id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6675 Problem after 'close' without 'vseries stop' d.e.richman@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Linux-5.13.0-39-generic-x86_64-with-glibc2.14 ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC) Description (Describe the actions that caused this problem to occur here) 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 > ui tool show ""Show Volume Menu"" > toolshed show > open > /home/drichman/Downloads/cryosparc_P5_3DVA_J118/cryosparc_P5_J118_component_000/*.mrc > vseries true Opened map series J118_component_000_frame_000.mrc as #1, 20 images, grid size 120,120,120, pixel 2.12, shown at level 0.33, step 1, values float32 > movieFramerate 10 Unknown command: movieFramerate 10 > mseries movieFramerate 10 Missing or invalid ""models"" argument: invalid models specifier > mseries slider #1 movieFramerate 10 > mseries slider #1 movieFramerate 10 bounce Expected a keyword > volume #1.1 level 0.1913 > coordset #1 bounce Missing ""bounce"" keyword's argument > mseries slider #1 movieFramerate 10 bounce true Expected a keyword > coordset #1 bounce true No structures specified > coordset #1 1-20 bounce true Expected a keyword > show #!1.1 models > hide #!1.1 models > hide #!1 models > show #!1.1 models > hide #!1.1 models > hide #!1 models > show #!1.2 models > hide #!1.2 models > hide #!1 models > show #!1.1 models > hide #!1 models > view #1.1 clip false No displayed objects specified. > show #!1.2 models > show #!1.3 models > hide #!1 models > vseries play #1 direction oscillate > vseries stop Missing or invalid ""series"" argument: empty atom specifier > vseries stop #1 > show #!1 models > vseries play #1 direction oscillate > vseries stop #1 > vseries play #1 direction oscillate maxFrameRate 10 > vseries stop #1 > vseries play #1 direction oscillate maxFrameRate 16 > volume #1.9 level 0.1913 color #b2b2b2 > volume #1.9 level 0.114 > vseries stop #1 > close > open > /home/drichman/Downloads/cryosparc_P5_3DVA_J118/cryosparc_P5_J118_component_001/*.mrc > vseries true Opened map series J118_component_001_frame_000.mrc as #1, 20 images, grid size 120,120,120, pixel 2.12, shown at level 0.343, step 1, values float32 > vseries play #1 direction oscillate maxFrameRate 16 > volume #1.1 level 0.3428 color #b2b2b2 > volume #1.1 level 0.08324 > vseries stop #1 > volume #1.11 level 0.272 > vseries play #1 direction oscillate maxFrameRate 16 > vseries stop #1 > close > open > /home/drichman/Downloads/cryosparc_P5_3DVA_J118/cryosparc_P5_J118_component_002/*.mrc > vseries true Opened map series J118_component_002_frame_000.mrc as #1, 20 images, grid size 120,120,120, pixel 2.12, shown at level 0.367, step 1, values float32 > volume #1.1 level 0.2206 > vseries play #1 direction oscillate maxFrameRate 16 > vseries play #1 direction oscillate maxFrameRate 8 > vseries stop #1 > vseries play #1 direction oscillate maxFrameRate 8 > vseries stop #1 > close > open > /home/drichman/Downloads/cryosparc_P5_3DVA/cryosparc_P5_J119_component_000/*.mrc > vseries true Opened map series J119_component_000_frame_000.mrc as #1, 20 images, grid size 120,120,120, pixel 2.12, shown at level 0.34, step 1, values float32 > volume #1.1 level 0.2455 > vseries play #1 direction oscillate maxFrameRate 8 > vseries stop #1 > open > /home/drichman/Downloads/cryosparc_P5_3DVA/cryosparc_P5_J119_component_001/*.mrc > vseries true Opened map series J119_component_001_frame_000.mrc as #2, 20 images, grid size 120,120,120, pixel 2.12, shown at level 0.357, step 1, values float32 > close > open > /home/drichman/Downloads/cryosparc_P5_3DVA/cryosparc_P5_J119_component_001/*.mrc > vseries true Opened map series J119_component_001_frame_000.mrc as #1, 20 images, grid size 120,120,120, pixel 2.12, shown at level 0.357, step 1, values float32 > volume #1.1 level 0.2311 > volume #1.1 level 0.2459 > vseries play #1 direction oscillate maxFrameRate 8 > vseries stop #1 > close > open > /home/drichman/Downloads/cryosparc_P5_3DVA/cryosparc_P5_J119_component_002/*.mrc > vseries true Opened map series J119_component_002_frame_000.mrc as #1, 20 images, grid size 120,120,120, pixel 2.12, shown at level 0.338, step 1, values float32 > volume #1.1 level 0.2742 > volume #1.1 level 0.2467 > vseries play #1 direction oscillate maxFrameRate 8 > vseries stop #1 > close > open > /home/drichman/Downloads/cryosparc_P5_3DVA/cryosparc_P5_J120_component_000/*.mrc > vseries true Opened map series J120_component_000_frame_000.mrc as #1, 20 images, grid size 120,120,120, pixel 2.12, shown at level 0.349, step 1, values float32 > vseries play #1 direction oscillate maxFrameRate 8 > vseries stop #1 > volume #1.15 level 0.309 > vseries play #1 direction oscillate maxFrameRate 8 > vseries stop #1 > close > open > /home/drichman/Downloads/cryosparc_P5_3DVA/cryosparc_P5_J120_component_001/*.mrc > vseries true Opened map series J120_component_001_frame_000.mrc as #1, 20 images, grid size 120,120,120, pixel 2.12, shown at level 0.363, step 1, values float32 > volume #1.1 level 0.3041 > vseries play #1 direction oscillate maxFrameRate 8 > close > open > /home/drichman/Downloads/cryosparc_P5_3DVA/cryosparc_P5_J120_component_002/*.mrc > vseries true Error processing trigger ""model display changed"": TypeError: object of type 'NoneType' has no len() File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 365, in get_display return self._any_displayed_positions and len(self._positions) > 0 See log for complete Python traceback. Error processing trigger ""model display changed"": TypeError: object of type 'NoneType' has no len() File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 365, in get_display return self._any_displayed_positions and len(self._positions) > 0 See log for complete Python traceback. Error processing trigger ""model display changed"": TypeError: object of type 'NoneType' has no len() File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 365, in get_display return self._any_displayed_positions and len(self._positions) > 0 See log for complete Python traceback. Error processing trigger ""model display changed"": TypeError: object of type 'NoneType' has no len() File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 365, in get_display return self._any_displayed_positions and len(self._positions) > 0 See log for complete Python traceback. Error processing trigger ""model display changed"": TypeError: object of type 'NoneType' has no len() File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 365, in get_display return self._any_displayed_positions and len(self._positions) > 0 See log for complete Python traceback. Error processing trigger ""model display changed"": TypeError: object of type 'NoneType' has no len() File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 365, in get_display return self._any_displayed_positions and len(self._positions) > 0 See log for complete Python traceback. Error processing trigger ""model display changed"": TypeError: object of type 'NoneType' has no len() File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 365, in get_display return self._any_displayed_positions and len(self._positions) > 0 See log for complete Python traceback. Error processing trigger ""model display changed"": TypeError: object of type 'NoneType' has no len() File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 365, in get_display return self._any_displayed_positions and len(self._positions) > 0 See log for complete Python traceback. Error processing trigger ""model display changed"": TypeError: object of type 'NoneType' has no len() File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 365, in get_display return self._any_displayed_positions and len(self._positions) > 0 See log for complete Python traceback. Error processing trigger ""model display changed"": TypeError: object of type 'NoneType' has no len() File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 365, in get_display return self._any_displayed_positions and len(self._positions) > 0 See log for complete Python traceback. Error processing trigger ""model display changed"": TypeError: object of type 'NoneType' has no len() File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 365, in get_display return self._any_displayed_positions and len(self._positions) > 0 See log for complete Python traceback. Error processing trigger ""model display changed"": TypeError: object of type 'NoneType' has no len() File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 365, in get_display return self._any_displayed_positions and len(self._positions) > 0 See log for complete Python traceback. Error processing trigger ""model display changed"": TypeError: object of type 'NoneType' has no len() File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 365, in get_display return self._any_displayed_positions and len(self._positions) > 0 See log for complete Python traceback. Error processing trigger ""model display changed"": TypeError: object of type 'NoneType' has no len() File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 365, in get_display return self._any_displayed_positions and len(self._positions) > 0 See log for complete Python traceback. Error processing trigger ""model display changed"": TypeError: object of type 'NoneType' has no len() File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 365, in get_display return self._any_displayed_positions and len(self._positions) > 0 See log for complete Python traceback. Error processing trigger ""model display changed"": TypeError: object of type 'NoneType' has no len() File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 365, in get_display return self._any_displayed_positions and len(self._positions) > 0 See log for complete Python traceback. Error processing trigger ""model display changed"": TypeError: object of type 'NoneType' has no len() File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 365, in get_display return self._any_displayed_positions and len(self._positions) > 0 See log for complete Python traceback. Error processing trigger ""model display changed"": TypeError: object of type 'NoneType' has no len() File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 365, in get_display return self._any_displayed_positions and len(self._positions) > 0 See log for complete Python traceback. Error processing trigger ""model display changed"": TypeError: object of type 'NoneType' has no len() File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 365, in get_display return self._any_displayed_positions and len(self._positions) > 0 See log for complete Python traceback. Error processing trigger ""model display changed"": TypeError: object of type 'NoneType' has no len() File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 365, in get_display return self._any_displayed_positions and len(self._positions) > 0 See log for complete Python traceback. Error processing trigger ""model display changed"": TypeError: object of type 'NoneType' has no len() File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 365, in get_display return self._any_displayed_positions and len(self._positions) > 0 See log for complete Python traceback. Error processing trigger ""model display changed"": TypeError: object of type 'NoneType' has no len() File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 365, in get_display return self._any_displayed_positions and len(self._positions) > 0 See log for complete Python traceback. Summary of feedback from opening files --- notes | Traceback (most recent call last): File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/model_panel/tool.py"", line 91, in lambda *args: self._initiate_fill_tree(*args, simple_change=True, countdown=(0,3))) File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/model_panel/tool.py"", line 162, in _initiate_fill_tree self._fill_tree(always_rebuild=always_rebuild) File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/model_panel/tool.py"", line 201, in _fill_tree self._get_info(model, all_selected_models, part_selected_models) File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/model_panel/tool.py"", line 275, in _get_info display = obj.display File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 365, in get_display return self._any_displayed_positions and len(self._positions) > 0 TypeError: object of type 'NoneType' has no len() Traceback (most recent call last): File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/model_panel/tool.py"", line 91, in lambda *args: self._initiate_fill_tree(*args, simple_change=True, countdown=(0,3))) File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/model_panel/tool.py"", line 162, in _initiate_fill_tree self._fill_tree(always_rebuild=always_rebuild) File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/model_panel/tool.py"", line 201, in _fill_tree self._get_info(model, all_selected_models, part_selected_models) File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/model_panel/tool.py"", line 275, in _get_info display = obj.display File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 365, in get_display return self._any_displayed_positions and len(self._positions) > 0 TypeError: object of type 'NoneType' has no len() Traceback (most recent call last): File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/model_panel/tool.py"", line 91, in lambda *args: self._initiate_fill_tree(*args, simple_change=True, countdown=(0,3))) File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/model_panel/tool.py"", line 162, in _initiate_fill_tree self._fill_tree(always_rebuild=always_rebuild) File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/model_panel/tool.py"", line 201, in _fill_tree self._get_info(model, all_selected_models, part_selected_models) File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/model_panel/tool.py"", line 275, in _get_info display = obj.display File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 365, in get_display return self._any_displayed_positions and len(self._positions) > 0 TypeError: object of type 'NoneType' has no len() Traceback (most recent call last): File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/model_panel/tool.py"", line 91, in lambda *args: self._initiate_fill_tree(*args, simple_change=True, countdown=(0,3))) File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/model_panel/tool.py"", line 162, in _initiate_fill_tree self._fill_tree(always_rebuild=always_rebuild) File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/model_panel/tool.py"", line 201, in _fill_tree self._get_info(model, all_selected_models, part_selected_models) File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/model_panel/tool.py"", line 275, in _get_info display = obj.display File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 365, in get_display return self._any_displayed_positions and len(self._positions) > 0 TypeError: object of type 'NoneType' has no len() Traceback (most recent call last): File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/model_panel/tool.py"", line 91, in lambda *args: self._initiate_fill_tree(*args, simple_change=True, countdown=(0,3))) File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/model_panel/tool.py"", line 162, in _initiate_fill_tree self._fill_tree(always_rebuild=always_rebuild) File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/model_panel/tool.py"", line 201, in _fill_tree self._get_info(model, all_selected_models, part_selected_models) File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/model_panel/tool.py"", line 275, in _get_info display = obj.display File ""/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 365, in get_display return self._any_displayed_positions and len(self._positions) > 0 TypeError: object of type 'NoneType' has no len() 17 messages similar to the above omitted Opened map series J120_component_002_frame_000.mrc as #1, 20 images, grid size 120,120,120, pixel 2.12, shown at level 0.357, step 1, values float32 OpenGL version: 3.3.0 NVIDIA 470.103.01 OpenGL renderer: NVIDIA GeForce RTX 2080 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: System manufacturer Model: System Product Name OS: Ubuntu 20.04 focal Architecture: 64bit ELF Virutal Machine: none CPU: 32 AMD Ryzen 9 3950X 16-Core Processor Cache Size: 512 KB Memory: total used free shared buff/cache available Mem: 125Gi 6.1Gi 91Gi 301Mi 27Gi 118Gi Swap: 2.0Gi 0B 2.0Gi Graphics: 09:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU102 [GeForce RTX 2080 Ti] [10de:1e04] (rev a1) Subsystem: eVga.com. Corp. TU102 [GeForce RTX 2080 Ti] [3842:2281] Kernel driver in use: nvidia Locale: ('en_US', 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 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-Clipper: 0.16.0 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-ISOLDE: 1.2.2 ChimeraX-Label: 1.0 ChimeraX-LinuxSupport: 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 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: 0.17 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 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: 1.2.0 }}} " defect closed normal Volume Data can't reproduce Eric Pettersen all ChimeraX