Opened 3 hours ago
#20469 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26200
ChimeraX Version: 1.12rc202606060206 (2026-06-06 02:06:12 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.12rc202606060206 (2026-06-06)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> C:/Users/Administrator/Desktop/创新实验室/实验/分子对接/DE1_IL12R_ternary_complex/MMFold_3.pdb
Chain information for MMFold_3.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
Computing secondary structure
> set bgColor white
> set bgColor #ffffff00
> select #1 /A:28,51,54,94,95,97,100,181
> /B:63,170,172,175,178,181,182,34,34,35,37,39,156,157
> /C:178,291,182,289,247,103,88,143
249 atoms, 227 bonds, 29 residues, 1 model selected
> show sel atoms
> select /A
1823 atoms, 1858 bonds, 247 residues, 1 model selected
> color sel cyan
> select /B
1486 atoms, 1509 bonds, 185 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium orchid
> select /C
2423 atoms, 2482 bonds, 304 residues, 1 model selected
> color sel light coral
> select clear
> select #1 /A:100@N /B:34@OE1
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance /A:100@N /B:34@OE1
Distance between /A GLY 100 N and /B GLU 34 OE1: 3.793Å
> hide #2.1 models
> select #1 /A:97@N /B:35@O
2 atoms, 2 residues, 1 model selected
> ui tool show Contacts
> ui tool show Distances
> distance /A:97@N /B:35@O
Distance between /A ARG 97 N and /B GLU 35 O: 2.439Å
> select #1 /A:51@NH1 /B:37@O
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance /A:51@NH1 /B:37@O
Distance between /A ARG 51 NH1 and /B ASP 37 O: 3.785Å
> select #1 /A:95@NE2 /B:156@OH
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance /A:95@NE2 /B:156@OH
Distance between /A GLN 95 NE2 and /B TYR 156 OH: 3.450Å
> select #1 /A:28@OG1 /B:157@NZ
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance /A:28@OG1 /B:157@NZ
Distance between /A THR 28 OG1 and /B LYS 157 NZ: 3.482Å
> select #1 /A:94@NH2 /B:37@OD1
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance /A:94@NH2 /B:37@OD1
Distance between /A ARG 94 NH2 and /B ASP 37 OD1: 3.665Å
> color sel lime
> select #1 /A:51@NH1 /B:39@OE2
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance /A:51@NH1 /B:39@OE2
Distance between /A ARG 51 NH1 and /B GLU 39 OE2: 2.529Å
> color sel lime
> select #1 /A:51@NH2 /B:39@OE2
Traceback (most recent call last):
File "E:\ChimeraX 1.12rc202606060206\bin\Lib\site-
packages\chimerax\core\safesave.py", line 112, in __exit__
os.replace(self._tmp_filename, self.name)
PermissionError: [WinError 5] 拒绝访问。:
'C:\\\Users\\\Administrator\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36264.1780922129.2782228.tmp'
-> 'C:\\\Users\\\Administrator\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "E:\ChimeraX 1.12rc202606060206\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "E:\ChimeraX 1.12rc202606060206\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 354, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "E:\ChimeraX 1.12rc202606060206\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 472, in add
self._history.enqueue((item, typed))
File "E:\ChimeraX 1.12rc202606060206\bin\Lib\site-
packages\chimerax\core\history.py", line 182, in enqueue
self.save()
File "E:\ChimeraX 1.12rc202606060206\bin\Lib\site-
packages\chimerax\core\history.py", line 212, in save
self._history.save(self._queue)
File "E:\ChimeraX 1.12rc202606060206\bin\Lib\site-
packages\chimerax\core\history.py", line 119, in save
with SaveTextFile(self._filename) as f:
File "E:\ChimeraX 1.12rc202606060206\bin\Lib\site-
packages\chimerax\core\safesave.py", line 122, in __exit__
os.replace(self._tmp_filename, self.name)
PermissionError: [WinError 5] 拒绝访问。:
'C:\\\Users\\\Administrator\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36264.1780922129.2782228.tmp'
-> 'C:\\\Users\\\Administrator\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'
Error processing trigger "command started":
PermissionError: [WinError 5] 拒绝访问。:
'C:\\\Users\\\Administrator\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36264.1780922129.2782228.tmp'
-> 'C:\\\Users\\\Administrator\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'
File "E:\ChimeraX 1.12rc202606060206\bin\Lib\site-
packages\chimerax\core\safesave.py", line 122, in __exit__
os.replace(self._tmp_filename, self.name)
See log for complete Python traceback.
2 atoms, 2 residues, 1 model selected
> select #1 /A:51@NH2 /B:39@OE2
Traceback (most recent call last):
File "E:\ChimeraX 1.12rc202606060206\bin\Lib\site-
packages\chimerax\core\safesave.py", line 112, in __exit__
os.replace(self._tmp_filename, self.name)
PermissionError: [WinError 5] 拒绝访问。:
'C:\\\Users\\\Administrator\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36264.1780922129.2782228.tmp'
-> 'C:\\\Users\\\Administrator\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "E:\ChimeraX 1.12rc202606060206\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "E:\ChimeraX 1.12rc202606060206\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 354, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "E:\ChimeraX 1.12rc202606060206\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 472, in add
self._history.enqueue((item, typed))
File "E:\ChimeraX 1.12rc202606060206\bin\Lib\site-
packages\chimerax\core\history.py", line 182, in enqueue
self.save()
File "E:\ChimeraX 1.12rc202606060206\bin\Lib\site-
packages\chimerax\core\history.py", line 212, in save
self._history.save(self._queue)
File "E:\ChimeraX 1.12rc202606060206\bin\Lib\site-
packages\chimerax\core\history.py", line 119, in save
with SaveTextFile(self._filename) as f:
File "E:\ChimeraX 1.12rc202606060206\bin\Lib\site-
packages\chimerax\core\safesave.py", line 122, in __exit__
os.replace(self._tmp_filename, self.name)
PermissionError: [WinError 5] 拒绝访问。:
'C:\\\Users\\\Administrator\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36264.1780922129.2782228.tmp'
-> 'C:\\\Users\\\Administrator\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'
Error processing trigger "command started":
PermissionError: [WinError 5] 拒绝访问。:
'C:\\\Users\\\Administrator\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.36264.1780922129.2782228.tmp'
-> 'C:\\\Users\\\Administrator\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'
File "E:\ChimeraX 1.12rc202606060206\bin\Lib\site-
packages\chimerax\core\safesave.py", line 122, in __exit__
os.replace(self._tmp_filename, self.name)
See log for complete Python traceback.
2 atoms, 2 residues, 1 model selected
OpenGL version: 3.3.0 - Build 32.0.101.7084
OpenGL renderer: Intel(R) UHD Graphics 770
OpenGL vendor: Intel
Python: 3.11.9
Locale: zh_CN.cp936
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: windows
Manufacturer: Dell Inc.
Model: OptiPlex Tower 7020
OS: Microsoft Windows 11 家庭版 中文版 (Build 26200.8457)
Memory: 16,851,447,808
MaxProcessMemory: 137,438,953,344
CPU: 12 12th Gen Intel(R) Core(TM) i5-12500
OSLanguage: zh-CN
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
asttokens: 3.0.1
attrs: 26.1.0
babel: 2.18.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 4.4.2
bs4: 0.0.2
build: 1.3.0
certifi: 2026.5.20
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: 1.12rc202606060206
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
comtypes: 1.4.11
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
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.4.0
OpenMM-CUDA-12: 8.4.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.7
pep517: 0.13.1
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
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
pywin32: 311
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: 1.2.1
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: 6.5.6
tqdm: 4.68.1
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2026.2
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
WMI: 1.5.1
yarl: 1.24.2
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