The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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===== Log before crash start =====
UCSF ChimeraX version: 1.5.dev202208060049 (2022-08-06)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/clemens.plaschka/Library/CloudStorage/OneDrive-
> VBC/papers/2022_Pacheco-Fiallos-
> Vorlaender/figures/scripts/Fig3e_TREX_EJC_overview_surface_thinRNA_T2_colors.cxc
> open ../../../../lab/coot/TREX-mRNP/hTREX_mRNA_nB_new.pdb
Chain information for hTREX_mRNA_nB_new.pdb #1
---
Chain | Description
2 4 | No description available
A a | No description available
B b | No description available
C K c k | No description available
E | No description available
F N n | No description available
G g | No description available
H h | No description available
I i | No description available
J j | No description available
L l | No description available
M m | No description available
O o | No description available
P p | No description available
e | No description available
f | No description available
> open ../../../../lab/coot/TREX-mRNP/models/HsUAP56_5suq_conf.pdb
Chain information for HsUAP56_5suq_conf.pdb #2
---
Chain | Description
H | No description available
Y | No description available
> open ../../../../lab/coot/TREX-mRNP/models/HsUAP56_5suq_conf.pdb
Chain information for HsUAP56_5suq_conf.pdb #3
---
Chain | Description
H | No description available
Y | No description available
> open ../pdbs/refine_run4_chainA-E-a-e_EJC-ALY_fit_to_TREX.pdb
Chain information for refine_run4_chainA-E-a-e_EJC-ALY_fit_to_TREX.pdb #4
---
Chain | Description
A a | No description available
B b | No description available
C c | No description available
D d | No description available
E e | No description available
> open ../../../../lab/coot/TREX-mRNP/hTREX_mRNA_nB_new.pdb
Chain information for hTREX_mRNA_nB_new.pdb #5
---
Chain | Description
2 4 | No description available
A a | No description available
B b | No description available
C K c k | No description available
E | No description available
F N n | No description available
G g | No description available
H h | No description available
I i | No description available
J j | No description available
L l | No description available
M m | No description available
O o | No description available
P p | No description available
e | No description available
f | No description available
> open ../../../../lab/coot/TREX-mRNP/hTREX_mRNA_nB_new.pdb
Chain information for hTREX_mRNA_nB_new.pdb #6
---
Chain | Description
2 4 | No description available
A a | No description available
B b | No description available
C K c k | No description available
E | No description available
F N n | No description available
G g | No description available
H h | No description available
I i | No description available
J j | No description available
L l | No description available
M m | No description available
O o | No description available
P p | No description available
e | No description available
f | No description available
> hide
> show nucleic
> hide protein|solvent|H
> surface hidePatches
> style (protein|nucleic|solvent) & @@draw_mode=0 stick
Changed 275695 atom styles
> cartoon
> cartoon style modeHelix default arrows true arrowsHelix false arrowScale 2
> width 2 thickness 0.4 sides 12 divisions 20
> cartoon style ~(nucleic|strand) xsection round
> cartoon style (nucleic|strand) xsection rectangle
> cartoon style protein modeHelix tube radius 2.2 sides 24 thickness 1.2
> cartoon style nucleic xsection round width 2 thickness 2
> nucleotides stubs
> lighting shadows false
> lighting simple
> camera ortho
> lighting soft intensity 0.2 fillIntensity 0.5 ambientIntensity 1
> windowsize 800 800
> size #1 pseudobondRadius 0.5
Changed 196 pseudobond radii
> select #1 minimumLength 1
196 pseudobonds, 1 model selected
> hide sel
> ~cartoon #2/H
> ~cartoon #3/H
> align #2/H toAtoms #1/H
RMSD between 1398 atom pairs is 0.760 angstroms
> align #5/j:500-2000 toAtoms #1/B:500-2000
RMSD between 4186 atom pairs is 0.001 angstroms
> align #3/H toAtoms #1/h
RMSD between 1398 atom pairs is 0.760 angstroms
> align #6/j:500-2000 toAtoms #1/b:500-2000
RMSD between 4186 atom pairs is 0.001 angstroms
> nucleotides #1,12#!8-9,13 fill
> style nucleic & #1,12#!8-9,13 stick
Changed 160 atom styles
> nucleotides #4,12#!8-9,13 fill
> style nucleic & #4,12#!8-9,13 stick
Changed 234 atom styles
> graphics silhouettes true
> set bgColor white
> ~cartoon
> hide #1-6 atoms
> surface #1
> ~surface #1/H,P,h,p,L,l,2,4
> cartoon #1/P,p,L,l,2,4 #4 #5/4,p,l #6/4,p,l
> show #1/2,4 #4/e,E #5/4 #6/4 atoms
> color #1/A,I,a,i lime green target abcspf
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,4
Processor Name: Unknown
Processor Speed: 2,4 GHz
Number of Processors: 1
Total Number of Cores: 10
L2 Cache: 20 MB
Memory: 64 GB
Software:
System Software Overview:
System Version: macOS 12.6 (21G115)
Kernel Version: Darwin 21.6.0
Time since boot: 12 days 1:20
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 24
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
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:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.10.8
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.0
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Looks like some native Mac code freed an object twice
"asi" : {"libsystem_c.dylib":["Over-release of NSResponder or subclass."]},