Opened 3 years ago

Closed 3 years ago

#7691 closed defect (fixed)

Clipper closing possible already-closed model during session reset

Reported by: chimerax-bug-report@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Sessions Version:
Keywords: Cc: pett, Greg Couch, Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-3.10.0-1160.42.2.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted

Current thread 0x00007fc6e1cfd740 (most recent call first):
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/atomic/molobject.py", line 1372 in delete
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/atomic/structure.py", line 115 in delete
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 342 in remove_drawings
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 349 in remove_all_drawings
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1207 in delete
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/models.py", line 96 in delete
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/clipper/symmetry.py", line 916 in delete
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/models.py", line 895 in close
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/models.py", line 574 in reset_state
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/session.py", line 535 in reset
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/std_commands/close.py", line 60 in close_session
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2856 in run
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 36 in run
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 680 in file_close_cb
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 1032 in 
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in 
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 87 in _run_code
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/brittanydrummond/Documents/AtDDD/RealSpaceRefine_29/23sept_5pm_roatmersfixed_real_space_refined_029.pdb

Chain information for 23sept_5pm_roatmersfixed_real_space_refined_029.pdb #1  
---  
Chain | Description  
D | No description available  
F | No description available  
G | No description available  
  

> open
> /home/brittanydrummond/Documents/AtDDD/RealSpaceRefine_29/dda1_48_70.pdb

Chain information for dda1_48_70.pdb #2  
---  
Chain | Description  
A | No description available  
  

> combine #1,2

> hide #2 models

> hide #1 models

> select #3/G:47@C #3/A:48@N

2 atoms, 2 residues, 1 model selected  

> ui tool show Rotamers

> ui tool show "Build Structure"

> bond sel

Created 1 bond  

> open /home/brittanydrummond/Documents/AtDDD/P60_J361_1.96A.mrc

Opened P60_J361_1.96A.mrc as #4, grid size 400,400,400, pixel 0.66, shown at
level 0.0153, step 2, values float32  

> volume #4 step 1

> volume #4 level 0.03845

> volume #4 level 0.07317

> ui tool show "Color Zone"

> color zone #4 near #3 distance 2.46

> color single #4

> color zone #4 near #3 distance 2.46

> color single #4

> color sel bychain

> select #3

21921 atoms, 22173 bonds, 1394 residues, 1 model selected  

> color sel bychain

> color zone #4 near #3 distance 2.46

> ~select #3

Nothing selected  

> toolshed show

> clipper associate #4 toModel #3

Opened P60_J361_1.96A.mrc as #3.1.1.1, grid size 400,400,400, pixel 0.66,
shown at level 0.0984, step 1, values float32  

> isodle start

Unknown command: isodle start  

> isoder start

Unknown command: isoder start  

> isolate start

Unknown command: isolate start  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 108 residues in model #1 to IUPAC-IUB
standards.  
Chain information for 23sept_5pm_roatmersfixed_real_space_refined_029.pdb  
---  
Chain | Description  
1.2/D | No description available  
1.2/F | No description available  
1.2/G | No description available  
  
Done loading forcefield  

> volume #3.1.1.1 level 0.05133

> ui mousemode right select

> select #3.2/G:47@CA

1 atom, 1 residue, 1 model selected  
ISOLDE: stopped sim  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/isolde/isolde.py", line 2749, in
_start_sim_or_toggle_pause  
self.start_sim()  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/isolde/isolde.py", line 2784, in
start_sim  
sm = self._sim_manager = Sim_Manager(self, self.selected_model, main_sel,  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 576, in __init__  
mobile_atoms = self.expand_mobile_selection(selected_atoms, expansion_mode)  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 971, in
expand_mobile_selection  
sel = selections.expand_selection_along_chains(core_atoms,  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/isolde/selections.py", line 39,
in expand_selection_along_chains  
raise TypeError('Selected atoms must all be in the same model!')  
TypeError: Selected atoms must all be in the same model!  
  
TypeError: Selected atoms must all be in the same model!  
  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/isolde/selections.py", line 39,
in expand_selection_along_chains  
raise TypeError('Selected atoms must all be in the same model!')  
  
See log for complete Python traceback.  
  

> ui mousemode right select

> select clear

> select #3.2/G:47@CA

1 atom, 1 residue, 1 model selected  
ISOLDE: stopped sim  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/isolde/isolde.py", line 2749, in
_start_sim_or_toggle_pause  
self.start_sim()  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/isolde/isolde.py", line 2784, in
start_sim  
sm = self._sim_manager = Sim_Manager(self, self.selected_model, main_sel,  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 576, in __init__  
mobile_atoms = self.expand_mobile_selection(selected_atoms, expansion_mode)  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 971, in
expand_mobile_selection  
sel = selections.expand_selection_along_chains(core_atoms,  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/isolde/selections.py", line 39,
in expand_selection_along_chains  
raise TypeError('Selected atoms must all be in the same model!')  
TypeError: Selected atoms must all be in the same model!  
  
TypeError: Selected atoms must all be in the same model!  
  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/isolde/selections.py", line 39,
in expand_selection_along_chains  
raise TypeError('Selected atoms must all be in the same model!')  
  
See log for complete Python traceback.  
  

> save "/home/brittanydrummond/Documents/AtDDD/RealSpaceRefine_29/combined
> map.pdb" relModel #3.1.1.1

> close session


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

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 430.40
OpenGL renderer: GeForce GTX 1070 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUS
Model: All Series
OS: Red Hat Enterprise Linux Server 7.9 Maipo
Architecture: 64bit ELF
Virutal Machine: none
CPU: 12 Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
Cache Size: 15360 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            27G         14G        6.7G        674M        5.7G         11G
	Swap:           15G        3.0M         15G

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104 [GeForce GTX 1070 Ti] [10de:1b82] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:119d]	
	Kernel driver in use: nvidia
Locale: ('en_NZ', 'UTF-8')
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: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    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: 2.6.1
    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: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    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: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 2.1.2
    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-ISOLDE: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    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: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    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
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    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: 1.6.1
    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: 1.13.7
    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
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    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: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by pett, 3 years ago

Cc: pett Greg Couch Tom Goddard added
Component: Unassigned → Sessions
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Clipper closing possible already-closed model during session reset

In 1.3, so possible already fixed?

comment:2 by Tristan Croll, 3 years ago

Resolution: → fixed
Status: assigned → closed

Going to close this as *probably* fixed - will revisit if it crops up again.

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