Opened 4 years ago

Closed 4 years ago

#5796 closed defect (can't reproduce)

Stack overflow, possibly due to screen locking

Reported by: nxb318@… Owned by: pett
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19043
ChimeraX Version: 1.3.dev202109080319 (2021-09-08 03:19:35 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: stack overflow

Thread 0x000024ac (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-packages\ChimeraX_main.py", line 880 in init
  File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-packages\ChimeraX_main.py", line 1029 in 
  File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\runpy.py", line 197 in _run_module_as_main

Windows fatal exception: stack overflow

Thread 0x000106c4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-packages\ChimeraX_main.py", line 880 in init
  File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-packages\ChimeraX_main.py", line 1029 in 
  File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.3.dev202109080319 (2021-09-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> C:\\\Users\\\nxb318\\\Documents\\\EM_related\\\rGluK2-3m-domoic_acid_processing\\\FROM_EXX\\\cls5_relion\\\run_class001-zflip.mrc

Opened run_class001-zflip.mrc as #1, grid size 420,420,420, pixel 1.06, shown
at level 0.00715, step 2, values float32  

> lighting soft

> volume #1 step 1

> volume #1 level 0.01312

> ui tool show "Hide Dust"

> surface dust #1 size 6.36

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls5_relion/Swissprot/swissmodel/cls5_LBDmonomer/models/02/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) cls5_LBD-monomer [more
info...]  
  
Chain information for model.pdb #2  
---  
Chain | Description  
A B C D | No description available  
  

> material transparentCastShadows true

> transparency 50

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls5_relion/model02_real_space_refined_007.pdb

Chain information for model02_real_space_refined_007.pdb #3  
---  
Chain | Description  
A B C D | No description available  
  

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> open 5kuf

5kuf title:  
GluK2EM with 2S,4R-4-methylglutamate [more info...]  
  
Chain information for 5kuf #4  
---  
Chain | Description | UniProt  
A

hide #3 models

hide #3 models

> show #!2 models

> hide #!2 models

> show #3 models

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls2_relion/model02_real_space_refined_008.pdb

| Chain information for model02_real_space_refined_008.pdb #4  
---  
Chain | Description  
A B C D | No description available  
  

> hide #3 models

> show #!2 models

> hide #!2 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #!2 models

> hide #!2 models

> hide #4 models

> show #3 models

> hide #3 models

> show #!2 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> hide #!2 models

> show #3 models

> hide #3 models

> show #4 models

> select #4/D:552

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #4/C:594

7 atoms, 7 bonds, 1 residue, 1 model selected  

> hide #4 models

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/run_class001-zflip.mrc

Opened run_class001-zflip.mrc as #5, grid size 420,420,420, pixel 1.06, shown
at level 0.00802, step 2, values float32  

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls2_relion/run_class001-zflip.mrc

Opened run_class001-zflip.mrc as #6, grid size 420,420,420, pixel 1.06, shown
at level 0.00731, step 2, values float32  

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls4_relion/run_class001-zflip.mrc

Opened run_class001-zflip.mrc as #7, grid size 420,420,420, pixel 1.06, shown
at level 0.00747, step 2, values float32  

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls5_relion/run_class001-zflip.mrc

Opened run_class001-zflip.mrc as #8, grid size 420,420,420, pixel 1.06, shown
at level 0.00715, step 2, values float32  

> volume #5 step 1

> volume #6 step 1

> volume #7 step 1

> volume #8 step 1

> volume #8 level 0.01312

> volume #7 level 0.01291

> volume #7 level 0.01447

> volume #6 level 0.01285

> volume #5 level 0.01196

> volume #5 level 0.01352

> volume #5 level 0.01609

> volume #5 level 0.01371

> volume #5 level 0.01573

> volume #6 level 0.01491

> volume #7 level 0.01563

> volume #8 level 0.0139

> ui tool show "Hide Dust"

> surface dust #5 size 6.36

> surface dust #6 size 6.36

> surface dust #7 size 6.36

> surface dust #8 size 6.36

> volume #5 level 0.0149

div>

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> show #!4 models

> hide #!4 models

> show #3 models

> select #3/B

6380 atoms, 6528 bonds, 806 residues, 1 model selected  

> color sel orange

> select clear

> hide #3 models

> show #!4 models

> hide #!4 models

> show #!4 models

> select #4/D:423@O

1 atom, 1 residue, 1 model selected  

> select clear

> select #4/D

5932 atoms, 6062 bonds, 2 pseudobonds, 751 residues, 2 models selected  

> color (#!4 & sel) orange

> select clear

> select #4/B

5932 atoms, 6062 bonds, 2 pseudobonds, 751 residues, 2 models selected  

> color (#!4 & sel) #b1ff7dff

> color (#!4 & sel) #aeff7cff

> color (#!4 & sel) #92ff74ff

> color (#!4 & sel) #88ff73ff

> color (#!4 & sel) #85ff72ff

> color (#!4 & sel) #80ff72ff

> color (#!4 & sel) #6eff6eff

> color (#!4 & sel) #6aff74ff

> select clear

> hide #!4 models

> show #3 models

> show #!4 models

> hide #!4 models

> show #!4 models

> color #3 #ff0f0f

> color #3 #ff8f06

> color #4 #fda000

> morph #3,4

Computed 51 frame morph #6  

> coordset #6 1,51

> hide #!6 models

> close #6

> show #3 models

> hide #3 models

> show #3 models

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_init_model_real_space_refined_004_loops.pdb

Chain information for cls1_init_model_real_space_refined_004_loops.pdb #6  
---  
Chain | Description  
A B C D | No description available  
  

> hide #3 models

> cartoon hide #6

> show #6 target ab

> style #6 sphere

Changed 23744 atom styles  

> ui tool show "Color Actions"

> color bychain

> show #3 models

> hide #6 models

> show #6 models

> hide #6 models

> show #6 models

> hide #6 models

> show #6 models

> hide #6 models

> show #6 models

> morph #4,6

Computed 51 frame morph #7  

> coordset #7 1,51

> close #7

> close #4

> morph #3,6

Computed 51 frame morph #4  

> coordset #4 1,51

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #3 models

> hide #3 models

> show #3 models

> show #6 models

> hide #3 models

> hide #6 models

> show #!4 models

> surface dust #1 size 6.35

> surface dust #1 size 6.34

> surface dust #1 size 6.31

> show #!1 models

> hide #!4 models

> show #3 models

> show #!4 models

> hide #3 models

> hide #!1 models

> close #4

> close

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls2_relion/run_class001-zflip.mrc

Opened run_class001-zflip.mrc as #1, grid size 420,420,420, pixel 1.06, shown
at level 0.00731, step 2, values float32  

> volume #1 step 1

> volume #1 level 0.01222

> volume #1 level 0.01304

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls5_relion/cls5_monomer-
> model02_real_space_refined_007.pdb

Chain information for cls5_monomer-model02_real_space_refined_007.pdb #2  
---  
Chain | Description  
A B C D | No description available  
  

> material transparentCastShadows true

> transparency 50

> hide #2 models

> show #2 models

> hide #!1 models

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls4_relion/run_class001-zflip.mrc

Opened run_class001-zflip.mrc as #3, grid size 420,420,420, pixel 1.06, shown
at level 0.00747, step 2, values float32  

> volume #3 step 1

> volume #3 level 0.01341

> select #2/C:585-625

331 atoms, 344 bonds, 41 residues, 1 model selected  

> show (sel-residues & sidechain) target ab

> hide #2 models

> show #!3 models

> close #3

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls2_relion/model02_real_space_refined_008.pdb
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls2_relion/run_class001-zflip.mrc

Chain information for model02_real_space_refined_008.pdb #3  
---  
Chain | Description  
A B C D | No description available  
  
Opened run_class001-zflip.mrc as #4, grid size 420,420,420, pixel 1.06, shown
at level 0.00731, step 2, values float32  

> volume #4 step 1

> volume #4 level 0.01404

> volume #4 level 0.01614

> select #3:777-789

404 atoms, 400 bonds, 52 residues, 1 model selected  

> show (sel-residues & sidechain) target ab

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #!4 models


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.3.dev202109080319 (2021-09-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 471.41
OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: OptiPlex 7071
OS: Microsoft Windows 10 Pro (Build 19043)
Memory: 34,140,291,072
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-9700 CPU @ 3.00GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.0
    chardet: 4.0.0
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.29.1
    ChimeraX-AtomicLibrary: 4.1.4
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.3
    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: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.4.1
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202109080319
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.4
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.1
    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
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    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: 2.0.1
    ChimeraX-MDcrds: 2.5
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.1.1
    ChimeraX-ModelPanel: 1.1
    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: 1.7
    ChimeraX-PDB: 2.6.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-Phenix: 0.3
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.3
    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: 1.6
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.12
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    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: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.10.0
    Cython: 0.29.23
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.4.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.20
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 2.11.3
    jupyter-client: 6.1.12
    jupyter-core: 4.7.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 1.1.1
    matplotlib: 3.4.2
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.6
    networkx: 2.6.2
    numexpr: 2.7.3
    numpy: 1.21.0
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pickleshare: 0.7.5
    Pillow: 8.2.0
    pip: 21.1.1
    pkginfo: 1.7.0
    prompt-toolkit: 3.0.20
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.9.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pywin32: 228
    pyzmq: 22.2.1
    qtconsole: 5.1.0
    QtPy: 1.11.0
    RandomWords: 0.3.0
    requests: 2.25.1
    scipy: 1.6.3
    setuptools: 57.0.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.0.1
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.0
    urllib3: 1.26.6
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.2
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (9)

comment:1 by pett, 4 years ago

Cc: Tom Goddard added
Component: Unassigned → Core
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Stack overflow

comment:2 by pett, 4 years ago

Status: accepted → feedback

Hi Nebojsa,

Thanks for reporting this problem. Do you remember what you were doing when this crash occurred?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

in reply to:  3 ; comment:3 by nxb318@…, 4 years ago 

Hello Eric,

I left the ChimeraX session open overnight. It had multiple files, the
total session (.cxs) file size is 2.2 gb since it has 20 objects (pdbs and
cryoem maps). In the morning, when I unlocked my PC, there was this report.

Hope this helps.

Best regards,

Nebojša Bogdanović, Ph.D
Department of Physiology and Biophysics,
School of Medicine,
Case Western Reserve University


On Thu, Dec 16, 2021 at 1:43 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

comment:4 by pett, 4 years ago

Status: feedback → accepted
Summary: Stack overflow → Stack overflow, possibly due to screen locking

I'm not sure we'll have any luck reproducing this, but we'll try. I guess the wise thing to do in the interim is save a session before leaving for the night!

--Eric

comment:5 by Tom Goddard, 4 years ago

It from the log like ChimeraX was doing nothing overnight and died in the Qt event loop. ChimeraX sets a Qt timer to call 60 times a second to render the graphics. If it sees nothing has changed it doesn't render. But I bet somehow this 60 times per second check all night long if the computer didn't sleep is behind the stack overflow and is probably a Qt window toolkit bug.

in reply to:  6 ; comment:6 by nxb318@…, 4 years ago 

Hello Eric,

Luckily, I've saved the session before leaving so no harm done. One
question though. I couldn't find the equivalent of the chimera command (vop
zflip #0) in ChimeraX. Could you please let me know what it is?

Best regards and thank you,
Nebojša Bogdanović, Ph.D

On Thu, Dec 16, 2021, 20:10 ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

in reply to:  7 ; comment:7 by goddard@…, 4 years ago 

In ChimeraX the "vop zflip" command is now called  "volume flip"

	https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#flip

In general all the Chimera vop subcommands now use command name "volume" instead of "vop".  In the case of zflip, I also wanted to allow x and y flip so I also renamed zflip to flip.

comment:8 by pett, 4 years ago

Screen locking did not cause a crash. Now leaving it running overnight to see what happens.

comment:9 by pett, 4 years ago

Resolution: → can't reproduce
Status: accepted → closed

Leaving ChimeraX running overnight also did not produce a crash. I don't know that there's much more I can do to try to replicate this.

Note: See TracTickets for help on using tickets.