id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8761 Crash in readcif::CIFFile::parse daniel.mejia@… Greg Couch "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.6rc202303292224 (2023-03-29 22:24:14 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x00007000158ce000 (most recent call first): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 316 in wait File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 574 in wait File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 1297 in run File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00007000148cb000 (most recent call first): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 316 in wait File 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""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py"", line 465 in collated_open File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py"", line 194 in provider_open File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/manager.py"", line 198 in open_data File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/mmcif/__init__.py"", line 97 in fetch File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py"", line 435 in remember_data_format File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py"", line 464 in collated_open File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py"", line 154 in provider_open File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py"", line 2897 in run File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py"", line 119 in cmd_open File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py"", line 2897 in run File 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""experiments"" : [ ] }, ""reportNotes"" : [ ""dyld_process_snapshot_create_for_process failed with 5"" ] } ===== Log before crash start ===== UCSF ChimeraX version: 1.6rc202303292224 (2023-03-29) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > devel build /Users/meji656/Sources/cysptm_chimerax running build running build_py running bdist_wheel installing to build/bdist.macosx-10.9-universal2/wheel running install running install_lib creating build/bdist.macosx-10.9-universal2/wheel creating build/bdist.macosx-10.9-universal2/wheel/chimerax creating build/bdist.macosx-10.9-universal2/wheel/chimerax/do_ptm copying build/lib/chimerax/do_ptm/do_ptm.py -> build/bdist.macosx-10.9-universal2/wheel/chimerax/do_ptm copying build/lib/chimerax/do_ptm/cmd.py -> build/bdist.macosx-10.9-universal2/wheel/chimerax/do_ptm copying build/lib/chimerax/do_ptm/__init__.py -> build/bdist.macosx-10.9-universal2/wheel/chimerax/do_ptm copying build/lib/chimerax/do_ptm/settings.py -> build/bdist.macosx-10.9-universal2/wheel/chimerax/do_ptm copying build/lib/chimerax/do_ptm/tool.py -> build/bdist.macosx-10.9-universal2/wheel/chimerax/do_ptm copying build/lib/chimerax/do_ptm/contextmenu.py -> build/bdist.macosx-10.9-universal2/wheel/chimerax/do_ptm running install_egg_info running egg_info writing ChimeraX_DoPTM.egg-info/PKG-INFO writing dependency_links to ChimeraX_DoPTM.egg-info/dependency_links.txt writing requirements to ChimeraX_DoPTM.egg-info/requires.txt writing top-level names to ChimeraX_DoPTM.egg-info/top_level.txt writing manifest file 'ChimeraX_DoPTM.egg-info/SOURCES.txt' Copying ChimeraX_DoPTM.egg-info to build/bdist.macosx-10.9-universal2/wheel/ChimeraX_DoPTM-0.1-py3.9.egg-info running install_scripts creating build/bdist.macosx-10.9-universal2/wheel/ChimeraX_DoPTM-0.1.dist- info/WHEEL creating 'dist/ChimeraX_DoPTM-0.1-py3-none-any.whl' and adding 'build/bdist.macosx-10.9-universal2/wheel' to it adding 'chimerax/do_ptm/__init__.py' adding 'chimerax/do_ptm/cmd.py' adding 'chimerax/do_ptm/contextmenu.py' adding 'chimerax/do_ptm/do_ptm.py' adding 'chimerax/do_ptm/settings.py' adding 'chimerax/do_ptm/tool.py' adding 'ChimeraX_DoPTM-0.1.dist-info/METADATA' adding 'ChimeraX_DoPTM-0.1.dist-info/WHEEL' adding 'ChimeraX_DoPTM-0.1.dist-info/top_level.txt' adding 'ChimeraX_DoPTM-0.1.dist-info/RECORD' removing build/bdist.macosx-10.9-universal2/wheel Distribution is in /Users/meji656/Sources/cysptm_chimerax/dist/ChimeraX_DoPTM-0.1-py3-none- any.whl > devel build /Users/meji656/Sources/cysptm_chimerax running build running build_py running bdist_wheel installing to build/bdist.macosx-10.9-universal2/wheel running install running install_lib creating build/bdist.macosx-10.9-universal2/wheel creating build/bdist.macosx-10.9-universal2/wheel/chimerax creating build/bdist.macosx-10.9-universal2/wheel/chimerax/do_ptm copying build/lib/chimerax/do_ptm/do_ptm.py -> build/bdist.macosx-10.9-universal2/wheel/chimerax/do_ptm copying build/lib/chimerax/do_ptm/cmd.py -> build/bdist.macosx-10.9-universal2/wheel/chimerax/do_ptm copying build/lib/chimerax/do_ptm/__init__.py -> build/bdist.macosx-10.9-universal2/wheel/chimerax/do_ptm copying build/lib/chimerax/do_ptm/settings.py -> build/bdist.macosx-10.9-universal2/wheel/chimerax/do_ptm copying build/lib/chimerax/do_ptm/tool.py -> build/bdist.macosx-10.9-universal2/wheel/chimerax/do_ptm copying build/lib/chimerax/do_ptm/contextmenu.py -> build/bdist.macosx-10.9-universal2/wheel/chimerax/do_ptm running install_egg_info running egg_info writing ChimeraX_DoPTM.egg-info/PKG-INFO writing dependency_links to ChimeraX_DoPTM.egg-info/dependency_links.txt writing requirements to ChimeraX_DoPTM.egg-info/requires.txt writing top-level names to ChimeraX_DoPTM.egg-info/top_level.txt writing manifest file 'ChimeraX_DoPTM.egg-info/SOURCES.txt' Copying ChimeraX_DoPTM.egg-info to build/bdist.macosx-10.9-universal2/wheel/ChimeraX_DoPTM-0.1-py3.9.egg-info running install_scripts creating build/bdist.macosx-10.9-universal2/wheel/ChimeraX_DoPTM-0.1.dist- info/WHEEL creating 'dist/ChimeraX_DoPTM-0.1-py3-none-any.whl' and adding 'build/bdist.macosx-10.9-universal2/wheel' to it adding 'chimerax/do_ptm/__init__.py' adding 'chimerax/do_ptm/cmd.py' adding 'chimerax/do_ptm/contextmenu.py' adding 'chimerax/do_ptm/do_ptm.py' adding 'chimerax/do_ptm/settings.py' adding 'chimerax/do_ptm/tool.py' adding 'ChimeraX_DoPTM-0.1.dist-info/METADATA' adding 'ChimeraX_DoPTM-0.1.dist-info/WHEEL' adding 'ChimeraX_DoPTM-0.1.dist-info/top_level.txt' adding 'ChimeraX_DoPTM-0.1.dist-info/RECORD' removing build/bdist.macosx-10.9-universal2/wheel Distribution is in /Users/meji656/Sources/cysptm_chimerax/dist/ChimeraX_DoPTM-0.1-py3-none- any.whl > toolshed install > /Users/meji656/Downloads/ChimeraX_RotamerLibsCysPTM-0.1-py3-none-any.whl Errors may have occurred when running pip: pip standard error: \--- [notice] A new release of pip is available: 23.0 -> 23.0.1 [notice] To update, run: /Applications/ChimeraX.app/Contents/MacOS/ChimeraX -m pip install --upgrade pip \--- pip standard output: \--- Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing /Users/meji656/Downloads/ChimeraX_RotamerLibsCysPTM-0.1-py3-none- any.whl Requirement already satisfied: ChimeraX-Core>=0.9 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-RotamerLibsCysPTM==0.1) (1.6rc202303292224) Requirement already satisfied: ChimeraX-RotamerLibMgr~=3.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-RotamerLibsCysPTM==0.1) (3.0) Installing collected packages: ChimeraX-RotamerLibsCysPTM Successfully installed ChimeraX-RotamerLibsCysPTM-0.1 \--- Successfully installed ChimeraX-RotamerLibsCysPTM-0.1 Installed ChimeraX-RotamerLibsCysPTM (0.1) > toolshed install /Users/meji656/Downloads/ChimeraX_DoPTM-0.1-py3-none- > any.whl Errors may have occurred when running pip: pip standard error: \--- [notice] A new release of pip is available: 23.0 -> 23.0.1 [notice] To update, run: /Applications/ChimeraX.app/Contents/MacOS/ChimeraX -m pip install --upgrade pip \--- pip standard output: \--- Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing /Users/meji656/Downloads/ChimeraX_DoPTM-0.1-py3-none-any.whl Requirement already satisfied: ChimeraX-RotamerLibMgr~=3.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-DoPTM==0.1) (3.0) Requirement already satisfied: ChimeraX-UI~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-DoPTM==0.1) (1.28.4) Requirement already satisfied: ChimeraX-Geometry~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-DoPTM==0.1) (1.3) Requirement already satisfied: ChimeraX-Hbonds~=2.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-DoPTM==0.1) (2.4) Requirement already satisfied: ChimeraX-Core~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-DoPTM==0.1) (1.6rc202303292224) Requirement already satisfied: ChimeraX-Atomic~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-DoPTM==0.1) (1.43.10) Requirement already satisfied: ChimeraX-Clashes~=2.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-DoPTM==0.1) (2.2.4) Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1) (2.0.1) Requirement already satisfied: ChimeraX-mmCIF~=2.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1) (2.12) Requirement already satisfied: ChimeraX-Graphics~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1) (1.1.1) Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1) (2.0.3) Requirement already satisfied: ChimeraX-AtomicLibrary~=10.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1) (10.0.6) Requirement already satisfied: ChimeraX-PDB~=2.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1) (2.7) Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1) (1.0.2) Requirement already satisfied: ChimeraX-Arrays~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1) (1.1) Requirement already satisfied: ChimeraX-AtomSearch~=2.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Clashes~=2.0->ChimeraX-DoPTM==0.1) (2.0.1) Requirement already satisfied: ChimeraX-ChemGroup~=2.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Hbonds~=2.0->ChimeraX-DoPTM==0.1) (2.0.1) Requirement already satisfied: ChimeraX-SelInspector~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-UI~=1.0->ChimeraX-DoPTM==0.1) (1.0) Requirement already satisfied: ChimeraX-MouseModes~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-UI~=1.0->ChimeraX-DoPTM==0.1) (1.2) Requirement already satisfied: ChimeraX-DataFormats~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1) (1.2.3) Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1) (1.5.1) Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1) (1.10.1) Requirement already satisfied: ChimeraX-Surface~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX- DoPTM==0.1) (1.0.1) Requirement already satisfied: ChimeraX-IO~=1.0.1 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-PDB~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1) (1.0.1) Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX- DoPTM==0.1) (1.0.1) Requirement already satisfied: ChimeraX-Map~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX- Atomic~=1.0->ChimeraX-DoPTM==0.1) (1.1.4) Requirement already satisfied: ChimeraX-StdCommands~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX- Atomic~=1.0->ChimeraX-DoPTM==0.1) (1.10.2) Requirement already satisfied: ChimeraX-MapData~=2.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX- Atomic~=1.0->ChimeraX-DoPTM==0.1) (2.0) Requirement already satisfied: ChimeraX-MapFilter~=2.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX- Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1) (2.0.1) Requirement already satisfied: ChimeraX-MapSeries~=2.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX- Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1) (2.1.1) Requirement already satisfied: ChimeraX-Dssp~=2.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX- Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1) (2.0) Requirement already satisfied: ChimeraX-MapFit~=2.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX- Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1) (2.0) Requirement already satisfied: ChimeraX-DistMonitor~=1.2 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX- Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1) (1.4) Installing collected packages: ChimeraX-DoPTM Successfully installed ChimeraX-DoPTM-0.1 \--- Successfully installed ChimeraX-DoPTM-0.1 Installed ChimeraX-DoPTM (0.1) > fetch 2d2i Unknown command: fetch 2d2i > clear Unknown command: clear > log clear > open 2d2i ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.6rc202303292224 (2023-03-29) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-20.2.50 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine OpenGL vendor: Intel Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 512 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1916.80.2.0.0 (iBridge: 20.16.3045.0.0,0) OS Loader Version: 564.40.4~66 Software: System Software Overview: System Version: macOS 13.2.1 (22D68) Kernel Version: Darwin 22.3.0 Time since boot: 2 days, 14 hours, 19 minutes Graphics/Displays: Intel Iris Plus Graphics: Chipset Model: Intel Iris Plus Graphics Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x8a53 Revision ID: 0x0007 Metal Support: Metal 3 Displays: DELL U2720Q: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 57WKX13 Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Connection Type: Thunderbolt/DisplayPort Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9 ChimeraX-AddH: 2.2.4 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6rc202303292224 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 ChimeraX-DoPTM: 0.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsCysPTM: 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: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.2 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.6 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.1.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.2.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.9.0 typing-extensions: 4.5.0 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Input/Output fixed Zach Pearson all ChimeraX