id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8282 Clipper: Cannot determine the correct value for the free reflections rruiz@… Tristan Croll "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description (Describe the actions that caused this problem to occur here) 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 > open ""/Users/rruiz/Library/CloudStorage/OneDrive- > UniversityofMarylandSchoolofMedicine/TG2/Xray structure/TG2_refine_6.pdb"" Chain information for TG2_refine_6.pdb #1 --- Chain | Description A D G J M P | No description available B E H K N Q | No description available C F I L O R | No description available > show cartoons > style sphere Changed 30910 atom styles > style sphere Changed 30910 atom styles > hide atoms > select ::name=""GDP"" 40 atoms, 42 bonds, 1 residue, 1 model selected > rainbow sel > select ::name=""GDP"" 40 atoms, 42 bonds, 1 residue, 1 model selected > color sel red > select ::name=""GDP"" 40 atoms, 42 bonds, 1 residue, 1 model selected > style sel sphere Changed 40 atom styles > open ""/Users/rruiz/Library/CloudStorage/OneDrive- > UniversityofMarylandSchoolofMedicine/TG2/Xray structure/TG2_refine_6.mtz"" Summary of feedback from opening /Users/rruiz/Library/CloudStorage/OneDrive- UniversityofMarylandSchoolofMedicine/TG2/Xray structure/TG2_refine_6.mtz --- warning | WARNING: multiple experimental reflection datasets found: (Original-experimental-data-mapped-to-asu) I-obs, SIGI-obs, (Experimental-data-used-in-refinement) F-obs-filtered, SIGF-obs-filtered Automatically choosing ""(Experimental-data-used-in-refinement) F-obs-filtered, SIGF-obs-filtered"". Traceback (most recent call last): File ""/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/graphics.py"", line 51, in event if self.handle_drag_and_drop(event): File ""/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/graphics.py"", line 116, in handle_drag_and_drop mw.dropEvent(event) File ""/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 574, in dropEvent _open_dropped_file(self.session, p) File ""/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 1919, in _open_dropped_file run(session, 'open %s' % FileNameArg.unparse(path)) File ""/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 181, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File ""/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 432, in collated_open return remember_data_format() File ""/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 403, in remember_data_format models, status = func(*func_args, **func_kw) File ""/Users/rruiz/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/clipper/__init__.py"", line 240, in open return open_structure_factors(session, data, **kw) File ""/Users/rruiz/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/clipper/cmd.py"", line 51, in open_structure_factors raise e File ""/Users/rruiz/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/clipper/cmd.py"", line 32, in open_structure_factors xmapset = mmgr.add_xmapset_from_file(path, oversampling_rate=over_sampling) File ""/Users/rruiz/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/clipper/maps/map_mgr.py"", line 306, in add_xmapset_from_file return XmapSet(self, mtzdata) File ""/Users/rruiz/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/clipper/maps/xmapset.py"", line 187, in __init__ self.init_maps(use_static_maps, use_live_maps, File ""/Users/rruiz/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/clipper/maps/xmapset.py"", line 252, in init_maps self._launch_live_xmap_mgr(crystal_data, fsigf_data) File ""/Users/rruiz/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/clipper/maps/xmapset.py"", line 435, in _launch_live_xmap_mgr xm = self._live_xmap_mgr = Xtal_thread_mgr(self.hklinfo, RuntimeError: Cannot determine the correct value for the free reflections in the given FreeR_flag array. Please convert your reflection file to CCP4 or PHENIX format using sftools or phenix.reflection_file_editor. RuntimeError: Cannot determine the correct value for the free reflections in the given FreeR_flag array. Please convert your reflection file to CCP4 or PHENIX format using sftools or phenix.reflection_file_editor. File ""/Users/rruiz/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/clipper/maps/xmapset.py"", line 435, in _launch_live_xmap_mgr xm = self._live_xmap_mgr = Xtal_thread_mgr(self.hklinfo, See log for complete Python traceback. > open ""/Users/rruiz/Library/CloudStorage/OneDrive- > UniversityofMarylandSchoolofMedicine/TG2/Xray structure/TG2_refine_6.mtz"" Summary of feedback from opening /Users/rruiz/Library/CloudStorage/OneDrive- UniversityofMarylandSchoolofMedicine/TG2/Xray structure/TG2_refine_6.mtz --- warning | WARNING: multiple experimental reflection datasets found: (Original-experimental-data-mapped-to-asu) I-obs, SIGI-obs, (Experimental-data-used-in-refinement) F-obs-filtered, SIGF-obs-filtered Automatically choosing ""(Experimental-data-used-in-refinement) F-obs-filtered, SIGF-obs-filtered"". note | | Chain information for TG2_refine_6.pdb #1 --- Chain | Description A D G J M P | No description available B E H K N Q | No description available C F I L O R | No description available Traceback (most recent call last): File ""/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/dialog.py"", line 155, in _qt_safe run(session, ""open "" + "" "".join([FileNameArg.unparse(p) for p in paths]) + ("""" File ""/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 181, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File ""/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 432, in collated_open return remember_data_format() File ""/private/var/folders/3d/rbyx9k813dv1vr2x6rs14fb40000gq/T/AppTranslocation/170C4310-8AF3-4576-BC9F-3D5D59818186/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 403, in remember_data_format models, status = func(*func_args, **func_kw) File ""/Users/rruiz/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/clipper/__init__.py"", line 240, in open return open_structure_factors(session, data, **kw) File ""/Users/rruiz/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/clipper/cmd.py"", line 51, in open_structure_factors raise e File ""/Users/rruiz/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/clipper/cmd.py"", line 32, in open_structure_factors xmapset = mmgr.add_xmapset_from_file(path, oversampling_rate=over_sampling) File ""/Users/rruiz/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/clipper/maps/map_mgr.py"", line 306, in add_xmapset_from_file return XmapSet(self, mtzdata) File ""/Users/rruiz/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/clipper/maps/xmapset.py"", line 187, in __init__ self.init_maps(use_static_maps, use_live_maps, File ""/Users/rruiz/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/clipper/maps/xmapset.py"", line 252, in init_maps self._launch_live_xmap_mgr(crystal_data, fsigf_data) File ""/Users/rruiz/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/clipper/maps/xmapset.py"", line 435, in _launch_live_xmap_mgr xm = self._live_xmap_mgr = Xtal_thread_mgr(self.hklinfo, RuntimeError: Cannot determine the correct value for the free reflections in the given FreeR_flag array. Please convert your reflection file to CCP4 or PHENIX format using sftools or phenix.reflection_file_editor. RuntimeError: Cannot determine the correct value for the free reflections in the given FreeR_flag array. Please convert your reflection file to CCP4 or PHENIX format using sftools or phenix.reflection_file_editor. File ""/Users/rruiz/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/clipper/maps/xmapset.py"", line 435, in _launch_live_xmap_mgr xm = self._live_xmap_mgr = Xtal_thread_mgr(self.hklinfo, See log for complete Python traceback. OpenGL version: 4.1 ATI-4.8.54 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 8-Core Intel Core i9 Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 32 GB System Firmware Version: 1731.120.10.0.0 (iBridge: 19.16.15071.0.0,0) OS Loader Version: 540.120.3~6 Software: System Software Overview: System Version: macOS 12.4 (21F79) Kernel Version: Darwin 21.5.0 Time since boot: 118 days 3:40 Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Family: Supported, Metal GPUFamily macOS 2 AMD Radeon Pro 5500M: Chipset Model: AMD Radeon Pro 5500M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0040 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32206U1-020 Option ROM Version: 113-D32206U1-020 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.5.30 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-ItemsInspection: 1.0 ChimeraX-Label: 1.1 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 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 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: 21.0 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 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 }}} " defect assigned normal Third Party all ChimeraX