![[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 13309)
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 13309)
| Ticket | Resolution | Summary | Owner | Reporter |
|---|---|---|---|---|
| #19536 | duplicate | Crash in swap_buffers waking from sleep, macOS 26.2 | ||
| Description |
The following bug report has been submitted:
Platform: macOS-26.2-arm64-arm-64bit
ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error
Current thread 0x0000000208d2ec40 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 248 in swap_buffers
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 561 in swap_buffers
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py", line 166 in status
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py", line 98 in _expose_event
File "/Applications/ChimeraX-1.11.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.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.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.map._map, chimerax.surface._surface, PIL._imaging, 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 (total: 47)
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REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
unused __TEXT 2ec8d4000-2ec8d8000 [ 16K] r--\/r-- SM=COW unused unknown system shared lib __TEXT
GAP OF 0x1bb728000 BYTES
---> commpage (reserved) 4a8000000-7a6800000 [ 12.0G] ---\/--- SM=NUL reserved VM address space (unallocated)
MALLOC_SMALL 7a6800000-7a6c00000 [ 4096K] rw-\/rwx SM=PRV ",
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unused __TEXT 2ec8d4000-2ec8d8000 [ 16K] r--\/r-- SM=COW unused unknown system shared lib __TEXT
GAP OF 0x1bb728000 BYTES
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MALLOC_SMALL 7a6800000-7a6c00000 [ 4096K] rw-\/rwx SM=PRV ",
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Writable regions: Total=845.1M written=7602K(1%) resident=1074K(0%) swapped_out=6528K(1%) unallocated=837.7M(99%)
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Activity Tracing 256K 1
AttributeGraph Data 1024K 1
CG image 1088K 36
ColorSync 176K 11
CoreAnimation 5568K 160
CoreGraphics 32K 2
CoreServices 624K 2
CoreUI image data 2960K 33
Foundation 432K 6
Kernel Alloc Once 48K 2
MALLOC 308.5M 112
MALLOC guard page 3248K 4
Mach message 64K 3
OpenGL GLSL 256K 3
PROTECTED_MEMORY 16K 1
STACK GUARD 56.7M 44
Stack 210.5M 44
VM_ALLOCATE 153.5M 187
VM_ALLOCATE (reserved) 160.0M 1 reserved VM address space (unallocated)
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__CTF 824 1
__DATA 43.1M 1125
__DATA_CONST 59.2M 1173
__DATA_DIRTY 8779K 902
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__OBJC_RW 2570K 1
__TEXT 1.4G 1187
__TEXT (graphics) 7264K 8
__TPRO_CONST 128K 2
dyld private memory 432K 6
mapped file 351.7M 74
page table in kernel 1074K 1
shared memory 3664K 21
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TOTAL 3.6G 6993
TOTAL, minus reserved VM space 3.4G 6993
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/yuanpengtao/Downloads/Structure2D_COMPOUND_CID_1587486.sdf
> format sdf
No such file/path:
/Users/yuanpengtao/Downloads/Structure2D_COMPOUND_CID_1587486.sdf
> open 8rq8 format mmcif fromDatabase pdb
8rq8 title:
Crystal structure of CRBN-midi in complex with mezigdomide [more info...]
Chain information for 8rq8 #1
---
Chain | Description | UniProt
A | Protein cereblon | CRBN_HUMAN 41-187 249-426
Non-standard residues in 8rq8 #1
---
QFC — Mezigdomide
ZN — zinc ion
> select :QFC
42 atoms, 47 bonds, 1 residue, 1 model selected
Must select at least one chain from each list
> ui tool show Contacts
> lighting full
> lighting soft
> lighting simple
> lighting soft
Unsupported scale factor (0.000000) detected on Display1
Desktop color scheme is light
Desktop color scheme is dark
Desktop color scheme is light
Desktop color scheme is dark
Desktop color scheme is light
Desktop color scheme is dark
Desktop color scheme is light
Unsupported scale factor (0.000000) detected on Display0
Desktop color scheme is dark
Unsupported scale factor (0.000000) detected on Display0
Desktop color scheme is light
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/yuanpengtao/Downloads/ChimeraX/AlphaFold/prediction_3/best_model.pdb
> format pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac14,2
Model Number: Z1610002FCH/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 13822.61.10
OS Loader Version: 13822.61.10
Software:
System Software Overview:
System Version: macOS 26.2 (25C56)
Kernel Version: Darwin 25.2.0
Time since boot: 6天10小时58分钟
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
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: No
Connection Type: Internal
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.11
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.25.1
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.2.5
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pytz: 2025.2
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.0.0
roman-numerals-py: 4.0.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.0.4
stack-data: 0.6.3
starlette: 0.50.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2025.3
urllib3: 2.6.2
uvicorn: 0.38.0
wcwidth: 0.2.14
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
|
|||
| #19535 | duplicate | Crash on Mac waking from sleep | ||
| Description |
The following bug report has been submitted:
Platform: macOS-15.7.1-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x0000000206d4a140 (most recent call first):
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, psutil._psutil_osx, psutil._psutil_posix, chimerax.surface._surface, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.xtc_utils, openmm.app.internal.compiled, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, lxml.builder, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 63)
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{
"uptime" : 5400,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac15,3",
"coalitionID" : 1700,
"osVersion" : {
"train" : "macOS 15.7.1",
"build" : "24G231",
"releaseType" : "User"
},
"captureTime" : "2025-12-23 11:21:41.2017 +1300",
"codeSigningMonitor" : 1,
"incident" : "6A6AE09C-7429-4D43-A982-744E4F61ACA9",
"pid" : 4690,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-12-23 10:05:34.7779 +1300",
"procStartAbsTime" : 22251877805,
"procExitAbsTime" : 131848131777,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.1","CFBundleVersion":"1.10.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"5E6B9D0E-B24A-5F0D-B03B-60D34F0A124C","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "B764343E-6690-75E4-BB9E-16AB9F8A0AF2",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["siriAssetIsNotReady","assetIsNotReady","notOptedIn"]},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "EFC49F7F-4351-4046-8320-4F37DC17BB24",
"sip" : "enabled",
"vmRegionInfo" : "0x6fd500187144 is not in any region. \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x00186fd500187144","rawCodes":[1,6878360061374788],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00186fd500187144 -> 0x00006fd500187144 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":4690},
"vmregioninfo" : "0x6fd500187144 is not in any region. \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n UNUSED SPACE AT END",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
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===== Log before crash start =====
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Master Chimerax Workspaces/PCH45
> Neck/PCH45_NeckFitting_6.cxs"
Opened PCH45_Neck_C6_3_40A_map_sharp.mrc as #3, grid size 416,416,416, pixel
1.37, shown at level 0.236, step 1, values float32
Opened Sheath[Unrefined]_C6Ring_R4?_ as #9, grid size 416,416,416, pixel 1.37,
shown at level 0.889, step 1, values float32
Opened Unnaccounted_for_Volumes as #14, grid size 416,416,416, pixel 1.37,
shown at level 0.662, step 1, values float32
Opened PCH45_Neck_C6_3_40A_map_sharp.mrc zone as #13, grid size 416,416,416,
pixel 1.37, shown at level 0.604, step 1, values float32
Opened Unaccounted_volumes_updated as #15, grid size 416,416,416, pixel 1.37,
shown at level 0.537, step 1, values float32
Opened PCH45_Neck_C6_3_40A_map_sharp.mrc zone as #18, grid size 416,416,416,
pixel 1.37, shown at level 0.887, step 1, values float32
Opened Unaccounted3 as #19, grid size 416,416,416, pixel 1.37, shown at level
0.457, step 1, values float32
Opened Gp24[Adaptor]_C6Ring_R4 as #24, grid size 416,416,416, pixel 1.37,
shown at level 0.82, step 1, values float32
Opened PCH45_Rough_Segmap cry.mrc as #23, grid size 416,416,416, pixel 1.37,
shown at level 0.497, step 1, values float32
Opened PCH45_Neck_C6_3_40A_map_sharp.mrc zone as #2, grid size 416,416,416,
pixel 1.37, shown at level 0.585, step 1, values float32
Opened PCH45_Neck_C6_3_40A_map_sharp.mrc zone as #25, grid size 416,416,416,
pixel 1.37, shown at level 0.585, step 1, values float32
Opened PCH45_Neck_C6_3_40A_map_sharp.mrc zone as #30, grid size 416,416,416,
pixel 1.37, shown at level 0.42, step 1, values float32
Opened PCH45_Gp182_AboveSheath_.mrc as #31, grid size 405,360,416, pixel
1.37,1.37,1.37, shown at level 0.431, step 1, values float32
> view name session-start
opened ChimeraX session
> hide #27 models
> lighting simple
> ui tool show "Side View"
> hide #29 models
> show #29 models
> volume #!9,13,24-25,30-31 showOutlineBox false
> hide #!30 models
> show #!30 models
> hide #!30 models
> show #!30 models
> hide #!30 models
> select add #30
1177 atoms, 1199 bonds, 146 residues, 3 models selected
> select add #31
1177 atoms, 1199 bonds, 146 residues, 5 models selected
> transparency sel & #31.1 50
> select subtract #30
1177 atoms, 1199 bonds, 146 residues, 3 models selected
> show #!30 models
> hide #!30 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> hide #!13 models
> show #!13 models
> hide #!12 models
> show #!12 models
> hide #!9 models
> show #!9 models
> select add #9
1177 atoms, 1199 bonds, 146 residues, 5 models selected
> select subtract #5
4 models selected
> vop subtract #9 #31 minrms True
Opened volume difference as #32, grid size 416,416,416, pixel 1.37, shown at
step 1, values float32
Minimum RMS scale factor for "PCH45_Gp182_AboveSheath_.mrc #31" above level
0.43098 is 0.63051
> select add #32
6 models selected
> show #!31 models
> select subtract #31
4 models selected
> select add #31
6 models selected
> select subtract #9
4 models selected
> vop subtract #31 #32 minrms True
Opened volume difference as #33, grid size 405,360,416, pixel 1.37,1.37,1.37,
shown at step 1, values float32
Minimum RMS scale factor for "volume difference #32" above level 0.88852 is 0
> hide #!33 models
> show #!33 models
> surface dust #13 size 13.7
> surface dust #24 size 13.7
> surface dust #25 size 13.7
> surface dust #33 size 13.7
> select add #33
6 models selected
> transparency sel & #33.1 50
> rename #33 PutativeGp183_C6Map
> select clear
> select add #33
2 models selected
> volume* threshold .82
Unknown command: volume* threshold .82
> volume threshold .82
Missing or invalid "volumes" argument: invalid density maps specifier
> volume threshold* .82
Expected a density maps specifier or a keyword
> volume threshold #* .82
Expected a keyword
> show #!32 models
> volume threshold #* level .82
Expected a keyword
> volume level #* .82
Invalid "level" argument: Expected a number
> volume threshold #* 0.82
Expected a keyword
> volume #* level 0.82
> volume #* transparency 0.25
> volume #* transparency 1
> volume #* transparency 0.75
> select clear
> volume #33 level 0.4049
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> hide #21 models
> hide #!24 models
> hide #!22 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> hide #26 models
> show #26 models
> hide #26 models
> show #26 models
> hide #26 models
> hide #29 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!13 models
> hide #11 models
> hide #!8 models
> surface dust #32 size 13.7
> surface dust #33 size 13.7
> hide #!33 models
> show #!33 models
> hide #!33 models
> show #1 models
> select add #4
1177 atoms, 1199 bonds, 146 residues, 1 model selected
> select add #1
258897 atoms, 267139 bonds, 31925 residues, 2 models selected
> hide #4 models
> select subtract #4
257720 atoms, 265940 bonds, 31779 residues, 1 model selected
> hide #5 models
> select clear
> select add #1
257720 atoms, 265940 bonds, 31779 residues, 1 model selected
> hide #1 models
> select subtract #1
Nothing selected
> show #5 models
> show #1 models
> hide #5 models
> show #4 models
> hide #4 models
> show #4 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> close #2
> hide #4 models
> show #4 models
> hide #4 models
> show #5 models
> hide #5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> select add #6
16068 atoms, 16236 bonds, 2208 residues, 13 models selected
> close #6
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> select add #32
2 models selected
> color #32 #ff00bbff models
> select clear
> show #!30 models
> hide #!30 models
> show #!30 models
> hide #!30 models
> show #27 models
> hide #27 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> show #11 models
> hide #11 models
> select add #1
257720 atoms, 265940 bonds, 31779 residues, 1 model selected
> color #32 #d6d6d6ff models
> select clear
> undo
> hide #11 models
> hide #!32 models
> show #!32 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> color #32 #ff009cff models
> select clear
> show #!3 models
> volume #!3,24,32 showOutlineBox false
> select add #3
2 models selected
> select clear
> select add #3
2 models selected
> volume #* level 0.5
> select clear
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> show #!8 models
> hide #!8 models
> show #!8 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #10 models
> hide #10 models
> show #10 models
> select add #10
3715 atoms, 3815 bonds, 462 residues, 1 model selected
Alignment identifier is 10/A
> select clear
> select #10/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #10/A:1-206
1653 atoms, 1694 bonds, 206 residues, 1 model selected
> select #10/A:201
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #10/A:1-201
1609 atoms, 1648 bonds, 201 residues, 1 model selected
> hide #!32 models
> show #!32 models
> select clear
> select #10/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #10/A:1-200
1595 atoms, 1632 bonds, 200 residues, 1 model selected
> delete sel
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Alphafolded
> Proteins/fold_pch45_gp25trimmed_first_1_200aa/fold_pch45_gp25trimmed_first_1_200aa_model_0.cif"
Chain information for fold_pch45_gp25trimmed_first_1_200aa_model_0.cif #2
---
Chain | Description
A | .
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Alphafolded
> Proteins/fold_pch45_gp25trimmed_first_1_200aa/fold_pch45_gp25trimmed_first_1_200aa_model_1.cif"
Chain information for fold_pch45_gp25trimmed_first_1_200aa_model_1.cif #6
---
Chain | Description
A | .
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Alphafolded
> Proteins/fold_pch45_gp25trimmed_first_1_200aa/fold_pch45_gp25trimmed_first_1_200aa_model_2.cif"
Chain information for fold_pch45_gp25trimmed_first_1_200aa_model_2.cif #34
---
Chain | Description
A | .
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Alphafolded
> Proteins/fold_pch45_gp25trimmed_first_1_200aa/fold_pch45_gp25trimmed_first_1_200aa_model_3.cif"
Chain information for fold_pch45_gp25trimmed_first_1_200aa_model_3.cif #35
---
Chain | Description
A | .
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Alphafolded
> Proteins/fold_pch45_gp25trimmed_first_1_200aa/fold_pch45_gp25trimmed_first_1_200aa_model_4.cif"
Chain information for fold_pch45_gp25trimmed_first_1_200aa_model_4.cif #36
---
Chain | Description
A | .
Computing secondary structure
> hide #2 models
> show #2 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #5 models
> hide #5 models
> show #4 models
> hide #4 models
> show #5 models
> hide #5 models
> hide #6 models
> show #6 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> close #9
> rename #10 Gp25_volzon10-coot11_200-462AA
> show #11 models
> hide #11 models
> show #11 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #11 models
> show #11 models
> hide #!12 models
> show #!12 models
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!12 models
> show #!12 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> hide #!3 models
> show #11 models
> hide #11 models
> show #!13 models
> hide #!13 models
> color #12 #002a9bff models
> show #!13 models
> hide #!13 models
> show #!13 models
> color #13 #003ba5ff models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> close #14
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!19 models
> hide #!19 models
> show #!15 models
> select add #15
2 models selected
> close #15
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #16 models
> hide #16 models
> show #16 models
> hide #!13 models
> hide #!12 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> hide #16 models
> show #16 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> hide #16 models
> show #16 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #!17 models
> hide #!17 models
> show #!17 models
> select add #17
13452 atoms, 13794 bonds, 1722 residues, 7 models selected
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #16 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> close #17
> hide #16 models
> show #16 models
> select add #16
2242 atoms, 2299 bonds, 287 residues, 1 model selected
> measure center #3
Center of mass grid index for PCH45_Neck_C6_3_40A_map_sharp.mrc = (208.00,
208.00, 143.67)
Center of mass xyz scene coordinates for PCH45_Neck_C6_3_40A_map_sharp.mrc =
(284.19, 284.19, 196.30)
> sym #16 c6 center 284.19, 284.19, 196.30
Made 6 copies for Tail_tube_monomerfit symmetry c6
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> color #8 #ff009cff models
> show #!8 models
> hide #!8 models
> show #!8 models
> show #!7 models
> hide #!7 models
> show #!7 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!7 models
> show #!7 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> show #!13 models
> hide #!13 models
> show #!13 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!13 models
> hide #!12 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> hide #!9 models
> show #11 models
> hide #11 models
> show #11 models
> select add #11
2242 atoms, 2299 bonds, 287 residues, 2 models selected
> hide #11 models
> show #11 models
> close #11
> show #!9 models
> hide #!9 models
> show #!9 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #!18 models
> hide #!18 models
> show #!18 models
> show #16 models
> hide #16 models
> select add #9
15694 atoms, 16093 bonds, 2009 residues, 8 models selected
> select subtract #9
2242 atoms, 2299 bonds, 287 residues, 1 model selected
> select add #9
15694 atoms, 16093 bonds, 2009 residues, 8 models selected
> hide #10 models
> show #10 models
> hide #!9 models
> show #!9 models
> hide #!18 models
> show #!18 models
> volume #!18,24 showOutlineBox false
> select clear
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> rename #18 TubeC6ringvolzone
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #20 models
> hide #20 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!19 models
> hide #!19 models
> show #20 models
> hide #20 models
> show #20 models
> close #20
> show #21 models
> hide #21 models
> show #21 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> hide #21 models
> show #21 models
> show #!22 models
> color #22 #51fb86ff models
> show #!24 models
> hide #!24 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> hide #21 models
> show #21 models
> hide #!22 models
> show #!22 models
> show #!24 models
> color #24 #00f90040 models
> color #24 #00fd92ff models
> hide #!24 models
> show #!24 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> hide #!24 models
> show #!24 models
> color #24 #51fb86ff models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> color #23 #d783ffff models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #1 models
> show #1 models
> hide #1 models
> hide #2 models
> show #2 models
> hide #2 models
> show #1 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> rename #13 Sheathring_Lowest_Volzon
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!13 models
> hide #21 models
> show #21 models
> hide #21 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> hide #34 models
> show #34 models
> hide #34 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> hide #!9 models
> hide #10 models
> show #10 models
> show #34 models
> ui tool show Matchmaker
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PCH45_C6_3_40_Wholemap_output_output.cif, chain r3 (#1) with
fold_pch45_gp25trimmed_first_1_200aa_model_0.cif, chain A (#2), sequence
alignment score = 301.2
RMSD between 69 pruned atom pairs is 0.661 angstroms; (across all 95 pairs:
3.337)
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> ui tool show Matchmaker
> matchmaker #6 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PCH45_C6_3_40_Wholemap_output_output.cif, chain r3 (#1) with
fold_pch45_gp25trimmed_first_1_200aa_model_1.cif, chain A (#6), sequence
alignment score = 301.2
RMSD between 70 pruned atom pairs is 0.691 angstroms; (across all 95 pairs:
3.338)
> ui tool show Matchmaker
> matchmaker #34-36 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PCH45_C6_3_40_Wholemap_output_output.cif, chain r3 (#1) with
fold_pch45_gp25trimmed_first_1_200aa_model_2.cif, chain A (#34), sequence
alignment score = 301.2
RMSD between 71 pruned atom pairs is 0.699 angstroms; (across all 95 pairs:
3.295)
Matchmaker PCH45_C6_3_40_Wholemap_output_output.cif, chain r3 (#1) with
fold_pch45_gp25trimmed_first_1_200aa_model_3.cif, chain A (#35), sequence
alignment score = 301.2
RMSD between 70 pruned atom pairs is 0.682 angstroms; (across all 95 pairs:
3.321)
Matchmaker PCH45_C6_3_40_Wholemap_output_output.cif, chain r3 (#1) with
fold_pch45_gp25trimmed_first_1_200aa_model_4.cif, chain A (#36), sequence
alignment score = 301.2
RMSD between 70 pruned atom pairs is 0.679 angstroms; (across all 95 pairs:
3.332)
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> select add #10
2120 atoms, 2182 bonds, 262 residues, 1 model selected
> select clear
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,3
Model Number: Z1C80004VX/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 13822.1.2
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.7.1 (24G231)
Kernel Version: Darwin 24.6.0
Time since boot: 1 hour, 32 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:
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
VN2410C:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 144.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.25.2
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
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: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ISOLDE: 1.10.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
|
|||
| #19533 | fixed | Boltz install command in nogui mode only installs torch on linux | ||
| Description |
Some faulty logic in the boltz install command caused it in nogui mode to not go beyond installing torch on linux and windows and not give any error. I only tried nogui install when I was setting up a boltz server so hadn't noticed before. |
|||
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.
