id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4831 Opening MRC file: getcwd: No such file or directory irina.grishkovskaya@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.15.7-x86_64-i386-64bit ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC) Description (Describe the actions that caused this problem to occur here) save mrc file Log: UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/irina.grishkovskaya/DRG1/Bud20/Krios/J2114/6n8k_JJ2114v2.pdb > format pdb No such file/path: /Users/irina.grishkovskaya/DRG1/Bud20/Krios/J2114/6n8k_JJ2114v2.pdb > ui tool show ""Command Line Interface"" > ui tool show ""Model Panel"" > open ""/Users/irina.grishkovskaya/Dropbox > (VBC)/Bergler_lab/Drg1_Manuscripts/Maps and > Models/models/RealSpaceRefine_67/DRGall_v7inputfin_cart_relax_0001_real_space_refined_067.pdb"" > format pdb Chain information for DRGall_v7inputfin_cart_relax_0001_real_space_refined_067.pdb #1 --- Chain | Description A | No description available B C E | No description available D | No description available F | No description available G | No description available > close > open > /Users/irina.grishkovskaya/DRG1/Bud20/Krios/deepEMhancer_results/wideTarget_cryosparc_P144_J2114_003_volume_map_flip.mrc > format mrc Opened wideTarget_cryosparc_P144_J2114_003_volume_map_flip.mrc as #1, grid size 480,480,480, pixel 1.38, shown at level 0.00126, step 2, values float32 > close > open > /Users/irina.grishkovskaya/DRG1/Bud20/Krios/relion_2114/deepEMhancer_results/highRes_run_class001.mrc Opened highRes_run_class001.mrc as #1, grid size 480,480,480, pixel 1.38, shown at level 0.0292, step 2, values float32 > volume #1 step 1 > volume #1 level 0.1647 > close > open > /Users/irina.grishkovskaya/DRG1/Bud20/Krios/relion_2114/deepEMhancer_results/tightTarget_run_class001.mrc Opened tightTarget_run_class001.mrc as #1, grid size 480,480,480, pixel 1.38, shown at level 0.000417, step 2, values float32 > volume #1 step 1 > volume #1 level 0.1759 > open > /Users/irina.grishkovskaya/DRG1/Bud20/Krios/relion_2114/deepEMhancer_results/wideTarget_run_class001.mrc Opened wideTarget_run_class001.mrc as #2, grid size 480,480,480, pixel 1.38, shown at level 0.0031, step 2, values float32 > volume #2 step 1 > volume #2 level 0.03636 > volume #2 level -0.005259 > volume #2 level 0.02467 > volume flip #2 axis z Opened wideTarget_run_class001.mrc z flip as #3, grid size 480,480,480, pixel 1.38, shown at step 1, values float32 > open > /Users/irina.grishkovskaya/DRG1/Bud20/Krios/relion_2114/210625_relion_all '/Users/irina.grishkovskaya/DRG1/Bud20/Krios/relion_2114/210625_relion_all' has no suffix > open > /Users/irina.grishkovskaya/DRG1/Bud20/Krios/relion_2114/210625_relion_all.pdb Chain information for 210625_relion_all.pdb #4 --- Chain | Description 1 | No description available 2 | No description available 3 | No description available 4 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available M2 | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available j | No description available k | No description available l | No description available o | No description available p | No description available q | No description available s | No description available u | No description available v | No description available y | No description available z | No description available > hide atoms > show cartoons > transparency #3.1 50 > set bgColor white > close #1 > close #2 > ui tool show ""Fit in Map"" Fit molecule 210625_relion_all.pdb (#4) to map wideTarget_run_class001.mrc z flip (#3) using 140596 atoms average map value = 0.3387, steps = 44 shifted from previous position = 0.0242 rotated from previous position = 0.0131 degrees atoms outside contour = 18373, contour level = 0.024672 Position of 210625_relion_all.pdb (#4) relative to wideTarget_run_class001.mrc z flip (#3) coordinates: Matrix rotation and translation 0.99999997 -0.00009087 -0.00020933 0.10595249 0.00009086 1.00000000 -0.00002058 -0.00249061 0.00020933 0.00002056 0.99999998 -0.06642199 Axis 0.08976002 -0.91360588 0.39656959 Axis point 289.78061388 0.00000000 512.34849578 Rotation angle (degrees) 0.01312814 Shift along axis -0.01455521 Fit molecule 210625_relion_all.pdb (#4) to map wideTarget_run_class001.mrc z flip (#3) using 140596 atoms average map value = 0.3387, steps = 40 shifted from previous position = 0.00152 rotated from previous position = 0.00102 degrees atoms outside contour = 18373, contour level = 0.024672 Position of 210625_relion_all.pdb (#4) relative to wideTarget_run_class001.mrc z flip (#3) coordinates: Matrix rotation and translation 0.99999998 -0.00007413 -0.00020980 0.10075919 0.00007413 1.00000000 -0.00002645 0.00641076 0.00020980 0.00002643 0.99999998 -0.06813662 Axis 0.11799236 -0.93628879 0.33081883 Axis point 298.55929612 0.00000000 489.59701403 Rotation angle (degrees) 0.01283861 Shift along axis -0.01665438 Fit molecule 210625_relion_all.pdb (#4) to map wideTarget_run_class001.mrc z flip (#3) using 140596 atoms average map value = 0.3388, steps = 28 shifted from previous position = 0.0233 rotated from previous position = 7.14e-05 degrees atoms outside contour = 18392, contour level = 0.024672 Position of 210625_relion_all.pdb (#4) relative to wideTarget_run_class001.mrc z flip (#3) coordinates: Matrix rotation and translation 0.99999998 -0.00007426 -0.00020937 0.09901143 0.00007426 1.00000000 -0.00002761 -0.01550909 0.00020937 0.00002759 0.99999998 -0.07494362 Axis 0.12329870 -0.93528485 0.33172229 Axis point 360.92998101 0.00000000 471.76702831 Rotation angle (degrees) 0.01282615 Shift along axis 0.00185293 > save > /Users/irina.grishkovskaya/DRG1/Bud20/Krios/relion_2114/deepEMhancer_results/2114relion_widetarget_flip.mrc > models #3 Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/save_command/dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/save_command/dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/save_command/dialog.py"", line 51, in display run(session, cmd) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/save_command/cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/save_command/cmd.py"", line 87, in provider_save provider_info.bundle_info.run_provider(session, provider_info.format_name, File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/__init__.py"", line 164, in save save_map(session, path, _name, **kw) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/volume.py"", line 3974, in save_map save_grid_data(grids, path, session, format_name, options) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map_data/fileformats.py"", line 297, in save_grid_data if matching_grid_path(glist, path): File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map_data/fileformats.py"", line 340, in matching_grid_path if realpath(gp) == rp: File ""/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py"", line 392, in realpath return abspath(path) File ""/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py"", line 379, in abspath cwd = os.getcwd() FileNotFoundError: [Errno 2] No such file or directory FileNotFoundError: [Errno 2] No such file or directory File ""/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py"", line 379, in abspath cwd = os.getcwd() See log for complete Python traceback. > save > /Users/irina.grishkovskaya/DRG1/Bud20/Krios/relion_2114/deepEMhancer_results/2114relion_wideTarget_run_class001flip.mrc > models #3 Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/save_command/dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/save_command/dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/save_command/dialog.py"", line 51, in display run(session, cmd) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/save_command/cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/save_command/cmd.py"", line 87, in provider_save provider_info.bundle_info.run_provider(session, provider_info.format_name, File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/__init__.py"", line 164, in save save_map(session, path, _name, **kw) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/volume.py"", line 3974, in save_map save_grid_data(grids, path, session, format_name, options) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map_data/fileformats.py"", line 297, in save_grid_data if matching_grid_path(glist, path): File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map_data/fileformats.py"", line 340, in matching_grid_path if realpath(gp) == rp: File ""/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py"", line 392, in realpath return abspath(path) File ""/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py"", line 379, in abspath cwd = os.getcwd() FileNotFoundError: [Errno 2] No such file or directory FileNotFoundError: [Errno 2] No such file or directory File ""/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py"", line 379, in abspath cwd = os.getcwd() See log for complete Python traceback. > save > /Users/irina.grishkovskaya/DRG1/Bud20/Krios/relion_2114/relion2114_wideTarget_run_class001flip.mrc > models #3 Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/save_command/dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/save_command/dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/save_command/dialog.py"", line 51, in display run(session, cmd) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/save_command/cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/save_command/cmd.py"", line 87, in provider_save provider_info.bundle_info.run_provider(session, provider_info.format_name, File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/__init__.py"", line 164, in save save_map(session, path, _name, **kw) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/volume.py"", line 3974, in save_map save_grid_data(grids, path, session, format_name, options) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map_data/fileformats.py"", line 297, in save_grid_data if matching_grid_path(glist, path): File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map_data/fileformats.py"", line 340, in matching_grid_path if realpath(gp) == rp: File ""/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py"", line 392, in realpath return abspath(path) File ""/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py"", line 379, in abspath cwd = os.getcwd() FileNotFoundError: [Errno 2] No such file or directory FileNotFoundError: [Errno 2] No such file or directory File ""/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py"", line 379, in abspath cwd = os.getcwd() See log for complete Python traceback. Window position QRect(1967,731 100x30) outside any known screen, using primary screen OpenGL version: 4.1 ATI-3.10.19 OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine OpenGL vendor: ATI Technologies Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro14,3 Processor Name: Quad-Core Intel Core i7 Processor Speed: 2.9 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 8 MB Hyper-Threading Technology: Enabled Memory: 16 GB Boot ROM Version: 429.60.3.0.0 SMC Version (system): 2.45f4 Software: System Software Overview: System Version: macOS 10.15.7 (19H114) Kernel Version: Darwin 19.6.0 Time since boot: 16 days 2:30 Graphics/Displays: Intel HD Graphics 630: Chipset Model: Intel HD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x591b Revision ID: 0x0004 Automatic Graphics Switching: Supported gMux Version: 4.0.29 [3.2.8] Metal: Supported, feature set macOS GPUFamily2 v1 Radeon Pro 560: Chipset Model: Radeon Pro 560 Type: GPU Bus: PCIe PCIe Lane Width: x8 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x67ef Revision ID: 0x00c0 ROM Revision: 113-C980AJ-927 VBIOS Version: 113-C9801AU-A02 EFI Driver Version: 01.A0.927 Automatic Graphics Switching: Supported gMux Version: 4.0.29 [3.2.8] Metal: Supported, feature set macOS GPUFamily2 v1 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2880 x 1800 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No 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: 2020.12.5 cftime: 1.5.0 chardet: 3.0.4 ChimeraX-AddCharge: 1.0.1 ChimeraX-AddH: 2.1.6 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.13.2 ChimeraX-AtomicLibrary: 3.1.3 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.5.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.2.1 ChimeraX-CommandLine: 1.1.4 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.5 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.1.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.3 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: 2.1 ChimeraX-Help: 1.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.0.2 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: 1.2.1 ChimeraX-MDcrds: 2.2 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.3 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.0.1 ChimeraX-ModelPanel: 1.0.1 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: 2.0.1 ChimeraX-OpenCommand: 1.5 ChimeraX-PDB: 2.4.1 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.1 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.4 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.3 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: 2.0.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.3.1 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: 1.0.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.7.6 ChimeraX-uniprot: 2.1 ChimeraX-UnitCell: 1.0 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: 0.29.21 decorator: 5.0.9 distlib: 0.3.1 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: 0.17 imagecodecs: 2020.5.30 imagesize: 1.2.0 ipykernel: 5.3.4 ipython: 7.18.1 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.7 jupyter-core: 4.7.1 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.6.2 lz4: 3.1.0 MarkupSafe: 2.0.1 matplotlib: 3.3.2 matplotlib-inline: 0.1.2 msgpack: 1.0.0 netCDF4: 1.5.4 networkx: 2.5 numexpr: 2.7.3 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.9 ParmEd: 3.2.0 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 21.0.1 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.18 psutil: 5.7.2 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.7.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 pyzmq: 22.0.3 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 setuptools: 50.3.2 sfftk-rw: 0.6.7.dev1 six: 1.15.0 snowballstemmer: 2.1.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 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 tables: 3.6.1 tifffile: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.0 wheel-filename: 1.3.0 }}} " defect closed normal Input/Output nonchimerax all ChimeraX