id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8149 Crash in event loop after volume step 1 on .mtz data chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.4rc202205140117 (2022-05-14 01:17:27 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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All rights reserved. How to cite UCSF ChimeraX > open ""/Users/nitsanyehishalom/Desktop/Studys/MS.c./Reserach/Results semester > 3/Structures/WT 5-13.pdb"" format pdb WT 5-13.pdb title: \--- [more info...] Chain information for WT 5-13.pdb #1 --- Chain | Description A | No description available B | No description available Non-standard residues in WT 5-13.pdb #1 --- CRO — (CRO) NA — (NA) SO4 — (SO4) > open ""/Users/nitsanyehishalom/Desktop/Studys/MS.c./Reserach/Results semester > 3/Structures/WT 5-13.mtz"" Summary of feedback from opening /Users/nitsanyehishalom/Desktop/Studys/MS.c./Reserach/Results semester 3/Structures/WT 5-13.mtz --- warnings | WARNING: multiple experimental reflection datasets found: (dataset) HKL_base, (dataset) F, SIGF Automatically choosing ""(dataset) F, SIGF"". No free flags detected in this dataset! Automatically generated a new random set with 2119 free from 119546 observed reflections. You should save your data to a new MTZ file and use this for any future rebuilding/refinement. note | Discarding unrecognised/unsupported data array /DEFAULT/1/FOM W Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 78,74,78, pixel 0.324,0.326,0.315, shown at level 0.934, step 1, values float32 Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 78,74,78, pixel 0.324,0.326,0.315, shown at level -0.206,0.206, step 1, values float32 Opened (LIVE) 2mFo-DFc_smooth_25 as #1.1.1.4, grid size 78,74,78, pixel 0.324,0.326,0.315, shown at level 0.211, step 1, values float32 Opened (STATIC) (dataset) FC, PHIC as #1.1.1.5, grid size 78,74,78, pixel 0.324,0.326,0.315, shown at level 1.02, step 1, values float32 Opened (STATIC) (dataset) FC_ALL, PHIC_ALL as #1.1.1.6, grid size 78,74,78, pixel 0.324,0.326,0.315, shown at level -1.1,1.1, step 1, values float32 Opened (STATIC) (dataset) FWT, PHWT as #1.1.1.7, grid size 78,74,78, pixel 0.324,0.326,0.315, shown at level 0.935, step 1, values float32 Opened (STATIC) (dataset) DELFWT, PHDELWT as #1.1.1.8, grid size 78,74,78, pixel 0.324,0.326,0.315, shown at level -0.339,0.339, step 1, values float32 Opened (STATIC) (dataset) FAN, PHAN as #1.1.1.9, grid size 78,74,78, pixel 0.324,0.326,0.315, shown at level -0.0611,0.0611, step 1, values float32 Opened (STATIC) (dataset) DELFAN, PHDELAN as #1.1.1.10, grid size 78,74,78, pixel 0.324,0.326,0.315, shown at level -0.0611,0.0611, step 1, values float32 Opened (STATIC) (dataset) FC_ALL_LS, PHIC_ALL_LS as #1.1.1.11, grid size 78,74,78, pixel 0.324,0.326,0.315, shown at level -1.11,1.11, step 1, values float32 WT 5-13.pdb title: \--- [more info...] Chain information for WT 5-13.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available Non-standard residues in WT 5-13.pdb #1.2 --- CRO — (CRO) NA — (NA) SO4 — (SO4) Opened crystallographic dataset from /Users/nitsanyehishalom/Desktop/Studys/MS.c./Reserach/Results semester 3/Structures/WT 5-13.mtz Found experimental reflection data: (dataset) F, SIGF Rwork: 0.1873; Rfree: 0.1853 Generated maps: Reflection Data (LIVE) 2mFo-DFc (LIVE) mFo-DFc (LIVE) 2mFo-DFc_smooth_25 (STATIC) (dataset) FC, PHIC (STATIC) (dataset) FC_ALL, PHIC_ALL (STATIC) (dataset) FWT, PHWT (STATIC) (dataset) DELFWT, PHDELWT (STATIC) (dataset) FAN, PHAN (STATIC) (dataset) DELFAN, PHDELAN (STATIC) (dataset) FC_ALL_LS, PHIC_ALL_LS Any unwanted maps may be safely closed via the Model panel. > ui tool show ""Surface Zone"" > ui tool show ""Map Coordinates"" Volume zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic models, 10 maps. > select #1.2 /A :210 7 atoms, 7 bonds, 1 residue, 1 model selected Volume zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic models, 10 maps. > transparency 0 > view sel > transparency 50 > transparency 0 > transparency 50 > hide ribbons > select down 7 atoms, 7 bonds, 1 residue, 1 model selected > select up 77 atoms, 78 bonds, 11 residues, 1 model selected > hide ~sel ribbons > hide ~sel > ui tool show ""Volume Viewer"" > volume #1.1.1.2 level 0.2708 > volume #1.1.1.2 level 0.2822 > volume #1.1.1.2 style mesh > close #1.1.1.3 Deleting (LIVE) mFo-DFc > close #1.1.1.4 Deleting (LIVE) 2mFo-DFc_smooth_25 > close #1.1.1.5 > close #1.1.1.6 > close #1.1.1.7 > close #1.1.1.8 > close #1.1.1.9 > close #1.1.1.10 > close #1.1.1.11 > surface dust #1.1.1.2 size 3.26 > volume #1.1.1.2 level 0.2156 > volume step 2 > volume step 1 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.4rc202205140117 (2022-05-14) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 83 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Model Number: Z15G000MKAE/A Chip: Unknown Total Number of Cores: 8 (6 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 8419.41.10 OS Loader Version: 8419.41.10 Software: System Software Overview: System Version: macOS 13.0.1 (22A400) Kernel Version: Darwin 22.1.0 Time since boot: 7 days, 18 hours, 27 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.10.8 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-Clipper: 0.18.0 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: 1.4rc202205140117 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 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: 1.18.2 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 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: 3.6.0 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: 21.0 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 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 ptyprocess: 0.7.0 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 pyzmq: 22.3.0 qtconsole: 5.3.0 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 Send2Trash: 1.8.0 SEQCROW: 1.5.10 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: 5.2.0 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect closed normal Volume Data can't reproduce Tristan Croll all ChimeraX