![[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 13347)
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 13347)
| Ticket | Resolution | Summary | Owner | Reporter |
|---|---|---|---|---|
| #19707 | fixed | Boltz prediction does not stop running when status message gets a connection refused error | ||
| Description |
The following bug report has been submitted:
Platform: macOS-26.1-arm64-arm-64bit
ChimeraX Version: 1.12.dev202512030954 (2025-12-03 09:54:27 UTC)
Description
Boltz prediction does not stop running when status message gets a connection refused error.
Log:
UCSF ChimeraX version: 1.12.dev202512030954 (2025-12-03)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/goddard/Desktop/boltz/boltz_ntca_model_0.cif_3/boltz_results_ntca_model_0.cif/predictions/ntca_model_0.cif/ntca_model_0.cif_model_0.cif
> format mmcif logInfo false
> ui tool show Boltz
> boltz predict protein /A name ntca_model_0.cif_model_0.cif useServer true
> serverHost 213.173.108.85 serverPort 11660
Running Boltz prediction of protein with 222 residues on gpu
Using cached multiple sequence alignment
/Users/goddard/Downloads/ChimeraX/BoltzMSA/9guk_C
Sending job request to server (655180 bytes)
Traceback (most recent call last):
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/boltz_gui.py", line 595, in _predict
self._run_prediction(options = ' '.join(options))
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/boltz_gui.py", line 612, in _run_prediction
br = run(self.session, cmd)
^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 87, in boltz_predict
br.start()
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 559, in start
self._run_boltz()
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 669, in _run_boltz
self._run_on_server()
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 706, in _run_on_server
job_id = predict_on_server(run_dir, self._server_host, self._server_port)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/server.py", line 290, in predict_on_server
msg = send_to_server(zip_data, host, port)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/server.py", line 339, in send_to_server
client_socket.sendall(zip_data)
TimeoutError: timed out
TimeoutError: timed out
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/server.py", line 339, in send_to_server
client_socket.sendall(zip_data)
See log for complete Python traceback.
> boltz predict protein /A name ntca_model_0.cif_model_0.cif useServer true
> serverHost 213.173.108.85 serverPort 11660
Running Boltz prediction of protein with 222 residues on gpu
Using cached multiple sequence alignment
/Users/goddard/Downloads/ChimeraX/BoltzMSA/9guk_C
Sending job request to server (655181 bytes)
Could not connect to 213.173.108.85:11660, connection refused
> boltz predict protein /A name ntca_model_0.cif_model_0.cif useServer true
> serverHost 213.173.108.85 serverPort 11660
Running Boltz prediction of protein with 222 residues on gpu
Using cached multiple sequence alignment
/Users/goddard/Downloads/ChimeraX/BoltzMSA/9guk_C
Sending job request to server (655180 bytes)
Server 213.173.108.85:11660 queued job ym44a6im
Confidence score 0.83, pTM 0.79, ipTM 0.00, pLDDT 0.83
Boltz prediction completed in 33 seconds (start boltz 0 sec, sequence search 0
sec, load weights 0 sec, structure inference 0 sec)
Please cite Boltz-1 Democratizing Biomolecular Interaction Modeling. BioRxiv
https://doi.org/10.1101/2024.11.19.624167 if you use these predictions.
> open
> /Users/goddard/Desktop/boltz/boltz_ntca_model_0.cif_model_0.cif_2/boltz_results_ntca_model_0.cif_model_0.cif/predictions/ntca_model_0.cif_model_0.cif/ntca_model_0.cif_model_0.cif_model_0.cif
> logInfo false
Matchmaker ntca_model_0.cif_model_0.cif, chain A (#1) with
ntca_model_0.cif_model_0.cif_model_0.cif, chain A (#2), sequence alignment
score = 1092.1
RMSD between 215 pruned atom pairs is 0.759 angstroms; (across all 222 pairs:
1.193)
> boltz predict protein #1/A name ntca_model_0.cif_model_0.cif useServer true
> serverHost 203.57.40.177 serverPort 10286
Running Boltz prediction of protein with 222 residues on gpu
Using cached multiple sequence alignment
/Users/goddard/Downloads/ChimeraX/BoltzMSA/9guk_C
Sending job request to server (655181 bytes)
Server 203.57.40.177:10286 queued job _rloxp9t
> hide #2 models
Traceback (most recent call last):
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 731, in _check_for_server_results
msg = get_results(self._job_id, self._run_dir, self._server_host,
self._server_port)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/server.py", line 307, in get_results
msg = send_to_server(f'status: {job_id}'.encode('utf-8'), host, port)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/server.py", line 334, in send_to_server
client_socket.connect((host, port)) # Connect to the server
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ConnectionRefusedError: [Errno 61] Connection refused
Error processing trigger "new frame":
ConnectionRefusedError: [Errno 61] Connection refused
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/server.py", line 334, in send_to_server
client_socket.connect((host, port)) # Connect to the server
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Cannot make a new prediction until the current prediction finishes.
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2 Ultra
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: 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: 13822.41.1
OS Loader Version: 13822.41.1
Software:
System Software Overview:
System Version: macOS 26.1 (25B78)
Kernel Version: Darwin 25.1.0
Time since boot: 52 days, 7 hours, 55 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:
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: 3.12.1
build: 1.3.0
certifi: 2025.8.3
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
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-CiliaBuilder: 1.0.9
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12.dev202512030954
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: 1.4.1
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-TutorialReadFormat: 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: 7.12.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.17
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.0
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
pandas: 2.3.3
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: 4.5.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
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: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.1
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.20
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-py: 3.1.0
rpds-py: 0.30.0
scipy: 1.16.3
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: 3.0.3
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: 6.5.2
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2025.2
urllib3: 2.5.0
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
|
|||
| #19706 | limitation | UCSF Guest wifi blocks connections to a boltz server | ||
| Description |
The following bug report has been submitted:
Platform: macOS-26.1-arm64-arm-64bit
ChimeraX Version: 1.12.dev202512030954 (2025-12-03 09:54:27 UTC)
Description
On UCSF Guest wifi the boltz server on RunPod does not work, seems to be blocked.
Log:
UCSF ChimeraX version: 1.12.dev202512030954 (2025-12-03)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show Boltz
Populating font family aliases took 49 ms. Replace uses of missing font family
"-webkit-standard" with one that exists to avoid this cost.
> boltz predict protein
> MLANENSLLTMFRELGSGKLPLQIEQFERGKTIFFPGDPAERVYLLVKGAVKLSRVYESGEEITVALLRENSVFGVLSLLTGQRSDRFYHAVAFTPVQLFSVPIEFMQKALIERPELANVMLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGIPSPDGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLRESKLIAIHKKRITVFNPVALSQQFS
> useServer true serverHost minsky.cgl.ucsf.edu serverPort 30172
Running Boltz prediction of protein with 222 residues on gpu
Using cached multiple sequence alignment
/Users/goddard/Downloads/ChimeraX/BoltzMSA/9guk_C
Sending job request to server (655127 bytes)
Server minsky.cgl.ucsf.edu:30172 queued job 5ciqwfi8
Confidence score 0.82, pTM 0.79, ipTM 0.00, pLDDT 0.83
Boltz prediction completed in 30 seconds (start boltz 0 sec, sequence search 0
sec, load weights 0 sec, structure inference 0 sec)
Please cite Boltz-1 Democratizing Biomolecular Interaction Modeling. BioRxiv
https://doi.org/10.1101/2024.11.19.624167 if you use these predictions.
> open
> /Users/goddard/Desktop/boltz/boltz_86/boltz_results_boltz_86/predictions/boltz_86/boltz_86_model_0.cif
> logInfo false
> hide #1 models
> boltz predict protein
> MLANENSLLTMFRELGSGKLPLQIEQFERGKTIFFPGDPAERVYLLVKGAVKLSRVYESGEEITVALLRENSVFGVLSLLTGQRSDRFYHAVAFTPVQLFSVPIEFMQKALIERPELANVMLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGIPSPDGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLRESKLIAIHKKRITVFNPVALSQQFS
> useServer true serverHost 213.173.108.85 serverPort 11660
Running Boltz prediction of protein with 222 residues on gpu
Using cached multiple sequence alignment
/Users/goddard/Downloads/ChimeraX/BoltzMSA/9guk_C
Sending job request to server (655127 bytes)
Server 213.173.108.85:11660 queued job jxotv6z_
Confidence score 0.83, pTM 0.80, ipTM 0.00, pLDDT 0.84
Boltz prediction completed in 33 seconds (start boltz 0 sec, sequence search 0
sec, load weights 0 sec, structure inference 0 sec)
> open
> /Users/goddard/Desktop/boltz/boltz_87/boltz_results_boltz_87/predictions/boltz_87/boltz_87_model_0.cif
> logInfo false
> hide #2 models
> boltz predict protein
> MLANENSLLTMFRELGSGKLPLQIEQFERGKTIFFPGDPAERVYLLVKGAVKLSRVYESGEEITVALLRENSVFGVLSLLTGQRSDRFYHAVAFTPVQLFSVPIEFMQKALIERPELANVMLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGIPSPDGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLRESKLIAIHKKRITVFNPVALSQQFS
> useServer true serverHost 213.173.108.85 serverPort 11660
Running Boltz prediction of protein with 222 residues on gpu
Using cached multiple sequence alignment
/Users/goddard/Downloads/ChimeraX/BoltzMSA/9guk_C
Sending job request to server (655127 bytes)
Server 213.173.108.85:11660 queued job 2l02g6o_
Confidence score 0.82, pTM 0.81, ipTM 0.00, pLDDT 0.83
Boltz prediction completed in 33 seconds (start boltz 0 sec, sequence search 0
sec, load weights 0 sec, structure inference 0 sec)
> open
> /Users/goddard/Desktop/boltz/boltz_88/boltz_results_boltz_88/predictions/boltz_88/boltz_88_model_0.cif
> logInfo false
> boltz predict protein
> MLANENSLLTMFRELGSGKLPLQIEQFERGKTIFFPGDPAERVYLLVKGAVKLSRVYESGEEITVALLRENSVFGVLSLLTGQRSDRFYHAVAFTPVQLFSVPIEFMQKALIERPELANVMLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGIPSPDGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLRESKLIAIHKKRITVFNPVALSQQFS
> useServer true serverHost 213.173.108.85 serverPort 11660
Running Boltz prediction of protein with 222 residues on gpu
Using cached multiple sequence alignment
/Users/goddard/Downloads/ChimeraX/BoltzMSA/9guk_C
Sending job request to server (655127 bytes)
Server 213.173.108.85:11660 queued job jzpavgyp
Confidence score 0.83, pTM 0.79, ipTM 0.00, pLDDT 0.83
Boltz prediction completed in 33 seconds (start boltz 0 sec, sequence search 0
sec, load weights 0 sec, structure inference 0 sec)
> open
> /Users/goddard/Desktop/boltz/boltz_89/boltz_results_boltz_89/predictions/boltz_89/boltz_89_model_0.cif
> logInfo false
> hide #3 models
> hide #4 models
> boltz predict protein
> MLANENSLLTMFRELGSGKLPLQIEQFERGKTIFFPGDPAERVYLLVKGAVKLSRVYESGEEITVALLRENSVFGVLSLLTGQRSDRFYHAVAFTPVQLFSVPIEFMQKALIERPELANVMLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGIPSPDGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLRESKLIAIHKKRITVFNPVALSQQFS
> useServer true serverHost 213.173.108.85 serverPort 11660
Running Boltz prediction of protein with 222 residues on gpu
Using cached multiple sequence alignment
/Users/goddard/Downloads/ChimeraX/BoltzMSA/9guk_C
Sending job request to server (655126 bytes)
Server 213.173.108.85:11660 queued job 1gu83vou
Confidence score 0.83, pTM 0.82, ipTM 0.00, pLDDT 0.83
Boltz prediction completed in 33 seconds (start boltz 0 sec, sequence search 0
sec, load weights 0 sec, structure inference 0 sec)
> open
> /Users/goddard/Desktop/boltz/boltz_90/boltz_results_boltz_90/predictions/boltz_90/boltz_90_model_0.cif
> logInfo false
> boltz predict protein
> MLANENSLLTMFRELGSGKLPLQIEQFERGKTIFFPGDPAERVYLLVKGAVKLSRVYESGEEITVALLRENSVFGVLSLLTGQRSDRFYHAVAFTPVQLFSVPIEFMQKALIERPELANVMLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGIPSPDGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLRESKLIAIHKKRITVFNPVALSQQFS
> useServer true serverHost 213.173.108.85 serverPort 11660
Running Boltz prediction of protein with 222 residues on gpu
Using cached multiple sequence alignment
/Users/goddard/Downloads/ChimeraX/BoltzMSA/9guk_C
Sending job request to server (655126 bytes)
Traceback (most recent call last):
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/boltz_gui.py", line 595, in _predict
self._run_prediction(options = ' '.join(options))
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/boltz_gui.py", line 612, in _run_prediction
br = run(self.session, cmd)
^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 87, in boltz_predict
br.start()
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 559, in start
self._run_boltz()
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 669, in _run_boltz
self._run_on_server()
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 706, in _run_on_server
job_id = predict_on_server(run_dir, self._server_host, self._server_port)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/server.py", line 290, in predict_on_server
msg = send_to_server(zip_data, host, port)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/server.py", line 338, in send_to_server
client_socket.sendall(zip_data)
BrokenPipeError: [Errno 32] Broken pipe
BrokenPipeError: [Errno 32] Broken pipe
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/server.py", line 338, in send_to_server
client_socket.sendall(zip_data)
See log for complete Python traceback.
> hide #5 models
> boltz predict protein
> MLANENSLLTMFRELGSGKLPLQIEQFERGKTIFFPGDPAERVYLLVKGAVKLSRVYESGEEITVALLRENSVFGVLSLLTGQRSDRFYHAVAFTPVQLFSVPIEFMQKALIERPELANVMLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGIPSPDGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLRESKLIAIHKKRITVFNPVALSQQFS
> useServer true serverHost 213.173.108.85 serverPort 11660
Running Boltz prediction of protein with 222 residues on gpu
Using cached multiple sequence alignment
/Users/goddard/Downloads/ChimeraX/BoltzMSA/9guk_C
Sending job request to server (655126 bytes)
Traceback (most recent call last):
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/boltz_gui.py", line 595, in _predict
self._run_prediction(options = ' '.join(options))
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/boltz_gui.py", line 612, in _run_prediction
br = run(self.session, cmd)
^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 87, in boltz_predict
br.start()
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 559, in start
self._run_boltz()
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 669, in _run_boltz
self._run_on_server()
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 706, in _run_on_server
job_id = predict_on_server(run_dir, self._server_host, self._server_port)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/server.py", line 290, in predict_on_server
msg = send_to_server(zip_data, host, port)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/server.py", line 338, in send_to_server
client_socket.sendall(zip_data)
BrokenPipeError: [Errno 32] Broken pipe
BrokenPipeError: [Errno 32] Broken pipe
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/server.py", line 338, in send_to_server
client_socket.sendall(zip_data)
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2 Ultra
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: 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: 13822.41.1
OS Loader Version: 13822.41.1
Software:
System Software Overview:
System Version: macOS 26.1 (25B78)
Kernel Version: Darwin 25.1.0
Time since boot: 52 days, 6 hours
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:
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: 3.12.1
build: 1.3.0
certifi: 2025.8.3
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
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-CiliaBuilder: 1.0.9
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12.dev202512030954
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: 1.4.1
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-TutorialReadFormat: 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: 7.12.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.17
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.0
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
pandas: 2.3.3
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: 4.5.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
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: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.1
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.20
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-py: 3.1.0
rpds-py: 0.30.0
scipy: 1.16.3
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: 3.0.3
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: 6.5.2
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2025.2
urllib3: 2.5.0
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
|
|||
| #19702 | duplicate | Crash on Mac waking from sleep | ||
| Description |
The following bug report has been submitted:
Platform: macOS-13.5.2-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 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
Thread 0x00000002ade7b000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002ace6f000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002abe63000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002aae57000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002a9e4b000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002a8e3f000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002a7e33000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002a6e27000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002a5e1b000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002a4e0f000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000297693000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000296687000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000029567b000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000029466f000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000293663000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001f490e080 (most recent call first):
File "/Applications/ChimeraX-1.10.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.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.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, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.pdb_lib._load_libs, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imaging, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 50)
{"app_name":"ChimeraX","timestamp":"2026-01-08 12:56:11.00 -0500","app_version":"1.10.0","slice_uuid":"9cf8124a-d876-34ad-b7ee-c011183ebc15","build_version":"1.10.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.5.2 (22G91)","roots_installed":0,"name":"ChimeraX","incident_id":"52EE29FA-25BE-4F83-BDBE-5F91576168DC"}
{
"uptime" : 1500000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,6",
"coalitionID" : 7869,
"osVersion" : {
"train" : "macOS 13.5.2",
"build" : "22G91",
"releaseType" : "User"
},
"captureTime" : "2026-01-08 12:56:09.4054 -0500",
"incident" : "52EE29FA-25BE-4F83-BDBE-5F91576168DC",
"pid" : 78030,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-12-17 09:38:45.5504 -0500",
"procStartAbsTime" : 32981471257570,
"procExitAbsTime" : 37015694014359,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.0","CFBundleVersion":"1.10.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"5941FB0E-C42A-5606-8409-DA443B737AF0","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "7F0B2FC0-5520-8CAC-651A-4D90B0F6E43F",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"sleepWakeUUID" : "6F092198-B16C-4C72-90A3-260E12147496",
"sip" : "enabled",
"vmRegionInfo" : "0x5d50941d670 is not in any region. Bytes after previous region: 5931505145457 Bytes before following region: 99140574783888\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x000005d50941d670","rawCodes":[1,6412541482608],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000005d50941d670"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":78030},
"vmregioninfo" : "0x5d50941d670 is not in any region. Bytes after previous region: 5931505145457 Bytes before following region: 99140574783888\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV ",
"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},
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"name" : "QtOpenGL.abi3.so"
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"name" : "QtOpenGLWidgets.abi3.so"
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"name" : "QtOpenGLWidgets"
},
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"size" : 237560,
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"name" : "libsystem_kernel.dylib"
},
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"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
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"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
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===== Log before crash start =====
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/om/Downloads/ODC_M1/ODC_M1 protein-refined_017.pdb"
Chain information for ODC_M1 protein-refined_017.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
G | No description available
H | No description available
I | No description available
> show cartoons
> hide atoms
> select /B:268-574
2500 atoms, 2554 bonds, 307 residues, 1 model selected
> select /B:268-574
2500 atoms, 2554 bonds, 307 residues, 1 model selected
> select add #1
21270 atoms, 21800 bonds, 13 pseudobonds, 2551 residues, 2 models selected
> select subtract #1
Nothing selected
> select /B:367
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
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
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
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
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
> open "/Users/om/Downloads/FINAL ODC_M1 protein-refined_017.pdb"
Chain information for FINAL ODC_M1 protein-refined_017.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
G | No description available
H | No description available
I | No description available
> open /Users/om/Downloads/D_9100124238_val-data_P1.cif
Summary of feedback from opening /Users/om/Downloads/D_9100124238_val-
data_P1.cif
---
warning | No mmCIF models found.
> open /Users/om/Downloads/D_9100124238_val-data_P1.cif
Summary of feedback from opening /Users/om/Downloads/D_9100124238_val-
data_P1.cif
---
warning | No mmCIF models found.
Desktop color scheme is dark
Desktop color scheme is light
> open /Volumes/current/fsc_example.xml
Opened fsc_example.xml
> open /Users/om/Downloads/Final_PDB/J177_fsc.xml
Opened J177_fsc.xml
> show sel cartoons
> hide sel atoms
> select add #1
21270 atoms, 21800 bonds, 13 pseudobonds, 2551 residues, 2 models selected
> select add #2
42540 atoms, 43600 bonds, 26 pseudobonds, 5102 residues, 4 models selected
> show sel cartoons
> hide sel atoms
> hide #!2 models
> select subtract #2
21270 atoms, 21800 bonds, 13 pseudobonds, 2551 residues, 2 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/H #2/H
Alignment identifier is 1
> select #1/H:1 #2/H:1
44 atoms, 48 bonds, 2 residues, 2 models selected
> select #1/H #2/H
1192 atoms, 1332 bonds, 58 residues, 2 models selected
1 [ID: 1] region 2 chains [1-29] RMSD: 0.000
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
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
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
> open "/Users/om/Downloads/Final_PDB/FINAL HsODC_protein.pdb"
Chain information for FINAL HsODC_protein.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
G | No description available
H | No description available
I | No description available
> select add #2
21866 atoms, 22466 bonds, 13 pseudobonds, 2580 residues, 3 models selected
> select subtract #2
596 atoms, 666 bonds, 29 residues, 1 model selected
> select add #1
21270 atoms, 21800 bonds, 13 pseudobonds, 2551 residues, 2 models selected
> select subtract #1
Nothing selected
> hide #!1 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 atoms
> show #!3 cartoons
> select #3/A:468-860
3063 atoms, 3115 bonds, 1 pseudobond, 388 residues, 2 models selected
> ui tool show "Color Actions"
> color sel bychain
> sequence chain #3/A
Alignment identifier is 3/A
> select #3/A:468-860
3063 atoms, 3115 bonds, 1 pseudobond, 388 residues, 2 models selected
> split #3
Split FINAL HsODC_protein.pdb (#3) into 8 models
Chain information for FINAL HsODC_protein.pdb A #3.1
---
Chain | Description
A | No description available
Chain information for FINAL HsODC_protein.pdb B #3.2
---
Chain | Description
B | No description available
Chain information for FINAL HsODC_protein.pdb C #3.3
---
Chain | Description
C | No description available
Chain information for FINAL HsODC_protein.pdb D #3.4
---
Chain | Description
D | No description available
Chain information for FINAL HsODC_protein.pdb E #3.5
---
Chain | Description
E | No description available
Chain information for FINAL HsODC_protein.pdb G #3.6
---
Chain | Description
G | No description available
Chain information for FINAL HsODC_protein.pdb H #3.7
---
Chain | Description
H | No description available
Chain information for FINAL HsODC_protein.pdb I #3.8
---
Chain | Description
I | No description available
> color #3.1 darkseagreen
> color #3.2 burlywood
> color #3.3 coral
> color #3.4 #498cffff
> color #3.5 mediumslateblue
> color #3.6 hotpink
> color #3.7 lightseagreen
> color #3.8 #ebebebff
> color #3.8 #d6d6d6ff
> color #3.8 #00fdffff
> color #3.8 #fffb00ff
> color #3.8 #8efa00ff
> color #3.8 #73fcd6ff
> color #3.8 #73fdffff
> color #3.8 #76d6ffff
> color #3.8 #73fcd6ff
> sequence chain #3.2/B
Alignment identifier is 3.2/B
> select #3.2/B:363
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.2/B:363-369
55 atoms, 55 bonds, 7 residues, 1 model selected
> select add #3.2
2500 atoms, 2554 bonds, 307 residues, 1 model selected
> select subtract #3.2
Nothing selected
> select add #3.2
2500 atoms, 2554 bonds, 307 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #3.2/B:369
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.2/B:363-369
55 atoms, 55 bonds, 7 residues, 1 model selected
> show sel cartoons
> select add #3.2
2500 atoms, 2554 bonds, 307 residues, 1 model selected
> select subtract #3.2
Nothing selected
> sequence chain #3.3/C
Alignment identifier is 3.3/C
> select #3.3/C:177
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3.3/C:177
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #3.3/C:178
17 atoms, 16 bonds, 2 residues, 1 model selected
> select add #3.3/C:179
29 atoms, 28 bonds, 3 residues, 1 model selected
> select add #3.3/C:180
35 atoms, 33 bonds, 4 residues, 1 model selected
> select add #3.3
4897 atoms, 5000 bonds, 6 pseudobonds, 606 residues, 2 models selected
> hide sel cartoons
> select #3.3/C:177
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3.3/C:177-181
43 atoms, 44 bonds, 5 residues, 1 model selected
> show sel cartoons
> select #3.3/C:181
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.3/C:181
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select add #3.3
4897 atoms, 5000 bonds, 6 pseudobonds, 606 residues, 2 models selected
> select subtract #3.3
Nothing selected
> select add #3.3
4897 atoms, 5000 bonds, 6 pseudobonds, 606 residues, 2 models selected
> show sel cartoons
> select subtract #3.3
Nothing selected
> select #3.3/C:698
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3.3/C:693-698
41 atoms, 41 bonds, 6 residues, 1 model selected
> select #3.3/C:693
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.3/C:693-695
24 atoms, 24 bonds, 3 residues, 1 model selected
> select #3.3/C:695
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.3/C:695-700
40 atoms, 40 bonds, 6 residues, 1 model selected
> select add #3.3
4897 atoms, 5000 bonds, 6 pseudobonds, 606 residues, 2 models selected
> select subtract #3.3
Nothing selected
> select add #3.2
2500 atoms, 2554 bonds, 307 residues, 1 model selected
> show sel cartoons
> select subtract #3.2
Nothing selected
> select add #3.4
3438 atoms, 3504 bonds, 422 residues, 1 model selected
> select subtract #3.4
Nothing selected
> select add #3.5
3208 atoms, 3285 bonds, 3 pseudobonds, 393 residues, 2 models selected
> select subtract #3.5
Nothing selected
> select add #3.6
2943 atoms, 2977 bonds, 3 pseudobonds, 375 residues, 2 models selected
> sequence chain #3.6/G
Alignment identifier is 3.6/G
> select #3.6/G:293
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3.6/G:293-298
48 atoms, 48 bonds, 6 residues, 1 model selected
> select #3.6/G:290
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.6/G:290-296
51 atoms, 50 bonds, 7 residues, 1 model selected
> select add #3.6
2943 atoms, 2977 bonds, 3 pseudobonds, 375 residues, 2 models selected
> select subtract #3.6
Nothing selected
> select add #3.1
3095 atoms, 3148 bonds, 1 pseudobond, 390 residues, 2 models selected
> sequence chain #3.1/A
Alignment identifier is 3.1/A
> select #3.1/A:589
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3.1/A:589-597
62 atoms, 62 bonds, 9 residues, 1 model selected
> select add #3.1
3095 atoms, 3148 bonds, 1 pseudobond, 390 residues, 2 models selected
> select subtract #3.1
Nothing selected
> select add #3.1
3095 atoms, 3148 bonds, 1 pseudobond, 390 residues, 2 models selected
> select subtract #3.1
Nothing selected
> select add #3.2
2500 atoms, 2554 bonds, 307 residues, 1 model selected
> select #3.1/A:504
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.1/A:504-512
79 atoms, 80 bonds, 9 residues, 1 model selected
> select add #3.1
3095 atoms, 3148 bonds, 1 pseudobond, 390 residues, 2 models selected
> select subtract #3.1
Nothing selected
> sequence chain #3.2/B
Alignment identifier is 3.2/B
> select #3.2/B:503
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.2/B:503-511
67 atoms, 68 bonds, 9 residues, 1 model selected
> select #3.2/B:471
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3.2/B:471-574
836 atoms, 851 bonds, 104 residues, 1 model selected
> select #3.2/B:470-471
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #3.2/B:268-471
1670 atoms, 1708 bonds, 204 residues, 1 model selected
> hide sel cartoons
> sequence chain #3.1/A
Alignment identifier is 3.1/A
> select
> #3.1/A:487-494,508-524,540-556,576-588,594-606,622-624,631-641,658-662,665-671,683-693,702-715,719-735,748-758,763-769,772-788,795-809,816-828,837-842,851-859
1743 atoms, 1750 bonds, 214 residues, 1 model selected
> select #3.1/A:769
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.1/A:468-769
2342 atoms, 2383 bonds, 1 pseudobond, 297 residues, 2 models selected
> select #3.1/A:765
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3.1/A:468-765
2312 atoms, 2353 bonds, 1 pseudobond, 293 residues, 2 models selected
> select #3.1/A:763-764
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #3.1/A:468-764
2305 atoms, 2346 bonds, 1 pseudobond, 292 residues, 2 models selected
> select #3.1/A:759
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3.1/A:468-759
2267 atoms, 2307 bonds, 1 pseudobond, 287 residues, 2 models selected
> hide sel cartoons
> sequence chain #2/C
Alignment identifier is 2/C
> select #2/C:707
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/C:451-707
1640 atoms, 1673 bonds, 2 pseudobonds, 205 residues, 2 models selected
> sequence chain #3.3/C
Alignment identifier is 3.3/C
> select #3.3/C:707
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3.3/C:599-707
798 atoms, 813 bonds, 1 pseudobond, 102 residues, 2 models selected
> select
> #3.3/C:26-28,40-64,67-86,111-113,115-126,138-140,144-157,181-192,222-224,227-240,256-260,265-270,281-294,304-316,321-338,340-345,348-356,360-368,370-378,381-387,391-425,435-444,447-449,451-462,465-481,488-500,548-566,570-572,576-578,584-591,595-604,606-608,613-615,628-638,645-660,670-690
3238 atoms, 3267 bonds, 392 residues, 1 model selected
> select #3.3/C:595
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.3/C:595-707
829 atoms, 845 bonds, 1 pseudobond, 106 residues, 2 models selected
> select #3.3/C:594
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3.3/C:1-594
4068 atoms, 4154 bonds, 5 pseudobonds, 500 residues, 2 models selected
> hide sel cartoons
> sequence chain #3.4/D
Alignment identifier is 3.4/D
> select #3.4/D:312
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.4/D:312-431
987 atoms, 1008 bonds, 120 residues, 1 model selected
> select #3.4/D:311
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.4/D:12-311
2419 atoms, 2462 bonds, 300 residues, 1 model selected
> hide sel cartoons
> select #3.4/D:307
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.4/D:307-311
37 atoms, 36 bonds, 5 residues, 1 model selected
> show sel cartoons
> select #3.4/D:307
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.4/D:307
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select
> #3.4/D:13-30,41-57,73-85,107-118,132-145,161-166,171-181,198-200,204-209,223-234,243-258,260-272,276-289,299-308,313-320,323-338,346-359,369-381,408-416,423-430
1953 atoms, 1968 bonds, 233 residues, 1 model selected
> select #3.4/D:308
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.4/D:308
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> sequence chain #3.5/E
Alignment identifier is 3.5/E
> select
> #3.5/E:12-22,43-54,69-83,99-111,127-132,137-148,162-164,184-191,201-215,222-236,238-242,250-267,304-318,321-327,349-352,359-369,378-389,413-422,427-430
1632 atoms, 1648 bonds, 196 residues, 1 model selected
> select #3.5/E:321
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3.5/E:321-435
790 atoms, 806 bonds, 1 pseudobond, 99 residues, 2 models selected
> select
> #3.5/E:12-22,43-54,69-83,99-111,127-132,137-148,162-164,184-191,201-215,222-236,238-242,250-267,304-318,321-327,349-352,359-369,378-389,413-422,427-430
1632 atoms, 1648 bonds, 196 residues, 1 model selected
> select #3.5/E:314
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3.5/E:314-435
848 atoms, 867 bonds, 1 pseudobond, 106 residues, 2 models selected
> select #3.5/E:303
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.5/E:303-435
939 atoms, 962 bonds, 1 pseudobond, 117 residues, 2 models selected
> select #3.5/E:298
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3.5/E:298-435
980 atoms, 1004 bonds, 1 pseudobond, 122 residues, 2 models selected
> select #3.5/E:297-298
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #3.5/E:297-435
985 atoms, 1009 bonds, 1 pseudobond, 123 residues, 2 models selected
> select #3.5/E:277
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.5/E:4-277
2191 atoms, 2243 bonds, 1 pseudobond, 268 residues, 2 models selected
> hide sel cartoons
> sequence chain #3.6/G
Alignment identifier is 3.6/G
> select #3.6/G:455
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.6/G:455-557
811 atoms, 817 bonds, 103 residues, 1 model selected
> select #3.6/G:443
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3.6/G:153-443
2092 atoms, 2119 bonds, 2 pseudobonds, 269 residues, 2 models selected
> hide sel cartoons
> ui tool show "Side View"
> lighting simple
> lighting soft
> set bgColor white
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting full
> lighting soft
> lighting simple
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
No map chosen to save
Permission denied reading directory "/Users/om/Desktop" while trying to
determine next unused file name image#.png.
> cd "/Users/om/Downloads/HsODC WH domain"
Current working directory is: /Users/om/Downloads/HsODC WH domain
> save "/Users/om/Downloads/HsODC WH domain/HsODC WH domains.png" width 1313
> height 830 supersample 4 transparentBackground true
> graphics silhouettes false
> select add #3
21270 atoms, 21800 bonds, 13 pseudobonds, 2551 residues, 13 models selected
> select subtract #3
Nothing selected
> select add #3
21270 atoms, 21800 bonds, 13 pseudobonds, 2551 residues, 13 models selected
> select subtract #3
Nothing selected
> hide #!3 models
> show #!3 models
> select add #3
21270 atoms, 21800 bonds, 13 pseudobonds, 2551 residues, 13 models selected
> show sel cartoons
> select subtract #3
Nothing selected
> select add #3.1
3095 atoms, 3148 bonds, 1 pseudobond, 390 residues, 2 models selected
> select add #3.7
3691 atoms, 3814 bonds, 1 pseudobond, 419 residues, 3 models selected
> select add #3.8
4284 atoms, 4480 bonds, 1 pseudobond, 448 residues, 4 models selected
> nucleotides sel stubs
> style sel stick
Changed 4284 atom styles
> style sel stick
Changed 4284 atom styles
> select subtract #3.1
1189 atoms, 1332 bonds, 58 residues, 2 models selected
> select add #3
21270 atoms, 21800 bonds, 13 pseudobonds, 2551 residues, 13 models selected
> select subtract #3
Nothing selected
> select add #3.7
596 atoms, 666 bonds, 29 residues, 1 model selected
> select add #3.8
1189 atoms, 1332 bonds, 58 residues, 2 models selected
> style sel stick
Changed 1189 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 1189 atom styles
> color sel bynucleotide
> nucleotides sel atoms
> style nucleic & sel stick
Changed 1189 atom styles
> style sel stick
Changed 1189 atom styles
> show sel atoms
> nucleotides sel stubs
> color sel bynucleotide
> color #3.7 #73fcd6ff
> color #3.8 #009051ff
> select subtract #3.7
593 atoms, 666 bonds, 29 residues, 1 model selected
> select subtract #3.8
Nothing selected
> sequence chain #3.1/A
Alignment identifier is 3.1/A
> sequence chain #3.1/A
Destroying pre-existing alignment with identifier 3.1/A
Alignment identifier is 3.1/A
> select add #3.1
3095 atoms, 3148 bonds, 1 pseudobond, 390 residues, 2 models selected
> select #3.1/A:597
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3.1/A:589-597
62 atoms, 62 bonds, 9 residues, 1 model selected
> select add #3.1
3095 atoms, 3148 bonds, 1 pseudobond, 390 residues, 2 models selected
> hide sel cartoons
> select #3.1/A:589
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3.1/A:589-597
62 atoms, 62 bonds, 9 residues, 1 model selected
> show sel cartoons
> sequence chain #3.2/B
Alignment identifier is 3.2/B
> select add #3.1
3095 atoms, 3148 bonds, 1 pseudobond, 390 residues, 2 models selected
> select subtract #3.1
Nothing selected
> select add #3.2
2500 atoms, 2554 bonds, 307 residues, 1 model selected
> hide sel cartoons
> select #3.2/B:363
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.2/B:363-369
55 atoms, 55 bonds, 7 residues, 1 model selected
> show sel cartoons
> select add #3.2
2500 atoms, 2554 bonds, 307 residues, 1 model selected
> select subtract #3.2
Nothing selected
> sequence chain #3.3/C
Alignment identifier is 3.3/C
> select add #3.3
4897 atoms, 5000 bonds, 6 pseudobonds, 606 residues, 2 models selected
> select subtract #3.3
Nothing selected
> select #3.3/C:158
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3.3/C:158-180
41 atoms, 41 bonds, 1 pseudobond, 5 residues, 2 models selected
> select #3.3/C:177
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3.3/C:177-180
35 atoms, 36 bonds, 4 residues, 1 model selected
> select add #3.3
4897 atoms, 5000 bonds, 6 pseudobonds, 606 residues, 2 models selected
> hide sel cartoons
> select #3.3/C:177
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3.3/C:177-180
35 atoms, 36 bonds, 4 residues, 1 model selected
> show sel cartoons
> select add #3.3
4897 atoms, 5000 bonds, 6 pseudobonds, 606 residues, 2 models selected
> select subtract #3.3
Nothing selected
> sequence chain #3.4/D
Alignment identifier is 3.4/D
> select #3.4/D:132
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3.4/D:123-132
74 atoms, 75 bonds, 10 residues, 1 model selected
> select #3.4/D:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.4/D:121-132
91 atoms, 92 bonds, 12 residues, 1 model selected
> select #3.4/D:131
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3.4/D:121-131
80 atoms, 80 bonds, 11 residues, 1 model selected
> select add #3.4
3438 atoms, 3504 bonds, 422 residues, 1 model selected
> select subtract #3.4
Nothing selected
> select add #3.4
3438 atoms, 3504 bonds, 422 residues, 1 model selected
> hide sel cartoons
> select #3.4/D:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.4/D:121-131
80 atoms, 80 bonds, 11 residues, 1 model selected
> show sel cartoons
> select add #3.4
3438 atoms, 3504 bonds, 422 residues, 1 model selected
> select subtract #3.4
Nothing selected
> sequence chain #3.6/G
Alignment identifier is 3.6/G
> select #3.6/G:290
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.6/G:290-296
51 atoms, 50 bonds, 7 residues, 1 model selected
> select #3.6/G:294
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.6/G:290-294
36 atoms, 35 bonds, 5 residues, 1 model selected
> select add #3.6
2943 atoms, 2977 bonds, 3 pseudobonds, 375 residues, 2 models selected
> select subtract #3.6
Nothing selected
> select add #3.6
2943 atoms, 2977 bonds, 3 pseudobonds, 375 residues, 2 models selected
> hide sel cartoons
> select #3.6/G:290
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.6/G:290-294
36 atoms, 35 bonds, 5 residues, 1 model selected
> show sel cartoons
> select add #3.6
2943 atoms, 2977 bonds, 3 pseudobonds, 375 residues, 2 models selected
> select subtract #3.6
Nothing selected
> select add #3.5
3208 atoms, 3285 bonds, 3 pseudobonds, 393 residues, 2 models selected
> hide sel cartoons
> ui tool show "Side View"
> lighting soft
> lighting simple
> lighting soft
> graphics silhouettes true
> select add #3.3
8105 atoms, 8285 bonds, 9 pseudobonds, 999 residues, 4 models selected
> sequence chain #3.3/C
Alignment identifier is 3.3/C
> select #3.3/C:158
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3.3/C:158-180
41 atoms, 41 bonds, 1 pseudobond, 5 residues, 2 models selected
> show sel cartoons
> select add #3.3
4897 atoms, 5000 bonds, 6 pseudobonds, 606 residues, 2 models selected
> select subtract #3.3
Nothing selected
> save "/Users/om/Downloads/HsODC WH domain/HsODC ISM.png" width 1313 height
> 830 supersample 3
===== Log before crash end =====
Log:
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: 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: Mac14,6
Model Number: Z1790005QLL/A
Chip: Apple M2 Max
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 32 GB
System Firmware Version: 8422.141.2
OS Loader Version: 8422.141.2
Software:
System Software Overview:
System Version: macOS 13.5.2 (22G91)
Kernel Version: Darwin 22.6.0
Time since boot: 125 days, 21 hours, 52 minutes
Graphics/Displays:
Apple M2 Max:
Chipset Model: Apple M2 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 38
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
HP E232:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.5.0
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: 14.1.18
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-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
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-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: 1.1.2
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: 7.9.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.4
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: 4.4.4
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
pyelftools: 0.32
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: 4.14.0
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
|
|||
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
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Last modified on Jan 4, 2017, 10:45:36 AM
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