![[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 14116)
| Ticket | Resolution | Summary | Owner | Reporter |
|---|---|---|---|---|
| #20776 | not a bug | Fetch identifier | ||
| #20775 | duplicate | KVFinder on old MacOS | ||
| #20773 | can't reproduce | Crash in NSAccessibility routines in Qt 6.10.2 and ChimeraX 1.12 |
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 14116)
| Ticket | Resolution | Summary | Owner | Reporter |
|---|---|---|---|---|
| #20776 | not a bug | Fetch identifier | ||
| Description |
The following bug report has been submitted:
Platform: Windows-10-10.0.26200
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Hello,
I recently unable to fetch predicted structures by their PDB ID. An example is P0CE95, which I have worked with regularly and always opened by fetch by ID. Please let me know if I am missing something. Thank you!
Log:
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 P0CE95 fromDatabase pdb format mmcif
PDB identifiers are either 4 or 8 characters long, got "P0CE95"
> open P0CE95 fromDatabase pdb format mmcif
PDB identifiers are either 4 or 8 characters long, got "P0CE95"
> open AF-P0CE95-F1 fromDatabase pdb format mmcif
PDB identifiers are either 4 or 8 characters long, got "AF-P0CE95-F1"
> open 6R9T fromDatabase pdb format mmcif
Summary of feedback from opening 6R9T fetched from pdb
---
note | Fetching compressed mmCIF 6r9t from http://files.rcsb.org/download/6r9t.cif
6r9t title:
Cryo-EM structure of autoinhibited human talin-1 [more info...]
Chain information for 6r9t #1
---
Chain | Description | UniProt
A | Talin-1 | TLN1_HUMAN 1-2541
> close session
> open AFP0CE95F1 fromDatabase pdb format mmcif
PDB identifiers are either 4 or 8 characters long, got "AFP0CE95F1"
> open p0ce95 fromDatabase pdb format mmcif ignoreCache true
PDB identifiers are either 4 or 8 characters long, got "p0ce95"
> open P0CE95 fromDatabase pdb format mmcif ignoreCache true
PDB identifiers are either 4 or 8 characters long, got "P0CE95"
> help help:user/fetch.html
QWindowsWindow::setGeometry: Unable to set geometry 1055x1108+1073+384 (frame:
1073x1155+1064+346) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1059x1117+1071+377 (frame:
1077x1164+1062+339) margins: 9, 38, 9, 9 minimum size: 840x882 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=1068, y=1150)))
QWindowsWindow::setGeometry: Unable to set geometry 750x609+1225+634 (frame:
768x656+1216+596) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 754x618+1223+627 (frame:
772x665+1214+589) margins: 9, 38, 9, 9 minimum size: 600x333 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=768, y=463)))
OpenGL version: 3.3.0 NVIDIA 596.08
OpenGL renderer: NVIDIA GeForce RTX 3050 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows
Manufacturer: Dell Inc.
Model: XPS 15 9520
OS: Microsoft Windows 11 Home (Build 26200)
Memory: 16,834,945,024
MaxProcessMemory: 137,438,953,344
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700H
OSLanguage: en-US
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
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: 2025.6.15
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
comtypes: 1.4.10
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
narwhals: 2.18.0
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: 2.4.3
numpy: 1.26.4
nvidia-cuda-cupti-cu12: 12.9.79
nvidia-cuda-nvcc-cu12: 12.9.86
nvidia-cuda-nvrtc-cu12: 12.9.86
nvidia-cuda-runtime-cu12: 12.9.79
nvidia-cufft-cu12: 11.4.1.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
plotly: 6.5.2
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pyKVFinder: 0.9.0
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
pywin32: 310
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
tomlkit: 0.14.0
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
WMI: 1.5.1
|
|||
| #20775 | duplicate | KVFinder on old MacOS | ||
| Description |
The following bug report has been submitted:
Platform: macOS-14.8.5-arm64-arm-64bit
ChimeraX Version: 1.12 (2026-06-12 03:42:34 UTC)
Description
I tried to use the cavity function but it failed
Log:
UCSF ChimeraX version: 1.12 (2026-06-12)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> close session
> open 4dpd
Summary of feedback from opening 4dpd fetched from pdb
---
notes | Fetching compressed mmCIF 4dpd from http://files.rcsb.org/download/4dpd.cif
Fetching CCD DHF from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/F/DHF/DHF.cif
Fetching CCD NAP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/NAP/NAP.cif
Fetching CCD UMP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/UMP/UMP.cif
4dpd title:
WILD TYPE PLASMODIUM FALCIPARUM DIHYDROFOLATE REDUCTASE-THYMIDYLATE SYNTHASE
(PfDHFR-TS), DHF COMPLEX, NADP+, dUMP [more info...]
Chain information for 4dpd #1
---
Chain | Description | UniProt
A B | Bifunctional dihydrofolate reductase-thymidylate synthase | A7UD81_PLAFA 1-608
Non-standard residues in 4dpd #1
---
DHF — dihydrofolic acid
NAP — nadp nicotinamide-adenine-dinucleotide phosphate
(2'-monophosphoadenosine 5'-diphosphoribose)
UMP — 2'-deoxyuridine 5'-monophosphate (DUMP)
> select /B
4719 atoms, 4640 bonds, 2 pseudobonds, 729 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select /B:2-605
Nothing selected
> select ::name="DHF"
32 atoms, 34 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 32 atom styles
> color sel purple
> open 4dpd
Summary of feedback from opening 4dpd fetched from pdb
---
warning | Cannot find consistent set of bond orders for ring system containing atom C12 in residue DHF /A:701
4dpd title:
WILD TYPE PLASMODIUM FALCIPARUM DIHYDROFOLATE REDUCTASE-THYMIDYLATE SYNTHASE
(PfDHFR-TS), DHF COMPLEX, NADP+, dUMP [more info...]
Chain information for 4dpd #2
---
Chain | Description | UniProt
A B | Bifunctional dihydrofolate reductase-thymidylate synthase | A7UD81_PLAFA 1-608
Non-standard residues in 4dpd #2
---
DHF — dihydrofolic acid
NAP — nadp nicotinamide-adenine-dinucleotide phosphate
(2'-monophosphoadenosine 5'-diphosphoribose)
UMP — 2'-deoxyuridine 5'-monophosphate (DUMP)
> select clear
> select #2/B
4719 atoms, 4640 bonds, 2 pseudobonds, 729 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #1/A:288
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:287
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:288
8 atoms, 7 bonds, 1 residue, 1 model selected
> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"
> label height 2
> surface sel
> surface (#!1 & sel)
> surface style solid
> ui tool show "Color Actions"
> color sel dark blue
> select clear
> surface
> ui tool show "Color Actions"
> color blue violet
> select ::name="DHF"
64 atoms, 68 bonds, 2 residues, 2 models selected
> select ::name="DHF"
64 atoms, 68 bonds, 2 residues, 2 models selected
> select sel :< 5
472 atoms, 464 bonds, 48 residues, 2 models selected
> show (#!1-2 & sel) target ab
> color (#!1-2 & sel) red
> select ::name="DHF"
64 atoms, 68 bonds, 2 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel restrict cross reveal true
Cannot find consistent set of bond orders for ring system containing atom C12
in residue DHF /A:701
28 hydrogen bonds found
> ui tool show Contacts
> contacts sel restrict cross ignoreHiddenModels true
136 contacts
> transparency sel 90
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #2/A
Alignment identifier is 1
> select
> #1/A:4-9,33-37,51-64,66-82,106-117,132-136,145-156,166-176,286-294,308-318,324-339,376-388,392-399,405-416,429-437,454-466,478-485,516-536,556-564,582-589
> #2/A:4-9,33-37,51-64,66-82,106-117,132-136,145-156,166-176,286-294,308-318,324-339,376-388,392-399,405-416,429-437,454-466,478-485,516-536,556-564,582-589
3702 atoms, 3750 bonds, 438 residues, 2 models selected
> select #1/A:299 #2/A:299
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #1/A:299-306 #2/A:299-306
134 atoms, 132 bonds, 16 residues, 2 models selected
Bifunctional Dihydrofolate Reductase-Thymidylate Synthase [ID: 1] region 2
chains [299-306] RMSD: 0.000
> surface hidePatches (#!1-2 & sel)
> select clear
> transparency 70
> select #1/A:368-369 #2/A:368-369
32 atoms, 30 bonds, 4 residues, 2 models selected
> select #1/A:368-369 #2/A:368-369
32 atoms, 30 bonds, 4 residues, 2 models selected
Bifunctional Dihydrofolate Reductase-Thymidylate Synthase [ID: 1] region 2
chains [368-369] RMSD: 0.000
> open 1DHF
Summary of feedback from opening 1DHF fetched from pdb
---
notes | Fetching compressed mmCIF 1dhf from http://files.rcsb.org/download/1dhf.cif
Fetching CCD FOL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/FOL/FOL.cif
1dhf title:
Crystal structures of recombinant human dihydrofolate reductase complexed with
folate and 5-deazofolate [more info...]
Chain information for 1dhf #5
---
Chain | Description | UniProt
A B | DIHYDROFOLATE REDUCTASE | DYR_HUMAN 1-186
Non-standard residues in 1dhf #5
---
FOL — folic acid
> select #5/B:4-185
1476 atoms, 1511 bonds, 182 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 4dpd_A SES surface, 53 of 481140 triangles, 4dpd_A SES surface,
53 of 481140 triangles, 36 atoms, 34 bonds
> delete atoms (#5 & sel)
> delete bonds (#5 & sel)
> surface hidePatches #1.3#2.2
> ui tool show Matchmaker
> matchmaker #5#!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4dpd, chain A (#1) with 1dhf, chain A (#5), sequence alignment
score = 313.5
RMSD between 148 pruned atom pairs is 0.835 angstroms; (across all 171 pairs:
1.723)
Matchmaker 4dpd, chain A (#1) with 4dpd, chain A (#2), sequence alignment
score = 3111.2
RMSD between 530 pruned atom pairs is 0.000 angstroms; (across all 530 pairs:
0.000)
> save /Users/hkalin/Desktop/malaria.png width 930 height 675 supersample 3
> save /Users/hkalin/Desktop/4DPD_workshop_vr_HK.glb
> color modify #*lightness 40
Missing or invalid "adjuster" argument: Should be one of 'blackness', 'blue',
'contrast', 'green', 'hue', 'lightness', 'red', 'saturation', or 'whiteness'
> color modify #*lightness40
Missing or invalid "adjuster" argument: Should be one of 'blackness', 'blue',
'contrast', 'green', 'hue', 'lightness', 'red', 'saturation', or 'whiteness'
> colormodify #*lightness40
Unknown command: colormodify #*lightness40
> colormodify #*lightness 40
Unknown command: colormodify #*lightness 40
> colormodify #*lightness 40
Unknown command: colormodify #*lightness 40
> color modify #*lightness 40
Missing or invalid "adjuster" argument: Should be one of 'blackness', 'blue',
'contrast', 'green', 'hue', 'lightness', 'red', 'saturation', or 'whiteness'
> color modify #lightness 40
Missing or invalid "adjuster" argument: Should be one of 'blackness', 'blue',
'contrast', 'green', 'hue', 'lightness', 'red', 'saturation', or 'whiteness'
> color modify #lightness +40
Missing or invalid "adjuster" argument: Should be one of 'blackness', 'blue',
'contrast', 'green', 'hue', 'lightness', 'red', 'saturation', or 'whiteness'
> color modify #lightness -40
Missing or invalid "adjuster" argument: Should be one of 'blackness', 'blue',
'contrast', 'green', 'hue', 'lightness', 'red', 'saturation', or 'whiteness'
> color modify #1 lightness -40
> color modify #1 lightness +40
> color modify #1 lightness +70
> color modify # lightness +70
Missing or invalid "adjuster" argument: Should be one of 'blackness', 'blue',
'contrast', 'green', 'hue', 'lightness', 'red', 'saturation', or 'whiteness'
> color modify lightness +70
> color modify #2 lightness +70
> color modify #2 hue +70
> color modify #1 hue +70
> color modify lightness +70
> color modify lightness -70
> color modify lightness -10
> color modify lightness +50
> style ball
Changed 11090 atom styles
> style sphere
Changed 11090 atom styles
> style sphere
Changed 11090 atom styles
> style stick
Changed 11090 atom styles
> style sphere
Changed 11090 atom styles
> style sphere
Changed 11090 atom styles
> style ball
Changed 11090 atom styles
Drag select of 811 atoms, 1236 residues, 170 pseudobonds, 718 bonds
> style sel sphere
Changed 10509 atom styles
> style sel ball
Changed 10509 atom styles
> style sel sphere
Changed 10509 atom styles
> set bgColor white
> set bgColor black
> style sel ball
Changed 10509 atom styles
> lighting simple
> style sel sphere
Changed 10509 atom styles
> select #1/A#2/A
9470 atoms, 9248 bonds, 170 pseudobonds, 1510 residues, 6 models selected
> select #1/A
4735 atoms, 4624 bonds, 44 pseudobonds, 755 residues, 4 models selected
> select clear
> select #1/A
4735 atoms, 4624 bonds, 44 pseudobonds, 755 residues, 4 models selected
> select #5/A
1570 atoms, 1545 bonds, 245 residues, 1 model selected
> close session
> open 5WG8
Summary of feedback from opening 5WG8 fetched from pdb
---
notes | Fetching compressed mmCIF 5wg8 from http://files.rcsb.org/download/5wg8.cif
Fetching CCD LB1 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/1/LB1/LB1.cif
Fetching CCD MN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/MN/MN.cif
Fetching CCD MPD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/MPD/MPD.cif
Fetching CCD MRD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/MRD/MRD.cif
5wg8 title:
Structure of PP5C with LB-100; 7-oxabicyclo[2.2.1]heptane-2,3-dicarbonyl
moiety modeled in the density [more info...]
Chain information for 5wg8 #1
---
Chain | Description | UniProt
A | Serine/threonine-protein phosphatase 5 | PPP5_HUMAN 169-499
Non-standard residues in 5wg8 #1
---
LB1 —
(1S,2R,3S,4R)-3-(4-methylpiperazine-1-carbonyl)-7-oxabicyclo[2.2.1]heptane-2-carboxylic
acid
MN — manganese (II) ion
MPD — (4S)-2-methyl-2,4-pentanediol
MRD — (4R)-2-methylpentane-2,4-diol
75 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
2553 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Drag select of 118 atoms, 320 residues, 11 pseudobonds, 104 bonds
No Surface models open
> select clear
No Surface models open
[Repeated 1 time(s)]
> select :LB1
11 atoms, 12 bonds, 1 residue, 1 model selected
> select :MN
2 atoms, 2 residues, 1 model selected
> select :MPD
8 atoms, 7 bonds, 1 residue, 1 model selected
> select :MRD
8 atoms, 7 bonds, 1 residue, 1 model selected
Drag select of 1 atoms
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 5wg8_A SES surface #1.2: minimum, 0.00, mean 0.00,
maximum 0.00
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for 5wg8_A SES surface #1.2: minimum, 0.00, mean 0.00,
maximum 0.00
To also show corresponding color key, enter the above coulombic command and
add key true
> show sel surfaces
> open 5WG8 fromDatabase pdb format mmcif
5wg8 title:
Structure of PP5C with LB-100; 7-oxabicyclo[2.2.1]heptane-2,3-dicarbonyl
moiety modeled in the density [more info...]
Chain information for 5wg8 #2
---
Chain | Description | UniProt
A | Serine/threonine-protein phosphatase 5 | PPP5_HUMAN 169-499
Non-standard residues in 5wg8 #2
---
LB1 —
(1S,2R,3S,4R)-3-(4-methylpiperazine-1-carbonyl)-7-oxabicyclo[2.2.1]heptane-2-carboxylic
acid
MN — manganese (II) ion
MPD — (4S)-2-methyl-2,4-pentanediol
MRD — (4R)-2-methylpentane-2,4-diol
75 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
2553 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> coulombic sel
Coulombic values for 5wg8_A SES surface #1.2: minimum, 0.00, mean 0.00,
maximum 0.00
To also show corresponding color key, enter the above coulombic command and
add key true
Drag select of 60 residues
Drag select of 26 residues
Drag select of 30 residues
Drag select of 64 residues
Drag select of 18 residues
> color modify #1 lightness 40
> color modify #* lightness 40
> color modify #1 lightness 40
> color modify #2 lightness 40
> color modify #2 lightness +40
> color modify #2 hue +40
> color modify #* hue +40
[Repeated 2 time(s)]
> color modify #* lightness +70
> select clear
[Repeated 1 time(s)]
> select #2/A
2815 atoms, 2613 bonds, 11 pseudobonds, 587 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting full
> lighting soft
> lighting simple
[Repeated 2 time(s)]
> lighting soft
> lighting simple
> ui tool show "Side View"
> view
[Repeated 1 time(s)]
> view orient
> lighting flat
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
Drag select of 106 atoms, 240 residues, 11 pseudobonds, 95 bonds
Drag select of 5wg8_A SES surface, 118 atoms, 320 residues, 11 pseudobonds,
104 bonds
> ui tool show "Find Cavities"
pyKVFinder module not installed; fetching from PyPi repository...
'pip install pyKVFinder' failed. Error from pip: error: subprocess-exited-
with-error
× Building wheel for pyKVFinder (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [58 lines of output]
running bdist_wheel
running build
running build_py
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/utils.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/main.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/argparser.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/hydropathy.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/export.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/spatial.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/depth.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/constitutional.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/geometry.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/cavity.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/openings.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/detect.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
running egg_info
writing pyKVFinder.egg-info/PKG-INFO
writing dependency_links to pyKVFinder.egg-info/dependency_links.txt
writing entry points to pyKVFinder.egg-info/entry_points.txt
writing requirements to pyKVFinder.egg-info/requires.txt
writing top-level names to pyKVFinder.egg-info/top_level.txt
reading manifest file 'pyKVFinder.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'requirements.txt'
adding license file 'LICENSE'
writing manifest file 'pyKVFinder.egg-info/SOURCES.txt'
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/WimleyWhite.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/EisenbergWeiss.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/ZhaoLondon.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/RadzickaWolfenden.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/MoonFleming.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/KyteDoolittle.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/HessaHeijne.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/vdw.dat ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/C1.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/PKI.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ClO4.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/custom-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/residues-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
running build_ext
building 'pyKVFinder._pyKVFinder' extension
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i
creating build/temp.macosx-10.9-universal2-cpython-311/C
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/gd/ww67f0hx1mg613mfry6rddqsxqlhrx/T/pip-build-env-
jap6z4xt/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12.app/Contents/include/python3.11 -c
C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o
-Xpreprocessor -fopenmp=libomp -O3 -ffast-math
error: unknown argument: '-fopenmp=libomp'
error: command '/usr/bin/clang' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem
with pip.
ERROR: Failed building wheel for pyKVFinder
error: failed-wheel-build-for-install
× Failed to build installable wheels for some pyproject.toml based projects
╰─> pyKVFinder
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/__init__.py", line 48, in check_pyKVFinder
import pyKVFinder
ModuleNotFoundError: No module named 'pyKVFinder'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 571, in start_tool
ti = api._api_caller.start_tool(api, session, self, tool_info)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1400, in start_tool
return cls._get_func(api, "start_tool")(session, ti.name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/__init__.py", line 42, in start_tool
check_pyKVFinder(session.logger)
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/__init__.py", line 54, in check_pyKVFinder
run(logger.session, pip_cmd, log=False)
File
"/Applications/ChimeraX-1.12.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
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/pip.py", line 84, in pip
run_logged_pip(pip_cmd, session.logger)
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/python_utils.py", line 148, in run_logged_pip
raise RuntimeError(s)
RuntimeError: error: subprocess-exited-with-error
× Building wheel for pyKVFinder (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [58 lines of output]
running bdist_wheel
running build
running build_py
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/utils.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/main.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/argparser.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/hydropathy.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/export.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/spatial.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/depth.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/constitutional.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/geometry.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/cavity.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/openings.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/detect.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
running egg_info
writing pyKVFinder.egg-info/PKG-INFO
writing dependency_links to pyKVFinder.egg-info/dependency_links.txt
writing entry points to pyKVFinder.egg-info/entry_points.txt
writing requirements to pyKVFinder.egg-info/requires.txt
writing top-level names to pyKVFinder.egg-info/top_level.txt
reading manifest file 'pyKVFinder.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'requirements.txt'
adding license file 'LICENSE'
writing manifest file 'pyKVFinder.egg-info/SOURCES.txt'
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/WimleyWhite.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/EisenbergWeiss.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/ZhaoLondon.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/RadzickaWolfenden.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/MoonFleming.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/KyteDoolittle.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/HessaHeijne.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/vdw.dat ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/C1.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/PKI.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ClO4.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/custom-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/residues-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
running build_ext
building 'pyKVFinder._pyKVFinder' extension
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i
creating build/temp.macosx-10.9-universal2-cpython-311/C
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/gd/ww67f0hx1mg613mfry6rddqsxqlhrx/T/pip-build-env-
jap6z4xt/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12.app/Contents/include/python3.11 -c
C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o
-Xpreprocessor -fopenmp=libomp -O3 -ffast-math
error: unknown argument: '-fopenmp=libomp'
error: command '/usr/bin/clang' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem
with pip.
ERROR: Failed building wheel for pyKVFinder
error: failed-wheel-build-for-install
× Failed to build installable wheels for some pyproject.toml based projects
╰─> pyKVFinder
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1955, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.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
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/cmd.py", line 219, in ui_tool_show
return bi.start_tool(session, name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 578, in start_tool
raise ToolshedError(
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:
error: subprocess-exited-with-error
× Building wheel for pyKVFinder (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [58 lines of output]
running bdist_wheel
running build
running build_py
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/utils.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/main.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/argparser.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/hydropathy.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/export.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/spatial.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/depth.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/constitutional.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/geometry.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/cavity.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/openings.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/detect.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
running egg_info
writing pyKVFinder.egg-info/PKG-INFO
writing dependency_links to pyKVFinder.egg-info/dependency_links.txt
writing entry points to pyKVFinder.egg-info/entry_points.txt
writing requirements to pyKVFinder.egg-info/requires.txt
writing top-level names to pyKVFinder.egg-info/top_level.txt
reading manifest file 'pyKVFinder.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'requirements.txt'
adding license file 'LICENSE'
writing manifest file 'pyKVFinder.egg-info/SOURCES.txt'
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/WimleyWhite.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/EisenbergWeiss.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/ZhaoLondon.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/RadzickaWolfenden.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/MoonFleming.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/KyteDoolittle.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/HessaHeijne.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/vdw.dat ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/C1.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/PKI.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ClO4.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/custom-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/residues-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
running build_ext
building 'pyKVFinder._pyKVFinder' extension
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i
creating build/temp.macosx-10.9-universal2-cpython-311/C
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/gd/ww67f0hx1mg613mfry6rddqsxqlhrx/T/pip-build-env-
jap6z4xt/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12.app/Contents/include/python3.11 -c
C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o
-Xpreprocessor -fopenmp=libomp -O3 -ffast-math
error: unknown argument: '-fopenmp=libomp'
error: command '/usr/bin/clang' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem
with pip.
ERROR: Failed building wheel for pyKVFinder
error: failed-wheel-build-for-install
× Failed to build installable wheels for some pyproject.toml based projects
╰─> pyKVFinder
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:
error: subprocess-exited-with-error
× Building wheel for pyKVFinder (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [58 lines of output]
running bdist_wheel
running build
running build_py
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/utils.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/main.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/argparser.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/hydropathy.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/export.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/spatial.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/depth.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/constitutional.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/geometry.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/cavity.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/openings.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/detect.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
running egg_info
writing pyKVFinder.egg-info/PKG-INFO
writing dependency_links to pyKVFinder.egg-info/dependency_links.txt
writing entry points to pyKVFinder.egg-info/entry_points.txt
writing requirements to pyKVFinder.egg-info/requires.txt
writing top-level names to pyKVFinder.egg-info/top_level.txt
reading manifest file 'pyKVFinder.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'requirements.txt'
adding license file 'LICENSE'
writing manifest file 'pyKVFinder.egg-info/SOURCES.txt'
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/WimleyWhite.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/EisenbergWeiss.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/ZhaoLondon.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/RadzickaWolfenden.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/MoonFleming.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/KyteDoolittle.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/HessaHeijne.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/vdw.dat ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/C1.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/PKI.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ClO4.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/custom-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/residues-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
running build_ext
building 'pyKVFinder._pyKVFinder' extension
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i
creating build/temp.macosx-10.9-universal2-cpython-311/C
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/gd/ww67f0hx1mg613mfry6rddqsxqlhrx/T/pip-build-env-
jap6z4xt/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12.app/Contents/include/python3.11 -c
C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o
-Xpreprocessor -fopenmp=libomp -O3 -ffast-math
error: unknown argument: '-fopenmp=libomp'
error: command '/usr/bin/clang' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem
with pip.
ERROR: Failed building wheel for pyKVFinder
error: failed-wheel-build-for-install
× Failed to build installable wheels for some pyproject.toml based projects
╰─> pyKVFinder
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 578, in start_tool
raise ToolshedError(
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.9
Locale: UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,6
Model Number: Z1AX0029VLL/A
Chip: Apple M3 Pro
Total Number of Cores: 12 (6 performance and 6 efficiency)
Memory: 36 GB
System Firmware Version: mBoot-18000.101.7
OS Loader Version: 10151.140.19.701.1
Software:
System Software Overview:
System Version: macOS 14.8.5 (23J423)
Kernel Version: Darwin 23.6.0
Time since boot: 3 hours, 20 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 18
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.6.2
aiohttp: 3.13.4
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.13.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 26.1.0
babel: 2.18.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 4.4.3
bs4: 0.0.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.7
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.67.1
ChimeraX-AtomicLibrary: 14.4
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4.1
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.4
ChimeraX-Cluster: 1.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.2.2
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.8.2
ChimeraX-Label: 1.5
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
ChimeraX-MatchMaker: 2.4.1
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.19
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.9
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.23
ChimeraX-ModelPanel: 1.6.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.4
ChimeraX-OpenFold: 1.0
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.13
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.6
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.12
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.18
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.4
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.50.8
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.4.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.14.1
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: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.16.0
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.18
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 2.0.0
iniconfig: 2.3.0
ipykernel: 7.1.0
ipython: 9.9.0
ipython_pygments_lexers: 1.1.1
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.8.0
jupyter_core: 5.9.1
kiwisolver: 1.5.0
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.2
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.1
narwhals: 2.22.1
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.4.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.7
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: 4.10.0
plotly: 6.8.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.5.2
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: 2.14.1
pydantic_core: 2.46.4
pydata-sphinx-theme: 0.18.0
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.5.1
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.10.2
PyQt6-Qt6: 6.10.2
PyQt6-WebEngine-commercial: 6.10.0
PyQt6-WebEngine-Qt6: 6.10.2
PyQt6_sip: 13.10.3
pytest: 9.0.3
pytest-cov: 7.1.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.32
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
rpds-py: 2026.5.1
scipy: 1.14.0
setuptools: 80.9.0
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: 3.4.4
stack-data: 0.6.3
starlette: 1.3.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 3.2.1
threadpoolctl: 3.6.0
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.7
tqdm: 4.68.2
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
Unidecode: 1.4.0
urllib3: 2.7.0
uvicorn: 0.49.0
wcwidth: 0.8.1
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
yarl: 1.24.2
|
|||
| #20773 | can't reproduce | Crash in NSAccessibility routines in Qt 6.10.2 and ChimeraX 1.12 | ||
| Description |
The following bug report has been submitted:
Platform: macOS-26.5.1-arm64-arm-64bit
ChimeraX Version: 1.12 (2026-06-12 03:42:34 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000001fbf85e80 (most recent call first):
File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 424 in event_loop
File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init
File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imaging, PIL._imagingmath, chimerax.segment._segment (total: 53)
{"app_name":"ChimeraX","timestamp":"2026-07-19 23:26:59.00 +0800","app_version":"1.12.0","slice_uuid":"544eb719-b770-3601-b425-1ceb237637ac","build_version":"1.12.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 26.5.1 (25F80)","roots_installed":0,"name":"ChimeraX","incident_id":"F9B561BE-C753-4782-8A0C-BADD5C9FF8DA"}
{
"uptime" : 330000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac16,11",
"coalitionID" : 11378,
"osVersion" : {
"train" : "macOS 26.5.1",
"build" : "25F80",
"releaseType" : "User"
},
"captureTime" : "2026-07-19 23:26:58.4219 +0800",
"codeSigningMonitor" : 2,
"incident" : "F9B561BE-C753-4782-8A0C-BADD5C9FF8DA",
"pid" : 97842,
"translated" : false,
"cpuType" : "ARM-64",
"procLaunch" : "2026-07-19 23:24:23.6950 +0800",
"procStartAbsTime" : 8017081166859,
"procExitAbsTime" : 8020794435498,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.12.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.12.0","CFBundleVersion":"1.12.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"FF35C813-1E2B-5B36-A4C8-104A06F3943A","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "DC15A465-326B-DBFD-FCFC-9FB4B18897EE",
"appleIntelligenceStatus" : {"reasons":["regionIneligible"],"state":"unavailable"},
"developerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRCuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkf\/f\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "318BA056-26E5-47A5-9B52-1C3015028BDB",
"sip" : "enabled",
"vmRegionInfo" : "0x1e8ed71656a5 is not in any region.
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x31751e8ed71656a5","rawCodes":[1,3563788278976370341],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x31751e8ed71656a5"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":97842},
"vmregioninfo" : "0x1e8ed71656a5 is not in any region.
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
UNUSED SPACE AT END",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : [{
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"vmSummary" : "ReadOnly portion of Libraries: Total=2.1G resident=0K(0%) swapped_out_or_unallocated=2.1G(100%)
Writable regions: Total=1.3G written=1586K(0%) resident=1586K(0%) swapped_out=0K(0%) unallocated=1.3G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 256K 2
Activity Tracing 256K 1
CG image 352K 5
CG raster data 208K 3
ColorSync 96K 5
CoreAnimation 912K 57
CoreGraphics 48K 3
CoreUI image data 1696K 21
Dispatch continuations 96.0M 1
Foundation 48K 2
Kernel Alloc Once 32K 1
MALLOC 425.8M 72
MALLOC guard page 3280K 4
Mach message 64K 3
OpenGL GLSL 256K 3
PROTECTED_MEMORY 16K 1
STACK GUARD 672K 42
Stack 202.4M 43
Stack Guard 56.0M 1
VM_ALLOCATE 300.5M 306
VM_ALLOCATE (reserved) 256.0M 1 reserved VM address space (unallocated)
__AUTH 6024K 634
__AUTH_CONST 89.5M 1026
__CTF 824 1
__DATA 42.0M 1108
__DATA_CONST 62.0M 1161
__DATA_DIRTY 8346K 881
__FONT_DATA 2352 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 605.4M 132
__OBJC_RO 79.1M 1
__OBJC_RW 2599K 1
__TEXT 1.5G 1183
__TPRO_CONST 128K 2
dyld private memory 304K 5
mapped file 802.0M 105
page table in kernel 1586K 1
shared memory 3696K 26
=========== ======= =======
TOTAL 4.4G 6846
TOTAL, minus reserved VM space 4.2G 6846
",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "69767d743106cf4a763010cfc2922d03fdd677ba",
"roots_installed" : 0,
"bug_type" : "309",
"trmStatus" : 8192,
"voucherInfos" : [{"originatorName":"SkyComputerUseService","proximateName":"SkyComputerUseService","thread_id":12849238}],
"trialInfo" : {
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{
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}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.12 (2026-06-12)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(NoModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(AltModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(MetaModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> close all
> open
> /Volumes/lfwsync/北理/CryoMV/CryoMV_Refine/AAAI/10516_external_metrics/cryoDRGN2/audit_good_bad_pair_map2map/good_pair_center01_center03_candidate03/direct_bp_unfiltered.mrc
Opened direct_bp_unfiltered.mrc as #1, grid size 256,256,256, pixel 1.05,
shown at level 0.0137, step 1, values float32
> open
> /Volumes/lfwsync/北理/CryoMV/CryoMV_Refine/AAAI/10516_external_metrics/local_flex_roi_compare/upper_flex_markers.pdb
Summary of feedback from opening
/Volumes/lfwsync/北理/CryoMV/CryoMV_Refine/AAAI/10516_external_metrics/local_flex_roi_compare/upper_flex_markers.pdb
---
warnings | Cannot find LINK/SSBOND residue mar (206 )
Cannot find LINK/SSBOND residue mar (207 )
Cannot find LINK/SSBOND residue mar (208 )
Cannot find LINK/SSBOND residue mar (209 )
Cannot find LINK/SSBOND residue mar (210 )
41 messages similar to the above omitted
note | Combining 2 symmetry atoms into MAR /kM:211 M
Chain information for upper_flex_markers.pdb #2
---
Chain | Description
kM | No description available
> volume #1 level 0.009
> volume gaussian #1 sDev 1.7 modelId #3
Opened direct_bp_unfiltered.mrc gaussian as #3, grid size 256,256,256, pixel
1.05, shown at step 1, values float32
> volume #3 level 0.0045
> hide #3 models
> mousemode rightMode "select toggle"
> ui tool show "Segment Map"
> view
Called accessibilityLabel on invalid object: 2147486648
Called accessibilityLabel on invalid object: 2147486659
Called accessibilityLabel on invalid object: 2147486648
Called accessibilityLabel on invalid object: 2147486659
Called accessibilityLabel on invalid object: 2147486648
Called accessibilityLabel on invalid object: 2147486659
Mismatch between Cocoa '\x4' and Carbon '\x0' for virtual key 119 with
QFlags(NoModifier)
Mismatch between Cocoa '\x4' and Carbon '\x0' for virtual key 119 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x4' and Carbon '\x0' for virtual key 119 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x4' and Carbon '\x0' for virtual key 119 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x4' and Carbon '\x0' for virtual key 119 with
QFlags(AltModifier)
Mismatch between Cocoa '\x4' and Carbon '\x0' for virtual key 119 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x4' and Carbon '\x0' for virtual key 119 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x4' and Carbon '\x0' for virtual key 119 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x4' and Carbon '\x0' for virtual key 119 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x4' and Carbon '\x0' for virtual key 119 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x4' and Carbon '\x0' for virtual key 119 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x4' and Carbon '\x0' for virtual key 119 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x4' and Carbon '\x0' for virtual key 119 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x4' and Carbon '\x0' for virtual key 119 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x4' and Carbon '\x0' for virtual key 119 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x4' and Carbon '\x0' for virtual key 119 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
Called accessibilityLabel on invalid object: 2147487317
Called accessibilityLabel on invalid object: 2147487328
Called accessibilityLabel on invalid object: 2147487317
Called accessibilityLabel on invalid object: 2147487328
Called accessibilityLabel on invalid object: 2147487317
Called accessibilityLabel on invalid object: 2147487328
Segmenting direct_bp_unfiltered.mrc gaussian, density threshold 0.004500
Only showing 60 of 420 regions.
Showing 60 of 420 region surfaces
Only showing 60 of 61 regions.
Showing 60 of 61 region surfaces
420 watershed regions, grouped to 61 regions
Showing direct_bp_unfiltered gaussian.seg - 61 regions, 60 surfaces
Called accessibilityLabel on invalid object: 2147487738
Called accessibilityLabel on invalid object: 2147487727
Called accessibilityLabel on invalid object: 2147487738
Called accessibilityLabel on invalid object: 2147487727
Called accessibilityLabel on invalid object: 2147487738
Called accessibilityLabel on invalid object: 2147488287
Called accessibilityLabel on invalid object: 2147488298
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #3 level 0.004344
> hide #!3 models
> show #!2 models
> volume #1 level 0.009
> volume #1 level 0.009483
> hide #!3 models
> close #2
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!1 models
> show #!4 models
> select add #4.9
1 model selected
> select add #4.6
2 models selected
> select add #4.24
3 models selected
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!3 models
> show #!4 models
> hide #!3 models
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.12 (2026-06-12)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M4 Pro
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac mini
Model Identifier: Mac16,11
Model Number: Z1JV0005KCH/A
Chip: Apple M4 Pro
Total Number of Cores: 12 (8 Performance and 4 Efficiency)
Memory: 48 GB
System Firmware Version: 18000.120.36
OS Loader Version: 18000.120.36
Software:
System Software Overview:
System Version: macOS 26.5.1 (25F80)
Kernel Version: Darwin 25.5.0
Time since boot: 3天20小时50分钟
Graphics/Displays:
Apple M4 Pro:
Chipset Model: Apple M4 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Q27P10:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 75.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.6.2
aiohttp: 3.13.4
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.13.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 26.1.0
babel: 2.18.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 4.4.3
bs4: 0.0.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.7
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.67.1
ChimeraX-AtomicLibrary: 14.4
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4.1
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.4
ChimeraX-Cluster: 1.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.2.2
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.8.2
ChimeraX-Label: 1.5
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
ChimeraX-MatchMaker: 2.4.1
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.19
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.9
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.23
ChimeraX-ModelPanel: 1.6.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.4
ChimeraX-OpenFold: 1.0
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.13
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.6
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.12
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.18
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.4
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.50.8
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.4.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.14.1
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: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.16.0
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.18
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 2.0.0
iniconfig: 2.3.0
ipykernel: 7.1.0
ipython: 9.9.0
ipython_pygments_lexers: 1.1.1
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.8.0
jupyter_core: 5.9.1
kiwisolver: 1.5.0
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.2
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.1
narwhals: 2.22.1
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.4.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.7
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: 4.10.0
plotly: 6.8.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.5.2
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: 2.14.1
pydantic_core: 2.46.4
pydata-sphinx-theme: 0.18.0
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.5.1
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.10.2
PyQt6-Qt6: 6.10.2
PyQt6-WebEngine-commercial: 6.10.0
PyQt6-WebEngine-Qt6: 6.10.2
PyQt6_sip: 13.10.3
pytest: 9.0.3
pytest-cov: 7.1.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.32
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
rpds-py: 2026.5.1
scipy: 1.14.0
setuptools: 80.9.0
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: 3.4.4
stack-data: 0.6.3
starlette: 1.3.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 3.2.1
threadpoolctl: 3.6.0
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.7
tqdm: 4.68.2
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
Unidecode: 1.4.0
urllib3: 2.7.0
uvicorn: 0.49.0
wcwidth: 0.8.1
webcolors: 24.11.1
wheel: 0.45.1
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
Last modified
10 years ago
Last modified on Jan 4, 2017, 10:45:36 AM
Note:
See TracWiki
for help on using the wiki.
