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 14104)
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 14104)
| Ticket | Resolution | Summary | Owner | Reporter |
|---|---|---|---|---|
| #20763 | fixed | Invalid escape sequence \* warning at startup in volume code | ||
| Description |
The following bug report has been submitted:
Platform: macOS-26.5.2-arm64-arm-64bit-Mach-O
ChimeraX Version: 1.13.dev202607151614 (2026-07-15 16:14:50 UTC)
Description
Getting a syntax warning about invalid escape sequence \* on startup from volume code.
Log:
Startup Messages
---
note | /Users/goddard/Desktop/ChimeraX July 15 2026.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-packages/chimerax/map/volume.py:4245: SyntaxWarning: "\\*" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\\\*"? A raw string is also an option.
Parameters below only supported by Chimera Map format (\\*.cmap)
UCSF ChimeraX version: 1.13.dev202607151614 (2026-07-15)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/goddard/Desktop/openfold/Q52085_2/Q52085/seed_42/Q52085_seed_42_sample_1_model.cif
> format mmcif logInfo false
> ui tool show Shell
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple
Python: 3.14.6
Locale: C.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac Studio
Model Identifier: Mac14,14
Model Number: Z1800003VLL/A
Chip: Apple M2 Ultra
Total Number of Cores: 24 (16 Performance and 8 Efficiency)
Memory: 64 GB
System Firmware Version: 18000.121.3
OS Loader Version: 18000.121.3
Software:
System Software Overview:
System Version: macOS 26.5.2 (25F84)
Kernel Version: Darwin 25.5.0
Time since boot: 16 days, 58 minutes
Graphics/Displays:
Apple M2 Ultra:
Chipset Model: Apple M2 Ultra
Type: GPU
Bus: Built-In
Total Number of Cores: 60
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
PHL 278B1:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.7.1
aiohttp: 3.11.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.14.2
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.2
attrs: 26.1.0
babel: 2.18.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 4.8.1
build: 1.5.0
certifi: 2026.6.17
cftime: 1.6.5
charset-normalizer: 3.4.9
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.3.1
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2.2
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: 1.70.2
ChimeraX-AtomicLibrary: 14.4.2
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: 1.13.dev202607151614
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.6
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.3
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.2.2
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.4
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: 1.8.5
ChimeraX-Label: 1.5
ChimeraX-LightingGUI: 1.0
ChimeraX-ListInfo: 1.3.1
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.3
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchAlign: 1.2.1
ChimeraX-MatchMaker: 2.4.1
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.19.2
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.4.3
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.17
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.24
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-NMRSTAR: 1.0.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.16.2
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: 1.10.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8.3
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: 1.5.3
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: 2.19.1
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-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.20
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: 1.53.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.5
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: 8.4.2
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.15.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
debugpy: 1.8.21
decorator: 5.3.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.63.0
frozenlist: 1.8.0
funcparserlib: 1.0.1
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h2: 4.3.0
h5py: 3.16.0
hpack: 4.2.0
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
hyperframe: 6.1.0
idna: 3.18
ihm: 2.2
imagecodecs: 2026.6.26
imagesize: 2.0.0
iniconfig: 2.3.0
ipykernel: 7.3.0
ipython: 9.14.1
ipython_pygments_lexers: 1.1.1
jedi: 0.20.0
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.9.1
jupyter_core: 5.9.1
kiwisolver: 1.5.0
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.4.5
Markdown: 3.8.2
markdown-it-py: 4.2.0
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.2
maturin: 1.14.1
mcp: 1.18.0
mdurl: 0.1.2
msgpack: 1.1.1
multidict: 6.7.1
ndindex: 1.10.1
nest-asyncio2: 1.7.2
netCDF4: 1.7.4
networkx: 3.3
numexpr: 2.14.1
numpy: 2.4.6
OpenMM: 8.4.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.7
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 12.3.0
pip: 26.1.2
pkginfo: 1.12.1.2
platformdirs: 4.10.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.5.2
psutil: 7.0.0
ptyprocess: 0.7.0
puccinialin: 0.1.13
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.13.4
pydantic-settings: 2.14.2
pydantic_core: 2.46.4
pydata-sphinx-theme: 0.20.0
Pygments: 2.18.0
pynmrstar: 3.5.1
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: 6.10.2
PyQt6-WebEngine-commercial: 6.10.0
PyQt6-WebEngine-Qt6: 6.10.2
PyQt6_sip: 13.10.3
pytest: 9.1.1
pytest-cov: 7.1.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.32
pyzmq: 27.1.0
qtconsole: 5.7.2
QtPy: 2.4.3
qtshim: 1.2.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
rich: 15.0.0
roman-numerals: 4.1.0
rpds-py: 2026.6.3
scipy: 1.18.0
setuptools: 82.0.1
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.1.1
sortedcontainers: 2.4.0
soupsieve: 2.8.4
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: 3.4.5
stack-data: 0.6.3
starlette: 1.3.1
superqt: 0.7.6
tables: 3.11.1
threadpoolctl: 3.6.0
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.7
tqdm: 4.68.4
traitlets: 5.15.1
typing-inspection: 0.4.2
typing_extensions: 4.16.0
urllib3: 2.7.0
uv: 0.11.26
uvicorn: 0.51.0
wcwidth: 0.8.2
webcolors: 24.11.1
wheel: 0.47.0
wheel-filename: 1.4.2
yarl: 1.24.2
|
|||
| #20761 | fixed | Color blobs mouse mode is choosing transparent colors | ||
| Description |
The following bug report has been submitted:
Platform: macOS-26.5.2-arm64-arm-64bit-Mach-O
ChimeraX Version: 1.13.dev202607102107 (2026-07-10 21:07:32 UTC)
Description
Color blobs mouse mode colors the first blob an opaque color but subsequent blobs get a transparent color. Why transparent? Same behavior in ChimeraX 1.12.
Log:
UCSF ChimeraX version: 1.13.dev202607102107 (2026-07-10)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 55878 format ccp4 fromDatabase emdb
Opened emdb 55878 as #1, grid size 440,440,440, pixel 0.65, shown at level
0.122, step 1, values float32, fit PDB 9tfv
> volume #1 level 0.441
> ui tool show "Measure and Color Blobs"
> measure blob #!1.1 triangleNumber 4008 color #0000ccff outline true
Surface emdb 55878 #1.1 blob:
volume = 17.426
area = 37.085
size = 5.2458 2.9716 2.2745
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/pick_blobs/pickblobs.py:268: RuntimeWarning: overflow
encountered in scalar add
alpha = (vc[v0][3] + vc[v1][3] + vc[v2][3]) // 3
> measure blob #!1.1 triangleNumber 20258 color #db566354 outline true
Surface emdb 55878 #1.1 blob:
volume = 602.14
area = 1025.3
size = 34.929 20.172 10.864
> measure blob #!1.1 triangleNumber 31281 color #ab967354 outline true
Surface emdb 55878 #1.1 blob:
volume = 82.877
area = 160.53
size = 20.15 6.2784 4.4765
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple
Python: 3.14.6
Locale: C.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac Studio
Model Identifier: Mac14,14
Model Number: Z1800003VLL/A
Chip: Apple M2 Ultra
Total Number of Cores: 24 (16 Performance and 8 Efficiency)
Memory: 64 GB
System Firmware Version: 18000.121.3
OS Loader Version: 18000.121.3
Software:
System Software Overview:
System Version: macOS 26.5.2 (25F84)
Kernel Version: Darwin 25.5.0
Time since boot: 14 days, 22 hours, 17 minutes
Graphics/Displays:
Apple M2 Ultra:
Chipset Model: Apple M2 Ultra
Type: GPU
Bus: Built-In
Total Number of Cores: 60
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
PHL 278B1:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.7.1
aiohttp: 3.13.4
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.14.1
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: 4.8.0
build: 1.5.0
certifi: 2026.6.17
cftime: 1.6.5
charset-normalizer: 3.4.9
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.3.1
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2.2
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: 1.70.2
ChimeraX-AtomicLibrary: 14.4.2
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: 1.13.dev202607102107
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.6
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DAQplugin: 1.0.0
ChimeraX-DataFormats: 1.2.4
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.2.2
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.4
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: 1.8.5
ChimeraX-Label: 1.5
ChimeraX-LightingGUI: 1.0
ChimeraX-ListInfo: 1.3.1
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.3
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchAlign: 1.2.1
ChimeraX-MatchMaker: 2.4.1
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.19.2
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.4.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.17
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.24
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-NMRSTAR: 1.0.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.16.2
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: 1.10.2
ChimeraX-ProNA3D: 0.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8.3
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: 2.19.1
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-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.20
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: 1.53.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.5
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: 8.4.2
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.15.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.8
debugpy: 1.8.21
decorator: 5.3.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
flatbuffers: 25.12.19
fonttools: 4.63.0
frozenlist: 1.8.0
funcparserlib: 1.0.1
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h2: 4.3.0
h5py: 3.16.0
hpack: 4.2.0
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
hyperframe: 6.1.0
idna: 3.18
ihm: 2.2
imagecodecs: 2026.6.26
imagesize: 2.0.0
iniconfig: 2.3.0
ipykernel: 7.3.0
ipython: 9.14.1
ipython_pygments_lexers: 1.1.1
jedi: 0.20.0
Jinja2: 3.1.6
joblib: 1.5.3
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.9.1
jupyter_core: 5.9.1
kiwisolver: 1.5.0
line_profiler: 5.0.0
llvmlite: 0.47.0
lxml: 6.0.2
lz4: 4.4.5
Markdown: 3.8.2
markdown-it-py: 4.2.0
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.2
mcp: 1.18.0
mdurl: 0.1.2
mlx: 0.31.2
mlx-metal: 0.31.2
mrcfile: 1.5.4
msgpack: 1.1.1
multidict: 6.7.1
narwhals: 2.23.0
ndindex: 1.10.1
nest-asyncio2: 1.7.2
netCDF4: 1.7.4
networkx: 3.3
numba: 0.65.1
numexpr: 2.14.1
numpy: 2.4.6
onnxruntime: 1.26.0
OpenMM: 8.4.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.7
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 26.1.2
pkginfo: 1.12.1.2
platformdirs: 4.10.0
plotly: 6.8.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.5.2
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: 2.13.4
pydantic-settings: 2.14.2
pydantic_core: 2.46.4
pydata-sphinx-theme: 0.20.0
Pygments: 2.18.0
pyKVFinder: 0.9.3
pynmrstar: 3.5.1
pynndescent: 0.6.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6: 6.10.2
PyQt6-Qt6: 6.10.2
PyQt6-WebEngine: 6.10.0
PyQt6-WebEngine-Qt6: 6.10.2
PyQt6_sip: 13.10.3
pytest: 9.1.1
pytest-cov: 7.1.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.32
pyzmq: 27.1.0
qtconsole: 5.7.2
QtPy: 2.4.3
qtshim: 1.2.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
rich: 15.0.0
roman-numerals: 4.1.0
rpds-py: 2026.6.3
scikit-learn: 1.9.0
scipy: 1.17.1
setuptools: 82.0.1
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.1.1
sortedcontainers: 2.4.0
soupsieve: 2.8.4
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: 3.4.5
stack-data: 0.6.3
starlette: 1.3.1
superqt: 0.7.6
tables: 3.11.1
threadpoolctl: 3.6.0
tifffile: 2025.3.13
tinyarray: 1.2.5
tomlkit: 0.15.0
tornado: 6.5.7
tqdm: 4.68.3
traitlets: 5.15.1
typing-inspection: 0.4.2
typing_extensions: 4.16.0
umap-learn: 0.5.12
urllib3: 2.7.0
uv: 0.11.26
uvicorn: 0.51.0
wcwidth: 0.8.2
webcolors: 24.11.1
wheel: 0.47.0
wheel-filename: 1.4.2
yarl: 1.24.2
|
|||
| #20760 | fixed | TypeError: setChecked(self, a0: bool): argument 1 has unexpected type 'numpy.bool' | ||
| Description |
The following bug report has been submitted:
Platform: macOS-26.5.2-arm64-arm-64bit-Mach-O
ChimeraX Version: 1.13.dev202607102107 (2026-07-10 21:07:32 UTC)
Description
Restoring a session hit this numpy 2 setChecked(numpy.bool) error this time in Volume Viewer that Eric saw yesterday in selection inspector.
Log:
UCSF ChimeraX version: 1.13.dev202607102107 (2026-07-10)
© 2016-2026 Regents of the University of California. All rights reserved.
> open /Users/goddard/Desktop/test.cxs format session
Opened emdb 55878 as #1, grid size 440,440,440, pixel 0.65, shown at level
0.122, step 1, values float32
Opened emdb 55878 gaussian as #3, grid size 440,440,440, pixel 0.65, shown at
level 0.0403, step 1, values float32
Traceback (most recent call last):
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
~~~~~~~~~~^^^^^^^^^^^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 5178, in models_opened
cb(vlist)
~~^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 190, in volume_opened_cb
self.display_volume_info(v)
~~~~~~~~~~~~~~~~~~~~~~~~^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 235, in display_volume_info
p.update_panel_widgets(volume)
~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 1628, in update_panel_widgets
self.add_histogram_pane(volume)
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 1508, in add_histogram_pane
hp.set_data_region(v)
~~~~~~~~~~~~~~~~~~^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 2112, in set_data_region
self.update_threshold_gui()
~~~~~~~~~~~~~~~~~~~~~~~~~^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 2675, in update_threshold_gui
self.update_shown_icon()
~~~~~~~~~~~~~~~~~~~~~~^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 2375, in update_shown_icon
s.setChecked(shown)
~~~~~~~~~~~~^^^^^^^
TypeError: setChecked(self, a0: bool): argument 1 has unexpected type
'numpy.bool'
Error processing trigger "add models":
TypeError: setChecked(self, a0: bool): argument 1 has unexpected type
'numpy.bool'
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 2375, in update_shown_icon
s.setChecked(shown)
~~~~~~~~~~~~^^^^^^^
See log for complete Python traceback.
Opened volume difference as #4, grid size 440,440,440, pixel 0.65, shown at
level 0.122, step 1, values float32
Traceback (most recent call last):
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
~~~~~~~~~~^^^^^^^^^^^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 5178, in models_opened
cb(vlist)
~~^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 190, in volume_opened_cb
self.display_volume_info(v)
~~~~~~~~~~~~~~~~~~~~~~~~^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 235, in display_volume_info
p.update_panel_widgets(volume)
~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 1628, in update_panel_widgets
self.add_histogram_pane(volume)
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 1508, in add_histogram_pane
hp.set_data_region(v)
~~~~~~~~~~~~~~~~~~^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 2112, in set_data_region
self.update_threshold_gui()
~~~~~~~~~~~~~~~~~~~~~~~~~^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 2675, in update_threshold_gui
self.update_shown_icon()
~~~~~~~~~~~~~~~~~~~~~~^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 2375, in update_shown_icon
s.setChecked(shown)
~~~~~~~~~~~~^^^^^^^
TypeError: setChecked(self, a0: bool): argument 1 has unexpected type
'numpy.bool'
Error processing trigger "add models":
TypeError: setChecked(self, a0: bool): argument 1 has unexpected type
'numpy.bool'
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 2375, in update_shown_icon
s.setChecked(shown)
~~~~~~~~~~~~^^^^^^^
See log for complete Python traceback.
Log from Tue Jul 14 14:48:37 2026UCSF ChimeraX version: 1.13.dev202607102107
(2026-07-10)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 55878 format ccp4 fromDatabase emdb
Opened emdb 55878 as #1, grid size 440,440,440, pixel 0.65, shown at level
0.122, step 1, values float32, fit PDB 9tfv
> open 9tfv format mmcif fromDatabase pdb
9tfv title:
Cryo-EM structure of the inward rectifying potassium channel 7.1 (Kir7.1)
[more info...]
Chain information for 9tfv #2
---
Chain | Description | UniProt
A B C D | Inward rectifier potassium channel 13 | KCJ13_HUMAN -16-360
Non-standard residues in 9tfv #2
---
K — potassium ion
> vop gaussian #1 sdev 1.95
Opened emdb 55878 gaussian as #3, grid size 440,440,440, pixel 0.65, shown at
step 1, values float32
> vop subtract #1 #3 minrms True
Opened volume difference as #4, grid size 440,440,440, pixel 0.65, shown at
step 1, values float32
Minimum RMS scale factor for "emdb 55878 gaussian #3" above level 0.040251 is
1.8434
> transparency #4.1 50
> transparency #4.1 0
> volume #!4 showOutlineBox true
> volume #!4 showOutlineBox false
> volume #!4 region all imageMode "full region"
> volume unzone #!4
> mousemode rightMode "crop volume"
> volume #!4 region all imageMode "full region"
> volume unzone #!4
> mousemode rightMode "crop volume"
> volume #!4 projectionMode 3d
> volume #!4 projectionMode 2d-xyz
> volume #!4 projectionMode rays
> volume #!4 projectionMode 3d
> volume #4 style surface
> fitmap #2 inMap #4
Fit molecule 9tfv (#2) to map volume difference (#4) using 17050 atoms
average map value = 0.129, steps = 60
shifted from previous position = 0.186
rotated from previous position = 0.156 degrees
atoms outside contour = 10740, contour level = 0.122
Position of 9tfv (#2) relative to volume difference (#4) coordinates:
Matrix rotation and translation
0.99999625 0.00271638 -0.00013520 -0.37481905
-0.00271637 0.99999634 0.00006726 0.38194553
0.00013538 -0.00006689 1.00000004 0.17593505
Axis -0.02465377 -0.04972999 -0.99845837
Axis point 137.02415586 139.85416498 0.00000000
Rotation angle (degrees) 0.15587735
Shift along axis -0.18541727
> ui tool show "Color Zone"
> color zone #4 near #2 distance 3.9
> color single #4
> color bychain
> color zone #4 near #2 distance 3.9
> volume splitbyzone #4
Opened volume difference 0 as #5.1, grid size 440,440,440, pixel 0.65, shown
at level 0.122, step 1, values float32
Opened volume difference 1 as #5.2, grid size 440,440,440, pixel 0.65, shown
at level 0.122, step 1, values float32
Opened volume difference 2 as #5.3, grid size 440,440,440, pixel 0.65, shown
at level 0.122, step 1, values float32
Opened volume difference 3 as #5.4, grid size 440,440,440, pixel 0.65, shown
at level 0.122, step 1, values float32
Opened volume difference 4 as #5.5, grid size 440,440,440, pixel 0.65, shown
at level 0.122, step 1, values float32
> hide #!5.1 models
> hide #!5.2 models
> show #!5.2 models
> close #5
> show #!1 models
> color single #4
> color zone #1 near #2 distance 3.9
> color zone #1 near #2 distance 4
> color zone #1 near #2 distance 2.34
> color single #1
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule 9tfv (#2) to map emdb 55878 (#1) using 17050 atoms
average map value = 0.2424, steps = 44
shifted from previous position = 0.00951
rotated from previous position = 0.0126 degrees
atoms outside contour = 6705, contour level = 0.122
Position of 9tfv (#2) relative to emdb 55878 (#1) coordinates:
Matrix rotation and translation
0.99999663 0.00257110 0.00001105 -0.36501687
-0.00257110 0.99999668 -0.00000848 0.37346891
-0.00001107 0.00000845 0.99999998 0.19084826
Axis 0.00329158 0.00430192 -0.99998533
Axis point 145.39276053 141.91233461 0.00000000
Rotation angle (degrees) 0.14731542
Shift along axis -0.19044031
Opened 9tfv map 5 as #5, grid size 68,68,84, pixel 1.67, shown at level 0.115,
step 1, values float32
> fitmap #2 inMap #1 resolution 5
Fit map 9tfv map 5 in map emdb 55878 using 34635 points
correlation = 0.4842, correlation about mean = 0.6234, overlap = 2049
steps = 40, shift = 0.0403, angle = 0.0107 degrees
Position of 9tfv map 5 (#5) relative to emdb 55878 (#1) coordinates:
Matrix rotation and translation
0.99999717 0.00239314 0.00002183 -0.35199047
-0.00239314 0.99999709 -0.00006173 0.35115167
-0.00002198 0.00006168 1.00000012 0.22334933
Axis 0.02577582 0.00914998 -0.99962587
Axis point 147.43512105 144.79145887 0.00000000
Rotation angle (degrees) 0.13716846
Shift along axis -0.22912558
Average map value = 0.2423 for 17050 atoms, 6703 outside contour
> close #5
> ui tool show "Hide Dust"
> surface dust #1 size 3.9
> surface dust #1 size 3.82
> surface dust #1 size 3.52
> surface undust #1
> ui tool show "Map Coordinates"
> save test.cxs
——— End of log from Tue Jul 14 14:48:37 2026 ———
> view name session-start
opened ChimeraX session
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple
Python: 3.14.6
Locale: C.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac Studio
Model Identifier: Mac14,14
Model Number: Z1800003VLL/A
Chip: Apple M2 Ultra
Total Number of Cores: 24 (16 Performance and 8 Efficiency)
Memory: 64 GB
System Firmware Version: 18000.121.3
OS Loader Version: 18000.121.3
Software:
System Software Overview:
System Version: macOS 26.5.2 (25F84)
Kernel Version: Darwin 25.5.0
Time since boot: 14 days, 22 hours, 1 minute
Graphics/Displays:
Apple M2 Ultra:
Chipset Model: Apple M2 Ultra
Type: GPU
Bus: Built-In
Total Number of Cores: 60
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
PHL 278B1:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.7.1
aiohttp: 3.13.4
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.14.1
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: 4.8.0
build: 1.5.0
certifi: 2026.6.17
cftime: 1.6.5
charset-normalizer: 3.4.9
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.3.1
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2.2
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: 1.70.2
ChimeraX-AtomicLibrary: 14.4.2
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: 1.13.dev202607102107
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.6
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DAQplugin: 1.0.0
ChimeraX-DataFormats: 1.2.4
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.2.2
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.4
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: 1.8.5
ChimeraX-Label: 1.5
ChimeraX-LightingGUI: 1.0
ChimeraX-ListInfo: 1.3.1
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.3
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchAlign: 1.2.1
ChimeraX-MatchMaker: 2.4.1
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.19.2
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.4.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.17
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.24
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-NMRSTAR: 1.0.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.16.2
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: 1.10.2
ChimeraX-ProNA3D: 0.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8.3
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: 2.19.1
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-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.20
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: 1.53.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.5
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: 8.4.2
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.15.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.8
debugpy: 1.8.21
decorator: 5.3.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
flatbuffers: 25.12.19
fonttools: 4.63.0
frozenlist: 1.8.0
funcparserlib: 1.0.1
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h2: 4.3.0
h5py: 3.16.0
hpack: 4.2.0
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
hyperframe: 6.1.0
idna: 3.18
ihm: 2.2
imagecodecs: 2026.6.26
imagesize: 2.0.0
iniconfig: 2.3.0
ipykernel: 7.3.0
ipython: 9.14.1
ipython_pygments_lexers: 1.1.1
jedi: 0.20.0
Jinja2: 3.1.6
joblib: 1.5.3
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.9.1
jupyter_core: 5.9.1
kiwisolver: 1.5.0
line_profiler: 5.0.0
llvmlite: 0.47.0
lxml: 6.0.2
lz4: 4.4.5
Markdown: 3.8.2
markdown-it-py: 4.2.0
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.2
mcp: 1.18.0
mdurl: 0.1.2
mlx: 0.31.2
mlx-metal: 0.31.2
mrcfile: 1.5.4
msgpack: 1.1.1
multidict: 6.7.1
narwhals: 2.23.0
ndindex: 1.10.1
nest-asyncio2: 1.7.2
netCDF4: 1.7.4
networkx: 3.3
numba: 0.65.1
numexpr: 2.14.1
numpy: 2.4.6
onnxruntime: 1.26.0
OpenMM: 8.4.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.7
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 26.1.2
pkginfo: 1.12.1.2
platformdirs: 4.10.0
plotly: 6.8.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.5.2
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: 2.13.4
pydantic-settings: 2.14.2
pydantic_core: 2.46.4
pydata-sphinx-theme: 0.20.0
Pygments: 2.18.0
pyKVFinder: 0.9.3
pynmrstar: 3.5.1
pynndescent: 0.6.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6: 6.10.2
PyQt6-Qt6: 6.10.2
PyQt6-WebEngine: 6.10.0
PyQt6-WebEngine-Qt6: 6.10.2
PyQt6_sip: 13.10.3
pytest: 9.1.1
pytest-cov: 7.1.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.32
pyzmq: 27.1.0
qtconsole: 5.7.2
QtPy: 2.4.3
qtshim: 1.2.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
rich: 15.0.0
roman-numerals: 4.1.0
rpds-py: 2026.6.3
scikit-learn: 1.9.0
scipy: 1.17.1
setuptools: 82.0.1
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.1.1
sortedcontainers: 2.4.0
soupsieve: 2.8.4
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: 3.4.5
stack-data: 0.6.3
starlette: 1.3.1
superqt: 0.7.6
tables: 3.11.1
threadpoolctl: 3.6.0
tifffile: 2025.3.13
tinyarray: 1.2.5
tomlkit: 0.15.0
tornado: 6.5.7
tqdm: 4.68.3
traitlets: 5.15.1
typing-inspection: 0.4.2
typing_extensions: 4.16.0
umap-learn: 0.5.12
urllib3: 2.7.0
uv: 0.11.26
uvicorn: 0.51.0
wcwidth: 0.8.2
webcolors: 24.11.1
wheel: 0.47.0
wheel-filename: 1.4.2
yarl: 1.24.2
|
|||
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