Opened 4 years ago

Closed 4 years ago

#5383 closed defect (can't reproduce)

v.session is None

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-4.4.0-210-generic-x86_64-with-debian-stretch-sid
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /media/newhd/RAD52_cryoEM_EMBL_Heidelberg_iNEXT_Marotta/PostProcess/4refinecleaning3symc11_3/postprocess_masked.mrc

Opened postprocess_masked.mrc, grid size 200,200,200, pixel 1.15, shown at
level 0.0257, step 1, values float32  

> volume #1 level 0.0333

> close session

> open
> /media/newhd/RAD52_cryoEM_EMBL_Heidelberg_iNEXT_Marotta/Refine3D/job079/run_class001.mrc

Opened run_class001.mrc, grid size 200,200,200, pixel 1.15, shown at level
0.0201, step 1, values float32  

> close session

> open
> /media/newhd/RAD52_cryoEM_EMBL_Heidelberg_iNEXT_Marotta/Refine3D/Cl2_cleaning3job077_symc11/run_class001.mrc

Opened run_class001.mrc, grid size 200,200,200, pixel 1.15, shown at level
0.021, step 1, values float32  

> set bgColor white

> volume #1 level 0.01113

> volume #1 level 0.02026

> open
> /media/newhd/RAD52_cryoEM_EMBL_Heidelberg_iNEXT_Marotta/Refine3D/Cl2_cleaning3job077_symc1/run_class001.mrc

Opened run_class001.mrc, grid size 200,200,200, pixel 1.15, shown at level
0.0201, step 1, values float32  

> select #2

2 models selected  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> volume #2 level 0.01705

> ~select #2

Nothing selected  

> vop add #1 model #3

> show #!1 models

> select #3

2 models selected  

> vop add #2 model #4

> show #!2 models

> ~select #3

Nothing selected  

> select #4

2 models selected  

> open
> /media/newhd/RAD52_cryoEM_EMBL_Heidelberg_iNEXT_Marotta/PostProcess/job085/postprocess_masked.mrc

Opened postprocess_masked.mrc, grid size 200,200,200, pixel 1.15, shown at
level 0.0257, step 1, values float32  

> ~select #4

Nothing selected  

> select #3

2 models selected  

> ~select #3

Nothing selected  

> vop add #3 model #5

> show #!3 models

> select #5

2 models selected  

> ~select #5

Nothing selected  

> select #3

2 models selected  

> hide #!3 models

> show #!3 models

> ~select #3

Nothing selected  

> save
> /media/newhd/RAD52_cryoEM_EMBL_Heidelberg_iNEXT_Marotta/ChimeraX/RefineJob078e079.cxs

> open
> /media/newhd/RAD52_cryoEM_EMBL_Heidelberg_iNEXT_Marotta/Refine3D/job086/run_class001.mrc

Opened run_class001.mrc, grid size 200,200,200, pixel 1.15, shown at level
0.0191, step 1, values float32  

> hide #!5 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> select #4

2 models selected  

> volume #4 level 0.0133

> close #1

> close #2

> close #3

> close #5

> hide #!4 models

> show #!4 models

> close #3

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2115, in close_map_cb  
log_equivalent_command(v.session, 'close #%s' % v.id_string)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/logging.py", line 29, in
log_equivalent_command  
command.run(command_text, log_only=True)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2767, in run  
prev_annos = self._process_positional_arguments()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2550, in
_process_positional_arguments  
value, text = self._parse_arg(anno, text, session, False)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2413, in _parse_arg  
value, replacement, rest = annotation.parse(text, session)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 1215, in parse  
models = aspec.evaluate(session).models  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 1039, in evaluate  
models = session.models.list(**kw)  
AttributeError: 'NoneType' object has no attribute 'models'  
  
AttributeError: 'NoneType' object has no attribute 'models'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 1039, in evaluate  
models = session.models.list(**kw)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2115, in close_map_cb  
log_equivalent_command(v.session, 'close #%s' % v.id_string)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/logging.py", line 29, in
log_equivalent_command  
command.run(command_text, log_only=True)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2767, in run  
prev_annos = self._process_positional_arguments()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2550, in
_process_positional_arguments  
value, text = self._parse_arg(anno, text, session, False)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2413, in _parse_arg  
value, replacement, rest = annotation.parse(text, session)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 1215, in parse  
models = aspec.evaluate(session).models  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 1039, in evaluate  
models = session.models.list(**kw)  
AttributeError: 'NoneType' object has no attribute 'models'  
  
AttributeError: 'NoneType' object has no attribute 'models'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 1039, in evaluate  
models = session.models.list(**kw)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 450.36.06
OpenGL renderer: GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: Ubuntu 16.04 xenial
Architecture: 64bit ELF
CPU: 28 Intel(R) Core(TM) i9-7940X CPU @ 3.10GHz
Cache Size: 19712 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           125G        3.1G         35G        113M         87G        121G
	Swap:           18G          0B         18G

Graphics:
	1a:00.0 VGA compatible controller [0300]: NVIDIA Corporation GV102 [10de:1e07] (rev a1)	
	Subsystem: ASUSTeK Computer Inc. Device [1043:866a]	
	Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 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: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → v.session is None

comment:2 by Tom Goddard, 4 years ago

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

The user closed model #3 which was a volume, then closed it again a few lines later and it gave an error. It seems somehow the first "close #3" command managed to delete the volume so its session attribute was set to None but somehow it was not removed from the open models list, so the user closed it again with "close #3".

Not sure how this could happen. This is an old ChimeraX 1.1 version. One remote guess is that the user didn't really execute "close #3". They used some other method to close the model, like the close icon on the volume viewer, or close button on model panel. And that tool logged the "close #3" command but actually did not run that command and instead mistakenly closed it with v.delete() instead of models.close([v]). Not worth looking for such code in this very old ChimeraX.

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