id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5383 v.session is None chimerax-bug-report@… Tom Goddard "{{{ 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 }}} " defect closed normal Volume Data can't reproduce all ChimeraX