id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7200 QMainWindowLayout::tabPosition called with out-of-bounds value '0' chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19043 ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- warning | Your computer has Intel graphics driver 7262 with a known bug that causes all Qt user interface panels to be blank. ChimeraX can partially fix this but may make some panel titlebars and edges black. Hopefully newer Intel graphics drivers will fix this. UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 2 TMV '2' has no suffix > open 2TMV Summary of feedback from opening 2TMV fetched from pdb --- note | Fetching compressed mmCIF 2tmv from http://files.rcsb.org/download/2tmv.cif 2tmv title: Visualization of protein-nucleic acid interactions In A virus. Refined structure of intact tobacco mosaic virus At 2.9 angstroms resolution by X-ray fiber diffraction [more info...] Chain information for 2tmv #1 --- Chain | Description | UniProt P | TMV coat protein | COAT_TMV R | RNA (5'-R(P*GP*ap*A)-3') | Non-standard residues in 2tmv #1 --- CA — calcium ion 2tmv mmCIF Assemblies --- 1| representative helical assembly 2| helical asymmetric unit 3| helical asymmetric unit, std helical frame > sym #1 assembly 2 > view > sym #1 assembly 1 > view > sym #1 assembly 3 > view > sym #1 assembly 3 > view > sym #1 assembly 1 > view > select /P:1-154 7272 atoms, 7416 bonds, 924 residues, 6 models selected > select /R:1-3 402 atoms, 450 bonds, 18 residues, 6 models selected > close > set bgColor white > open 1za7 Summary of feedback from opening 1za7 fetched from pdb --- note | Fetching compressed mmCIF 1za7 from http://files.rcsb.org/download/1za7.cif 1za7 title: The crystal structure of salt stable cowpea cholorotic mottle virus at 2.7 angstroms resolution. [more info...] Chain information for 1za7 #1 --- Chain | Description | UniProt A B C | Coat protein | COAT_CCMV 1za7 mmCIF Assemblies --- 1| complete icosahedral assembly 2| icosahedral asymmetric unit 3| icosahedral pentamer 4| icosahedral 23 hexamer 5| icosahedral asymmetric unit, std point frame 6| crystal asymmetric unit, crystal frame > sym #1 assembly 1 > view > show #2 surfaces > hide #!2 models > show #!2 models > open 1ny7 Summary of feedback from opening 1ny7 fetched from pdb --- note | Fetching compressed mmCIF 1ny7 from http://files.rcsb.org/download/1ny7.cif 1ny7 title: Cowpea mosaic virus (CPMV) [more info...] Chain information for 1ny7 #3 --- Chain | Description | UniProt 1 | cowpea mosaic virus, small (S) subunit | VGNM_CPMV 2 | cowpea mosaic virus, large (L) subunit | VGNM_CPMV 1ny7 mmCIF Assemblies --- 1| complete icosahedral assembly 2| icosahedral asymmetric unit 3| icosahedral pentamer 4| icosahedral 23 hexamer 5| icosahedral asymmetric unit, std point frame 6| crystal asymmetric unit, crystal frame > sym #3 assembly 1 > view > select add #4 4407 atoms, 4458 bonds, 622 residues, 1 model selected > ui windowfill toggle [Repeated 1 time(s)] > move x 1000 models #4 > move x -300 models #4 > move x -70 models #4 [Repeated 1 time(s)] > show sel surfaces > color #4.1 white transparency 0 > color #4.1 mediumslateblue transparency 0 > color #4.2 darkseagreen transparency 0 > open 1qj7 Summary of feedback from opening 1qj7 fetched from pdb --- notes | Fetching compressed mmCIF 1qj7 from http://files.rcsb.org/download/1qj7.cif Fetching CCD GR1 from http://ligand-expo.rcsb.org/reports/G/GR1/GR1.cif Fetching CCD TYS from http://ligand-expo.rcsb.org/reports/T/TYS/TYS.cif 1qj7 title: Novel Covalent Active Site Thrombin Inhibitors [more info...] Chain information for 1qj7 #5 --- Chain | Description | UniProt A | thrombin | THRB_HUMAN B | thrombin | THRB_HUMAN I | hirugen | ITHA_HIRME Non-standard residues in 1qj7 #5 --- GR1 — 6-carbamimidoyl-2-[5-(3-diethylcarbamoyl-phenyl)-2-hydroxy- indan-1-yl]-hexanoic acid (GR179849) > close #5 > open 1qjz Summary of feedback from opening 1qjz fetched from pdb --- note | Fetching compressed mmCIF 1qjz from http://files.rcsb.org/download/1qjz.cif 1qjz title: Three Dimensional Structure of Physalis Mottle Virus : Implications for the Viral Assembly [more info...] Chain information for 1qjz #5 --- Chain | Description | UniProt A B C | coat protein | COAT_PHMV 1qjz mmCIF Assemblies --- 1| complete icosahedral assembly 2| icosahedral asymmetric unit 3| icosahedral pentamer 4| icosahedral 23 hexamer 5| icosahedral asymmetric unit, std point frame > sym #5 assembly 1 > view > select up 4407 atoms, 4458 bonds, 622 residues, 3 models selected > select up 24372 atoms, 24526 bonds, 3568 residues, 8 models selected > move x 1000 models #6 > move x -70 models #6 > show sel & #6#!2,4 surfaces > select subtract #4 19965 atoms, 20068 bonds, 2946 residues, 13 models selected > hide #!4 models > close #3 > close #4 > move x -300 models #6 > save ReviewFigure format tiff width 1200 > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > save ReviewFigure format tiff width 1200 > cd ""C:/Users/Bon DTE Lab/Google Drive/Grad School/MS2 Viral Capsids/PDB > Files"" Current working directory is: C:\Users\Bon DTE Lab\Google Drive\Grad School\MS2 Viral Capsids\PDB Files > save ReviewFigure format tiff width 1200 height 692 transparentBackground > true QMainWindowLayout::tabPosition called with out-of-bounds value '0' Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.4\bin\lib\site-packages\chimerax\ui\gui.py"", line 2283, in dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e) File ""C:\Program Files\ChimeraX 1.4\bin\lib\site-packages\chimerax\ui\gui.py"", line 668, in close_request all_windows = self.tool_instance_to_windows[tool_instance] KeyError: None KeyError: None File ""C:\Program Files\ChimeraX 1.4\bin\lib\site-packages\chimerax\ui\gui.py"", line 668, in close_request all_windows = self.tool_instance_to_windows[tool_instance] See log for complete Python traceback. QMainWindowLayout::tabPosition called with out-of-bounds value '0' OpenGL version: 3.3.0 - Build 26.20.100.7262 OpenGL renderer: Intel(R) UHD Graphics 630 OpenGL vendor: Intel Python: 3.9.11 Locale: en_US.cp1252 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: windows Manufacturer: Acer Model: Aspire TC-865 OS: Microsoft Windows 10 Home (Build 19043) Memory: 17,061,081,088 MaxProcessMemory: 137,438,953,344 CPU: 6 Intel(R) Core(TM) i5-8400 CPU @ 2.80GHz OSLanguage: en-US Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2022.5.18.1 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 comtypes: 1.1.10 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: 21.3 ParmEd: 3.4.3 parso: 0.8.3 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 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 pywin32: 303 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 WMI: 1.5.1 }}} " defect closed normal Window Toolkit can't reproduce Tom Goddard all ChimeraX