![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 21 months ago
Closed 21 months ago
#14415 closed defect (can't reproduce)
Crash using menus
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.2.1-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
"uptime" : 450000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac14,7",
"coalitionID" : 14062,
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"build" : "23C71",
"releaseType" : "User"
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"captureTime" : "2024-01-19 12:11:21.8139 +0100",
"codeSigningMonitor" : 1,
"incident" : "8AE507C5-7A14-43A7-BB2E-E4BF6DBD4087",
"pid" : 40750,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-01-19 11:52:01.7514 +0100",
"procStartAbsTime" : 10794111227981,
"procExitAbsTime" : 10821947111445,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "E0980AAA-4D03-9661-045F-A0B406409F0E",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
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"sleepWakeUUID" : "BE07D36D-3FAA-44C4-A73C-64D6951B2EDE",
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===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/syed.zawar/Desktop/PC_Data/Vannini
> Lab/Manuscript/Figures/colorcoded_model.cxs"
Log from Tue Jan 16 18:11:27 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/syed.zawar/Downloads/FL_OC1_Final_Isolde_Run2_real_space_refined_006_clean_trimmed.pdb
Chain information for
FL_OC1_Final_Isolde_Run2_real_space_refined_006_clean_trimmed.pdb #1
---
Chain | Description
A | No description available
C | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
> color /T medium purple
> color /X salmon
> color /Z pale goldenrod
> color /b medium orchid
> color /d dark khaki
> color /e cyan
> color /f lavender
> color /g snow
> color /h sky blue
> color /i medium spring green
> color /K medium aquamarine
> color /L papaya whip
> color /M olive
> color /N cornflower blue
> color /O light steel blue
> color /P gold
> color /Q light pink
> color /S orange
> color /U teal
> color /Y plum
> color /V royal blue
> color /W deep sky blue
> color /A pink
> color /C burly wood
> color /a coral
> save "/Users/syed.zawar/Desktop/PC_Data/Vannini
> Lab/Manuscript/Figures/colorcoded_model.cxs"
——— End of log from Tue Jan 16 18:11:27 2024 ———
opened ChimeraX session
> open 7AEA
7aea title:
Cryo-EM structure of human RNA Polymerase III elongation complex 2 [more
info...]
Chain information for 7aea #2
---
Chain | Description | UniProt
A | DNA-directed RNA polymerase III subunit RPC1 | RPC1_HUMAN 1-1390
B | DNA-directed RNA polymerase III subunit RPC2 | RPC2_HUMAN 1-1133
C | DNA-directed RNA polymerases I and III subunit RPAC1 | RPAC1_HUMAN 1-346
D | DNA-directed RNA polymerase III subunit RPC9 | RPC9_HUMAN 1-148
E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | RPAB1_HUMAN
1-210
F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | RPAB2_HUMAN
1-127
G | DNA-directed RNA polymerase III subunit RPC8 | RPC8_HUMAN 1-204
H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | RPAB3_HUMAN
1-150
I | DNA-directed RNA polymerase III subunit RPC10 | RPC10_HUMAN 1-108
J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | RPAB5_HUMAN
1-67
K | DNA-directed RNA polymerases I and III subunit RPAC2 | RPAC2_HUMAN 1-133
L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | RPAB4_HUMAN
1-58
M | DNA-directed RNA polymerase III subunit RPC5 | RPC5_HUMAN 1-708
N | DNA-directed RNA polymerase III subunit RPC4 | RPC4_HUMAN 1-398
O | DNA-directed RNA polymerase III subunit RPC3 | RPC3_HUMAN 1-534
P | DNA-directed RNA polymerase III subunit RPC6 | RPC6_HUMAN 1-316
Q | DNA-directed RNA polymerase III subunit RPC7 | RPC7_HUMAN 1-223
R | RNA |
S | Non-template DNA |
T | Template DNA |
Non-standard residues in 7aea #2
---
MG — magnesium ion
SF4 — iron/sulfur cluster
ZN — zinc ion
> open 7AE1
7ae1 title:
Cryo-EM structure of human RNA Polymerase III elongation complex 1 [more
info...]
Chain information for 7ae1 #3
---
Chain | Description | UniProt
A | DNA-directed RNA polymerase III subunit RPC1 | RPC1_HUMAN 1-1390
B | DNA-directed RNA polymerase III subunit RPC2 | RPC2_HUMAN 1-1133
C | DNA-directed RNA polymerases I and III subunit RPAC1 | RPAC1_HUMAN 1-346
D | DNA-directed RNA polymerase III subunit RPC9 | RPC9_HUMAN 1-148
E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | RPAB1_HUMAN
1-210
F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | RPAB2_HUMAN
1-127
G | DNA-directed RNA polymerase III subunit RPC8 | RPC8_HUMAN 1-204
H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | RPAB3_HUMAN
1-150
I | DNA-directed RNA polymerase III subunit RPC10 | RPC10_HUMAN 1-108
J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | RPAB5_HUMAN
1-67
K | DNA-directed RNA polymerases I and III subunit RPAC2 | RPAC2_HUMAN 1-133
L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | RPAB4_HUMAN
1-58
M | DNA-directed RNA polymerase III subunit RPC5 | RPC5_HUMAN 1-708
N | DNA-directed RNA polymerase III subunit RPC4 | RPC4_HUMAN 1-398
O | DNA-directed RNA polymerase III subunit RPC3 | RPC3_HUMAN 1-534
P | DNA-directed RNA polymerase III subunit RPC6 | RPC6_HUMAN 1-316
Q | DNA-directed RNA polymerase III subunit RPC7 | RPC7_HUMAN 1-223
R | RNA |
S | Non-template DNA |
T | Template-DNA |
Non-standard residues in 7ae1 #3
---
MG — magnesium ion
SF4 — iron/sulfur cluster
ZN — zinc ion
> hide atoms
> show cartoons
> set bgColor white
> lighting soft
> graphics silhouettes true
> ui tool show Matchmaker
> matchmaker #1/T to #3/A pairing ss
Parameters
---
Chain pairing | ss
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 7ae1, chain A (#3) with
FL_OC1_Final_Isolde_Run2_real_space_refined_006_clean_trimmed.pdb, chain T
(#1), sequence alignment score = 6737.7
RMSD between 1200 pruned atom pairs is 1.028 angstroms; (across all 1381
pairs: 1.459)
> color #1 #929000ff
> color #2 #008f00ff
> color #3 #009193ff
> select #3/M:6-433
3211 atoms, 3282 bonds, 1 pseudobond, 400 residues, 2 models selected
> select #2/M:6-422
3025 atoms, 3089 bonds, 2 pseudobonds, 375 residues, 2 models selected
> select clear
> select add #2
42422 atoms, 43304 bonds, 86 pseudobonds, 5271 residues, 4 models selected
> select subtract #2
Nothing selected
> select add #3
42608 atoms, 43497 bonds, 83 pseudobonds, 5296 residues, 4 models selected
> select subtract #3
Nothing selected
> ui tool show "Side View"
> open "/Users/syed.zawar/Desktop/PC_Data/Vannini
> Lab/ModelBuilding/Model_building_into_states/OC1/OC1_Class0_P66_J325__localfilter.mrc"
Opened OC1_Class0_P66_J325__localfilter.mrc as #4, grid size 280,280,280,
pixel 1.43, shown at level 0.365, step 2, values float32
> volume #4 step 1
> volume #4 level 1.048
> hide #!4 models
> select #1/a
1184 atoms, 1216 bonds, 141 residues, 1 model selected
> color/ a coral
Unknown command: color/ a coral
> color / a coral
> color / C burly wood
> color / #1 C burly wood
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #1/ C burly wood
> color #1/ a coral
> color #1/ A pink
> select clear
> save /Users/syed.zawar/Desktop/image78.png supersample 3
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,7
Model Number: Z16R000RDT/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.61.4
OS Loader Version: 10151.61.4
Software:
System Software Overview:
System Version: macOS 14.2.1 (23C71)
Kernel Version: Darwin 23.2.0
Time since boot: 14 days, 41 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
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
HP Z27k G3:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.21.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.6.0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
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: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 21 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash using menus |
comment:2 by , 21 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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