The following bug report has been submitted:
Platform: macOS-13.4-arm64-arm-64bit
ChimeraX Version: 1.10.dev202501140846 (2025-01-14 08:46:23 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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Log:
UCSF ChimeraX version: 1.10.dev202501140846 (2025-01-14)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/zhaochunqiu/Desktop/结构作图/S-L-18-water.cxs
Log from Tue Apr 8 23:15:31 2025UCSF ChimeraX version: 1.10.dev202501140846
(2025-01-14)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/zhaochunqiu/Desktop/结构作图/S-L-18-water.cxs
Log from Tue Apr 8 21:23:26 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.10.dev202501140846 (2025-01-14)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/zhaochunqiu/Desktop/1.pdb /Users/zhaochunqiu/Desktop/17.pdb
> /Users/zhaochunqiu/Desktop/16.pdb /Users/zhaochunqiu/Desktop/15.pdb
> /Users/zhaochunqiu/Desktop/14.pdb /Users/zhaochunqiu/Desktop/13.pdb
> /Users/zhaochunqiu/Desktop/12.pdb /Users/zhaochunqiu/Desktop/11.pdb
> /Users/zhaochunqiu/Desktop/10.pdb /Users/zhaochunqiu/Desktop/9.pdb
> /Users/zhaochunqiu/Desktop/8.pdb /Users/zhaochunqiu/Desktop/7.pdb
> /Users/zhaochunqiu/Desktop/6.pdb /Users/zhaochunqiu/Desktop/5.pdb
> /Users/zhaochunqiu/Desktop/4.pdb /Users/zhaochunqiu/Desktop/3.pdb
> /Users/zhaochunqiu/Desktop/2.pdb
Chain information for 1.pdb #1
---
Chain | Description
A B | No description available
H | No description available
Chain information for 17.pdb #2
---
Chain | Description
A B | No description available
H | No description available
Chain information for 16.pdb #3
---
Chain | Description
A B | No description available
H | No description available
Chain information for 15.pdb #4
---
Chain | Description
A B | No description available
H | No description available
Chain information for 14.pdb #5
---
Chain | Description
A B | No description available
H | No description available
Chain information for 13.pdb #6
---
Chain | Description
A B | No description available
H | No description available
Chain information for 12.pdb #7
---
Chain | Description
A B | No description available
H | No description available
Chain information for 11.pdb #8
---
Chain | Description
A B | No description available
H | No description available
Chain information for 10.pdb #9
---
Chain | Description
A B | No description available
H | No description available
Chain information for 9.pdb #10
---
Chain | Description
A B | No description available
H | No description available
Chain information for 8.pdb #11
---
Chain | Description
A B | No description available
H | No description available
Chain information for 7.pdb #12
---
Chain | Description
A B | No description available
H | No description available
Chain information for 6.pdb #13
---
Chain | Description
A B | No description available
H | No description available
Chain information for 5.pdb #14
---
Chain | Description
A B | No description available
H | No description available
Chain information for 4.pdb #15
---
Chain | Description
A B | No description available
H | No description available
Chain information for 3.pdb #16
---
Chain | Description
A B | No description available
H | No description available
Chain information for 2.pdb #17
---
Chain | Description
A B | No description available
H | No description available
Computing secondary structure
> open /Users/zhaochunqiu/Desktop/xxx.pdb
Chain information for xxx.pdb #18
---
Chain | Description
A B | No description available
H | No description available
> select
> #1/A#2/A#3/A#4/A#5/A#6/A#7/A#8/A#9/A#10/A#11/A#12/A#13/A#14/A#15/A#16/A#17/A#18/A
18612 atoms, 18954 bonds, 2430 residues, 18 models selected
> ui tool show "Color Actions"
> color sel pale turquoise
> select
> #1/B#2/B#3/B#4/B#5/B#6/B#7/B#8/B#9/B#10/B#11/B#12/B#13/B#14/B#15/B#16/B#17/B#18/B
18612 atoms, 18954 bonds, 2430 residues, 18 models selected
> ui tool show "Color Actions"
> color sel pale turquoise
> select
> #1/H#2/H#3/H#4/H#5/H#6/H#7/H#8/H#9/H#10/H#11/H#12/H#13/H#14/H#15/H#16/H#17/H#18/H
65232 atoms, 66780 bonds, 54 pseudobonds, 8082 residues, 36 models selected
> ui tool show "Color Actions"
> color sel plum
> select add #18
67300 atoms, 68886 bonds, 54 pseudobonds, 8352 residues, 36 models selected
> select add #17
69368 atoms, 70992 bonds, 54 pseudobonds, 8622 residues, 36 models selected
> select subtract #17
63676 atoms, 65176 bonds, 51 pseudobonds, 7903 residues, 34 models selected
> select subtract #18
57984 atoms, 59360 bonds, 48 pseudobonds, 7184 residues, 32 models selected
> select add #16
60052 atoms, 61466 bonds, 48 pseudobonds, 7454 residues, 32 models selected
> select subtract #16
54360 atoms, 55650 bonds, 45 pseudobonds, 6735 residues, 30 models selected
> select add #15
56428 atoms, 57756 bonds, 45 pseudobonds, 7005 residues, 30 models selected
> select subtract #15
50736 atoms, 51940 bonds, 42 pseudobonds, 6286 residues, 28 models selected
> select add #14
52804 atoms, 54046 bonds, 42 pseudobonds, 6556 residues, 28 models selected
> select subtract #14
47112 atoms, 48230 bonds, 39 pseudobonds, 5837 residues, 26 models selected
> select add #13
49180 atoms, 50336 bonds, 39 pseudobonds, 6107 residues, 26 models selected
> select subtract #13
43488 atoms, 44520 bonds, 36 pseudobonds, 5388 residues, 24 models selected
> select add #12
45556 atoms, 46626 bonds, 36 pseudobonds, 5658 residues, 24 models selected
> select subtract #12
39864 atoms, 40810 bonds, 33 pseudobonds, 4939 residues, 22 models selected
> select add #11
41932 atoms, 42916 bonds, 33 pseudobonds, 5209 residues, 22 models selected
> select subtract #11
36240 atoms, 37100 bonds, 30 pseudobonds, 4490 residues, 20 models selected
> select up
56920 atoms, 58160 bonds, 30 pseudobonds, 7190 residues, 20 models selected
> select up
56920 atoms, 58160 bonds, 30 pseudobonds, 7190 residues, 20 models selected
> select down
30 pseudobonds, 10 models selected
> set bgColor white
> open /Users/zhaochunqiu/Desktop/loop1/water-156-178-to-S-L-merge.pdb
> open /Users/zhaochunqiu/Desktop/loop2/water-68-78-merge.pdb
> select add #19
630 atoms, 30 pseudobonds, 630 residues, 11 models selected
> select add #20
1530 atoms, 30 pseudobonds, 1530 residues, 12 models selected
> color (#19-20 & sel) gray
> select subtract #19
900 atoms, 30 pseudobonds, 900 residues, 11 models selected
> select subtract #20
30 pseudobonds, 10 models selected
> lighting soft
[Repeated 2 time(s)]
> save /Users/zhaochunqiu/Desktop/结构作图/S-L-18-water.cxs
——— End of log from Tue Apr 8 21:23:26 2025 ———
> view name session-start
opened ChimeraX session
> select add #19
630 atoms, 30 pseudobonds, 630 residues, 11 models selected
> select add #20
1530 atoms, 30 pseudobonds, 1530 residues, 12 models selected
> color (#19-20 & sel) red
> select subtract #19
900 atoms, 30 pseudobonds, 900 residues, 11 models selected
> select subtract #20
30 pseudobonds, 10 models selected
> style ball
Changed 103986 atom styles
> select add #20
900 atoms, 30 pseudobonds, 900 residues, 11 models selected
> color (#20 & sel) gray
> select add #19
1530 atoms, 30 pseudobonds, 1530 residues, 12 models selected
> color (#19-20 & sel) gray
> select subtract #19
900 atoms, 30 pseudobonds, 900 residues, 11 models selected
> select subtract #20
30 pseudobonds, 10 models selected
> style ball
Changed 103986 atom styles
> select add #19
630 atoms, 30 pseudobonds, 630 residues, 11 models selected
> select add #20
1530 atoms, 30 pseudobonds, 1530 residues, 12 models selected
> ui tool show "Color Actions"
> color sel plum
> select subtract #19
900 atoms, 30 pseudobonds, 900 residues, 11 models selected
> select subtract #20
30 pseudobonds, 10 models selected
> save /Users/zhaochunqiu/Desktop/结构作图/S-L-18-water.cxs
——— End of log from Tue Apr 8 23:15:31 2025 ———
> view name session-start
opened ChimeraX session
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.8.0, Qt 6.8.1
Qt runtime version: 6.8.1
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir10,1
Model Number: MGN63CH/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 8422.121.1
OS Loader Version: 8422.121.1
Software:
System Software Overview:
System Version: macOS 13.4 (22F66)
Kernel Version: Darwin 22.5.0
Time since boot: 15小时7分钟
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 7
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
anyio: 4.8.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.2.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.1
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.dev202501140846
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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
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: 1.5.1
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
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
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.7
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: 1.1.2
ChimeraX-ProfileGrids: 1.0.1
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: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.15
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
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: 2.5.1
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: 1.43
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
coverage: 7.6.10
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.11
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.0.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.5
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.8
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
pluggy: 1.5.0
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.1
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.0
PyQt6-Qt6: 6.8.1
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.1
PyQt6_sip: 13.9.1
pytest: 8.3.4
pytest-cov: 6.0.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
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: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.3.0
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Duplicate of #16627. Fixed by Qt 6.8.2