(cmd + " %s")(session)
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 594, in run_expanded_command
run(session, cmd)
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 537, in run
run_command(session, command, **kw)
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\coulombic\cmd.py", line 102, in cmd_coulombic
assign_charges(session, needs_assignment, his_scheme, charge_method,
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\coulombic\coulombic.py", line 110, in assign_charges
add_charges(session, charged_residues, method=charge_method, status=status,
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\add_charge\charge.py", line 34, in add_charges
uncharged_res_types = add_standard_charges(session, residues, status=status,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\add_charge\charge.py", line 81, in add_standard_charges
defattr(session, attr_file, restriction=structures, summary=False)
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\std_commands\defattr.py", line 187, in defattr
raise SyntaxError("Error evaluating atom specifier (%s) on line %d of %s: %s"
SyntaxError: Error evaluating atom specifier (::amber_name=ARG @oxt,ot2,2oct)
on line 179 of D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\add_charge\amber_name.defattr: tuple index out of range
SyntaxError: Error evaluating atom specifier (::amber_name=ARG @oxt,ot2,2oct)
on line 179 of D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\add_charge\amber_name.defattr: tuple index out of range
File "D:\Soft\Work\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\std_commands\defattr.py", line 187, in defattr
raise SyntaxError("Error evaluating atom specifier (%s) on line %d of %s: %s"
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 591.74
OpenGL renderer: NVIDIA GeForce RTX 4080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.9
Locale: en_US.cp1252
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: windows
Manufacturer: Gigabyte Technology Co., Ltd.
Model: Z790 AORUS ELITE AX
OS: Microsoft Windows 11 Enterprise (Build 26100)
Memory: 137,254,060,032
MaxProcessMemory: 137,438,953,344
CPU: 32 13th Gen Intel(R) Core(TM) i9-13900KF
OSLanguage: en-US
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2026.1.4
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
comtypes: 1.4.11
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pywin32: 311
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
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: 3.2.0
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
tzdata: 2025.3
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.3.2
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
WMI: 1.5.1
yarl: 1.22.0
|
|||
Query Language
query: TracLinks and the [[TicketQuery]] macro both use a mini “query language” for specifying query filters. Filters are separated by ampersands (&). Each filter consists of the ticket field name, an operator and one or more values. More than one value are separated by a pipe (|), meaning that the filter matches any of the values. To include a literal & or | in a value, escape the character with a backslash (\).
The available operators are:
= | the field content exactly matches one of the values |
~= | the field content contains one or more of the values |
^= | the field content starts with one of the values |
$= | the field content ends with one of the values |
All of these operators can also be negated:
!= | the field content matches none of the values |
!~= | the field content does not contain any of the values |
!^= | the field content does not start with any of the values |
!$= | the field content does not end with any of the values |
The date fields created and modified can be constrained by using the = operator and specifying a value containing two dates separated by two dots (..). Either end of the date range can be left empty, meaning that the corresponding end of the range is open. The date parser understands a few natural date specifications like "3 weeks ago", "last month" and "now", as well as Bugzilla-style date specifications like "1d", "2w", "3m" or "4y" for 1 day, 2 weeks, 3 months and 4 years, respectively. Spaces in date specifications can be omitted to avoid having to quote the query string.
created=2007-01-01..2008-01-01 | query tickets created in 2007 |
created=lastmonth..thismonth | query tickets created during the previous month |
modified=1weekago.. | query tickets that have been modified in the last week |
modified=..30daysago | query tickets that have been inactive for the last 30 days |
See also: TracTickets, TracReports, TracGuide, TicketQuery
Last modified
9 years ago
Last modified on Jan 4, 2017, 10:45:36 AM
Note:
See TracWiki
for help on using the wiki.
