id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7090 Toolbar buttons not created when ISOLDE installed sean.connell@… Greg Couch "{{{ The following bug report has been submitted: Platform: macOS-10.15.7-x86_64-i386-64bit ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > cd /Users/sconnell/Downloads Current working directory is: /Users/sconnell/Downloads > devel install ChimeraX_Clipper-0.18.0-cp39-cp39-macosx_10_13_x86_64.whl Bundle info file 'ChimeraX_Clipper-0.18.0-cp39-cp39-macosx_10_13_x86_64.whl/bundle_info.xml' is missing > toolshed show > toolshed install ChimeraX_Clipper-0.18.0-cp39-cp39-macosx_10_13_x86_64.whl Errors may have occurred when running pip: pip standard error: \--- WARNING: Value for scheme.platlib does not match. Please report this to distutils: /Users/sconnell/Library/Application Support/ChimeraX/1.4/site- packages sysconfig: /Users/sconnell/Library/Python/3.9/lib/python/site-packages WARNING: Value for scheme.purelib does not match. Please report this to distutils: /Users/sconnell/Library/Application Support/ChimeraX/1.4/site- packages sysconfig: /Users/sconnell/Library/Python/3.9/lib/python/site-packages WARNING: Value for scheme.headers does not match. Please report this to distutils: /Users/sconnell/Library/Application Support/ChimeraX/include/python3.9/ChimeraX-Clipper sysconfig: /Users/sconnell/Library/Python/3.9/include/ChimeraX-Clipper WARNING: Value for scheme.scripts does not match. Please report this to distutils: /Users/sconnell/Library/Application Support/ChimeraX/bin sysconfig: /Users/sconnell/Library/Python/3.9/bin WARNING: Value for scheme.data does not match. Please report this to distutils: /Users/sconnell/Library/Application Support/ChimeraX sysconfig: /Users/sconnell/Library/Python/3.9 WARNING: Additional context: user = True home = None root = None prefix = None WARNING: Value for scheme.headers does not match. Please report this to distutils: /Users/sconnell/Library/Application Support/ChimeraX/include/python3.9/UNKNOWN sysconfig: /Users/sconnell/Library/Python/3.9/include/UNKNOWN WARNING: You are using pip version 21.3.1; however, version 22.1.2 is available. You should consider upgrading via the '/Applications/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -m pip install --upgrade pip' command. \--- pip standard output: \--- Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing ./ChimeraX_Clipper-0.18.0-cp39-cp39-macosx_10_13_x86_64.whl Requirement already satisfied: ChimeraX-Arrays~=1.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Clipper==0.18.0) (1.0) Requirement already satisfied: ChimeraX-AtomicLibrary~=7.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Clipper==0.18.0) (7.0) Requirement already satisfied: ChimeraX-Core~=1.4.dev202203030220 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Clipper==0.18.0) (1.4) Requirement already satisfied: ChimeraX-Atomic~=1.36 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Clipper==0.18.0) (1.39.1) Requirement already satisfied: ChimeraX-mmCIF~=2.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (2.7) Requirement already satisfied: ChimeraX-Graphics~=1.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.1) Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.0.2) Requirement already satisfied: ChimeraX-PDB~=2.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (2.6.6) Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (2.0.1) Requirement already satisfied: ChimeraX-Geometry~=1.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.2) Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (2.0.2) Requirement already satisfied: ChimeraX-DataFormats~=1.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.36->ChimeraX- Clipper==0.18.0) (1.2.2) Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.36->ChimeraX- Clipper==0.18.0) (1.5.1) Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.36->ChimeraX- Clipper==0.18.0) (1.9) Requirement already satisfied: ChimeraX-UI~=1.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX- Clipper==0.18.0) (1.18.3) Requirement already satisfied: ChimeraX-Surface~=1.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX- Clipper==0.18.0) (1.0) Requirement already satisfied: ChimeraX-IO~=1.0.1 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-PDB~=2.0->ChimeraX-Atomic~=1.36->ChimeraX- Clipper==0.18.0) (1.0.1) Requirement already satisfied: ChimeraX-Map~=1.0 in /Applications/ChimeraX-1.4.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~=1.36->ChimeraX-Clipper==0.18.0) (1.1) Requirement already satisfied: ChimeraX-MapData~=2.0 in /Applications/ChimeraX-1.4.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~=1.36->ChimeraX-Clipper==0.18.0) (2.0) Requirement already satisfied: ChimeraX-StdCommands~=1.0 in /Applications/ChimeraX-1.4.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~=1.36->ChimeraX-Clipper==0.18.0) (1.8) Requirement already satisfied: ChimeraX-MouseModes~=1.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX- Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.1) Requirement already satisfied: ChimeraX-SelInspector~=1.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX- Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.0) Requirement already satisfied: ChimeraX-MapFilter~=2.0 in /Applications/ChimeraX-1.4.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~=1.36->ChimeraX-Clipper==0.18.0) (2.0) Requirement already satisfied: ChimeraX-MapSeries~=2.0 in /Applications/ChimeraX-1.4.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~=1.36->ChimeraX-Clipper==0.18.0) (2.1) Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX- Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.0) Requirement already satisfied: ChimeraX-MapFit~=2.0 in /Applications/ChimeraX-1.4.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~=1.36->ChimeraX-Clipper==0.18.0) (2.0) Requirement already satisfied: ChimeraX-Dssp~=2.0 in /Applications/ChimeraX-1.4.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~=1.36->ChimeraX-Clipper==0.18.0) (2.0) Installing collected packages: ChimeraX-Clipper Successfully installed ChimeraX-Clipper-0.18.0 \--- Successfully installed ChimeraX-Clipper-0.18.0 Installed ChimeraX-Clipper (0.18.0) > toolshed install ChimeraX_ISOLDE-1.4b1-cp39-cp39-macosx_10_13_x86_64.whl Errors may have occurred when running pip: pip standard error: \--- WARNING: Value for scheme.platlib does not match. Please report this to distutils: /Users/sconnell/Library/Application Support/ChimeraX/1.4/site- packages sysconfig: /Users/sconnell/Library/Python/3.9/lib/python/site-packages WARNING: Value for scheme.purelib does not match. Please report this to distutils: /Users/sconnell/Library/Application Support/ChimeraX/1.4/site- packages sysconfig: /Users/sconnell/Library/Python/3.9/lib/python/site-packages WARNING: Value for scheme.headers does not match. Please report this to distutils: /Users/sconnell/Library/Application Support/ChimeraX/include/python3.9/ChimeraX-ISOLDE sysconfig: /Users/sconnell/Library/Python/3.9/include/ChimeraX-ISOLDE WARNING: Value for scheme.scripts does not match. Please report this to distutils: /Users/sconnell/Library/Application Support/ChimeraX/bin sysconfig: /Users/sconnell/Library/Python/3.9/bin WARNING: Value for scheme.data does not match. Please report this to distutils: /Users/sconnell/Library/Application Support/ChimeraX sysconfig: /Users/sconnell/Library/Python/3.9 WARNING: Additional context: user = True home = None root = None prefix = None WARNING: Value for scheme.headers does not match. Please report this to distutils: /Users/sconnell/Library/Application Support/ChimeraX/include/python3.9/UNKNOWN sysconfig: /Users/sconnell/Library/Python/3.9/include/UNKNOWN WARNING: You are using pip version 21.3.1; however, version 22.1.2 is available. You should consider upgrading via the '/Applications/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -m pip install --upgrade pip' command. \--- pip standard output: \--- Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing ./ChimeraX_ISOLDE-1.4b1-cp39-cp39-macosx_10_13_x86_64.whl Requirement already satisfied: ChimeraX-Clipper~=0.18.0 in /Users/sconnell/Library/Application Support/ChimeraX/1.4/site-packages (from ChimeraX-ISOLDE==1.4b1) (0.18.0) Requirement already satisfied: ChimeraX-Core~=1.4.dev202203030220 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-ISOLDE==1.4b1) (1.4) Requirement already satisfied: ChimeraX-AtomicLibrary~=7.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-ISOLDE==1.4b1) (7.0) Requirement already satisfied: ChimeraX-Arrays~=1.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-ISOLDE==1.4b1) (1.0) Requirement already satisfied: ChimeraX-Atomic~=1.36 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-ISOLDE==1.4b1) (1.39.1) Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.4b1) (2.0.1) Requirement already satisfied: ChimeraX-Geometry~=1.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.4b1) (1.2) Requirement already satisfied: ChimeraX-PDB~=2.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.4b1) (2.6.6) Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.4b1) (1.0.2) Requirement already satisfied: ChimeraX-Graphics~=1.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.4b1) (1.1) Requirement already satisfied: ChimeraX-mmCIF~=2.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.4b1) (2.7) Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.4b1) (2.0.2) Requirement already satisfied: ChimeraX-DataFormats~=1.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.36->ChimeraX- ISOLDE==1.4b1) (1.2.2) Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.36->ChimeraX- ISOLDE==1.4b1) (1.5.1) Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.36->ChimeraX- ISOLDE==1.4b1) (1.9) Requirement already satisfied: ChimeraX-Surface~=1.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX- ISOLDE==1.4b1) (1.0) Requirement already satisfied: ChimeraX-UI~=1.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX- ISOLDE==1.4b1) (1.18.3) Requirement already satisfied: ChimeraX-IO~=1.0.1 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-PDB~=2.0->ChimeraX-Atomic~=1.36->ChimeraX- ISOLDE==1.4b1) (1.0.1) Requirement already satisfied: ChimeraX-MapData~=2.0 in /Applications/ChimeraX-1.4.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~=1.36->ChimeraX-ISOLDE==1.4b1) (2.0) Requirement already satisfied: ChimeraX-Map~=1.0 in /Applications/ChimeraX-1.4.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~=1.36->ChimeraX-ISOLDE==1.4b1) (1.1) Requirement already satisfied: ChimeraX-StdCommands~=1.0 in /Applications/ChimeraX-1.4.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~=1.36->ChimeraX-ISOLDE==1.4b1) (1.8) Requirement already satisfied: ChimeraX-SelInspector~=1.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX- Atomic~=1.36->ChimeraX-ISOLDE==1.4b1) (1.0) Requirement already satisfied: ChimeraX-MouseModes~=1.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX- Atomic~=1.36->ChimeraX-ISOLDE==1.4b1) (1.1) Requirement already satisfied: ChimeraX-MapSeries~=2.0 in /Applications/ChimeraX-1.4.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~=1.36->ChimeraX-ISOLDE==1.4b1) (2.1) Requirement already satisfied: ChimeraX-MapFilter~=2.0 in /Applications/ChimeraX-1.4.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~=1.36->ChimeraX-ISOLDE==1.4b1) (2.0) Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in /Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX- Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-ISOLDE==1.4b1) (1.0) Requirement already satisfied: ChimeraX-MapFit~=2.0 in /Applications/ChimeraX-1.4.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~=1.36->ChimeraX-ISOLDE==1.4b1) (2.0) Requirement already satisfied: ChimeraX-Dssp~=2.0 in /Applications/ChimeraX-1.4.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~=1.36->ChimeraX-ISOLDE==1.4b1) (2.0) Installing collected packages: ChimeraX-ISOLDE Successfully installed ChimeraX-ISOLDE-1.4b1 \--- Successfully installed ChimeraX-ISOLDE-1.4b1 Installed ChimeraX-ISOLDE (1.4b1) Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/triggerset.py"", line 134, in invoke return self._func(self._name, data) File ""/Users/sconnell/Library/Application Support/ChimeraX/1.4/site- packages/chimerax/isolde/toolbar.py"", line 127, in _set_button_starting_states self.set_enabled(key, True) File ""/Users/sconnell/Library/Application Support/ChimeraX/1.4/site- packages/chimerax/isolde/toolbar.py"", line 113, in set_enabled self.session.toolbar.set_enabled(enabled, tab, section, display_name) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/toolbar/manager.py"", line 164, in set_enabled tb.set_enabled(enabled, tab_title, section_title, button_title) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/toolbar/tool.py"", line 246, in set_enabled self.ttb.set_enabled(enabled, tab_title, section_title, button_title) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/tabbedtoolbar.py"", line 496, in set_enabled raise ValueError(f""Didn't find section '{section_title}' in tab '{tab_title}'"") ValueError: Didn't find section 'Main' in tab 'ISOLDE' Populating font family aliases took 519 ms. Replace uses of missing font family "".AppleSystemUIFont"" with one that exists to avoid this cost. Error processing trigger ""new frame"": ValueError: Didn't find section 'Main' in tab 'ISOLDE' File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/tabbedtoolbar.py"", line 496, in set_enabled raise ValueError(f""Didn't find section '{section_title}' in tab '{tab_title}'"") See log for complete Python traceback. > cd > /Users/sconnell/Downloads/GE81112-Oct20201/GE81112/maps/30S-GE81112-PID1604-73/Complex- > C_MergeAB/Starting_aln_models Current working directory is: /Users/sconnell/Downloads/GE81112-Oct20201/GE81112/maps/30S-GE81112-PID1604-73/Complex- C_MergeAB/Starting_aln_models > open > /Users/sconnell/Downloads/GE81112-Oct20201/GE81112/maps/30S-GE81112-PID1604-73/Complex- > C_MergeAB/Starting_aln_models/Combined_model_001.pdb Chain information for Combined_model_001.pdb #1 --- Chain | Description 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 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 v | No description available > isolde start > set selectionWidth 4 Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Users/sconnell/Library/Application Support/ChimeraX/1.4/site- packages/chimerax/isolde/cmd/cmd.py"", line 29, in isolde_start get_singleton(session) File ""/Users/sconnell/Library/Application Support/ChimeraX/1.4/site- packages/chimerax/isolde/cmd/cmd.py"", line 20, in get_singleton return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=create) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/tools.py"", line 193, in get_singleton tinst = tool_class(session, tool_name, **kw) File ""/Users/sconnell/Library/Application Support/ChimeraX/1.4/site- packages/chimerax/isolde/tool.py"", line 27, in __init__ isolde = Isolde(session) File ""/Users/sconnell/Library/Application Support/ChimeraX/1.4/site- packages/chimerax/isolde/isolde.py"", line 301, in __init__ session._isolde_tb.isolde_started() File ""/Users/sconnell/Library/Application Support/ChimeraX/1.4/site- packages/chimerax/isolde/toolbar.py"", line 136, in isolde_started self.set_enabled('Start ISOLDE', False) File ""/Users/sconnell/Library/Application Support/ChimeraX/1.4/site- packages/chimerax/isolde/toolbar.py"", line 113, in set_enabled self.session.toolbar.set_enabled(enabled, tab, section, display_name) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/toolbar/manager.py"", line 164, in set_enabled tb.set_enabled(enabled, tab_title, section_title, button_title) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/toolbar/tool.py"", line 246, in set_enabled self.ttb.set_enabled(enabled, tab_title, section_title, button_title) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/tabbedtoolbar.py"", line 496, in set_enabled raise ValueError(f""Didn't find section '{section_title}' in tab '{tab_title}'"") ValueError: Didn't find section 'Main' in tab 'ISOLDE' ValueError: Didn't find section 'Main' in tab 'ISOLDE' File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/tabbedtoolbar.py"", line 496, in set_enabled raise ValueError(f""Didn't find section '{section_title}' in tab '{tab_title}'"") See log for complete Python traceback. > isolde start OpenGL version: 4.1 NVIDIA-14.0.32 355.11.11.10.10.143 OpenGL renderer: NVIDIA GeForce GTX 675MX OpenGL Engine OpenGL vendor: NVIDIA Corporation Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: cocoa Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac13,2 Processor Name: Quad-Core Intel Core i7 Processor Speed: 3,4 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: 32 GB Boot ROM Version: 429.0.0.0.0 SMC Version (system): 2.11f16 Software: System Software Overview: System Version: macOS 10.15.7 (19H1922) Kernel Version: Darwin 19.6.0 Time since boot: 24 days 14:56 Graphics/Displays: NVIDIA GeForce GTX 675MX: Chipset Model: NVIDIA GeForce GTX 675MX Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 1 GB Vendor: NVIDIA (0x10de) Device ID: 0x11a2 Revision ID: 0x00a2 ROM Revision: 3707 Metal: Supported, feature set macOS GPUFamily1 v4 Displays: iMac: Display Type: LCD Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.10.8 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.18.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.1.5 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.4b1 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.9 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.18.3 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.0 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 23.1.0 qtconsole: 5.3.0 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect assigned normal Core Tristan Croll chimera-programmers all ChimeraX