id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5226 Save dialog: wrapped C/C++ object of type SaveOptionsWidget has been deleted Dbarrero@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Darwin-19.4.0-x86_64-i386-64bit ChimeraX Version: 1.0 (2020-05-08) Description (Describe the actions that caused this problem to occur here) Selected a chain, changed color, and clicked save Log: UCSF ChimeraX version: 1.0rc202005080235 (2020-05-08) © 2016-2020 Regents of the University of California. All rights reserved. > open /Users/dbarrero/Desktop/dam1_phos_sites.cxs format session Log from Fri Jul 16 09:42:07 2021UCSF ChimeraX version: 1.0rc202005080235 (2020-05-08) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/dbarrero/Desktop/PDB_FILES/6cfz.pdb format pdb 6cfz.pdb title: Structure of the dash/DAM1 complex shows its role At the yeast kinetochore- microtubule interface [more info...] Chain information for 6cfz.pdb #1 --- Chain | Description A | DASH/DAM1 complex subunit ASK1 B | DASH/DAM1 complex subunit DAD3 C | DASH/DAM1 complex subunit DAD2 D | DASH/DAM1 complex subunit DUO1 E | DASH/DAM1 complex subunit DAD4 F | DASH/DAM1 complex subunit DAD1 G | DASH/DAM1 complex subunit HSK3 H | DASH/DAM1 complex subunit DAM1 I | DASH/DAM1 complex subunit SPC19 J | DASH/DAM1 complex subunit SPC34 > open /Users/dbarrero/Desktop/6cfz.cif 6cfz.cif title: Structure of the DASH/Dam1 complex shows its role at the yeast kinetochore- microtubule interface [more info...] Chain information for 6cfz.cif #2 --- Chain | Description A | Ask1 B | Dad3 C | Dad2 D | Duo1 E | Dad4 F | Dad1,Dad1 G | Hsk3 H | Dam1 I | Spc19 J | Spc34 6cfz.cif mmCIF Assemblies --- 1| complete point assembly 2| point asymmetric unit 3| point asymmetric unit, std point frame > hide #!2 models > show #!2 models > hide #2.1 models > show #2.1 models > hide #!1 models > sym biomt Missing or invalid ""structures"" argument: invalid atomic structures specifier > sym #2 assembly 1 > view > show #!1 models > hide #2.1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > view #!1 clip false > show #!1 cartoons > style #!1 stick Changed 12006 atom styles > hide #!1 atoms > lighting flat > lighting flat > lighting shadows true intensity 0.5 > graphics silhouettes false > lighting shadows false > lighting full > lighting soft > lighting simple > lighting soft > select 1/B:48 Expected an objects specifier or a keyword > select #1/B:48 11 atoms, 10 bonds, 1 model selected > color sel orange red > show sel target ab > graphics silhouettes true > select clear > select #1/B:48 11 atoms, 10 bonds, 1 model selected > toolshed show ""Color Actions"" > toolshed show ""Color Actions"" > color sel byelement > select clear > select #1/B:52 14 atoms, 13 bonds, 1 model selected > color sel orange red > toolshed show ""Color Actions"" > color sel byelement > show sel target ab > select clear > select #1/J:145 7 atoms, 6 bonds, 1 model selected > color sel orange red > show sel target ab > toolshed show ""Color Actions"" > color sel byelement > show sel target ab > select #1/J:192 24 atoms, 23 bonds, 1 model selected > color sel orange red > show sel target ab > color sel byelement > select clear > select #1/J:199 17 atoms, 16 bonds, 1 model selected > color sel orange red > show sel target ab > color sel byelement > select clear > select #1/A:26 14 atoms, 13 bonds, 1 model selected > color sel orange red > show sel target ab > color sel byelement > select clear > view #!1 clip false > show #!3 models > style #!1,3 stick Changed 24012 atom styles > hide #!1,3 atoms > hide #!1,3 atoms > show #!1,3 atoms > show #!1,3 cartoons > hide #!1,3 atoms > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > undo > undo > undo > undo > undo > undo > undo > undo > undo > undo > select #1/A:26 14 atoms, 13 bonds, 1 model selected > select #1/J:199 17 atoms, 16 bonds, 1 model selected > select #1/A:26 14 atoms, 13 bonds, 1 model selected > hide #!3 models > show #!3 models > show sel cartoons > sym #2 assembly 1 > view > select #1 12006 atoms, 12093 bonds, 4 pseudobonds, 2 models selected > ~select #1 Nothing selected > select #3.1 2 pseudobonds, 1 model selected > select #3 12006 atoms, 12093 bonds, 2 pseudobonds, 2 models selected > close > open /Users/dbarrero/Desktop/6cfz.cif format mmcif 6cfz.cif title: Structure of the DASH/Dam1 complex shows its role at the yeast kinetochore- microtubule interface [more info...] Chain information for 6cfz.cif #1 --- Chain | Description A | Ask1 B | Dad3 C | Dad2 D | Duo1 E | Dad4 F | Dad1,Dad1 G | Hsk3 H | Dam1 I | Spc19 J | Spc34 6cfz.cif mmCIF Assemblies --- 1| complete point assembly 2| point asymmetric unit 3| point asymmetric unit, std point frame > style stick Changed 12006 atom styles > show cartoons > hide atoms > sym #1 assembly 1 > view > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > view #!2 clip false > view #!2 clip false > lighting soft > set bgColor gray > select #1/A:26 14 atoms, 13 bonds, 1 model selected > color sel orange red > show sel target ab > select #2 12006 atoms, 12093 bonds, 2 pseudobonds, 2 models selected > show #!2 models > select #1/A:26 14 atoms, 13 bonds, 1 model selected > color sel red > select #2/A:26 14 atoms, 13 bonds, 1 model selected > color sel orange red > show sel target ab > select #2/b:48 11 atoms, 10 bonds, 1 model selected > color sel orange red > show sel target ab > select #1/b:48 11 atoms, 10 bonds, 1 model selected > show sel target ab > color sel orange red > select #1/b:52 14 atoms, 13 bonds, 1 model selected > color sel orange red > show sel target ab > select #2/b:52 14 atoms, 13 bonds, 1 model selected > show sel target ab > color sel orange red > select #2/J:145 7 atoms, 6 bonds, 1 model selected > color sel orange red > show sel target ab > select #1/J:145 7 atoms, 6 bonds, 1 model selected > color sel orange red > select #1/J:192 24 atoms, 23 bonds, 1 model selected > color sel orange red > show sel target ab > select #2/J:192 24 atoms, 23 bonds, 1 model selected > color sel orange red > show sel target ab > select #2/J:199 17 atoms, 16 bonds, 1 model selected > show sel target ab > color sel orange red > show sel target ab > color sel orange red > select #2/A:26 14 atoms, 13 bonds, 1 model selected > select clear > save /Users/dbarrero/Desktop/dam1_phos_sites.cxs opened ChimeraX session > hide #!2 models > select #1 12006 atoms, 12093 bonds, 2 pseudobonds, 2 models selected > hide sel atoms > color (#!1 & sel) dim gray > set bgColor white > select /C 2448 atoms, 2458 bonds, 2 pseudobonds, 4 models selected > color (#!1 & sel) cornflower blue > select /A 2148 atoms, 2170 bonds, 2 models selected > toolshed show ""Color Actions"" > color sel gold > select #1 12006 atoms, 12093 bonds, 2 pseudobonds, 2 models selected > ~select #1 Nothing selected > save /Users/dbarrero/Desktop/Ian:bakerlab/Dad2_Ask1_decamer.png width 1032 > height 760 supersample 3 > toolshed show ""Show Sequence Viewer"" > sequence chain #1/A #2/A Alignment identifier is 1 > select #1 12006 atoms, 12093 bonds, 2 pseudobonds, 2 models selected > toolshed show ""Show Sequence Viewer"" > sequence chain #1/A #2/A Alignment identifier is 1 > save /Users/dbarrero/Desktop/Ian:bakerlab/Dad2_Ask1.cxs > select #1 12006 atoms, 12093 bonds, 2 pseudobonds, 2 models selected > color (#!1 & sel) dark gray > color (#!1 & sel) dim gray > select /C 2448 atoms, 2458 bonds, 2 pseudobonds, 4 models selected > color (#!1 & sel) cornflower blue > select /G 1722 atoms, 1734 bonds, 2 models selected > toolshed show ""Color Actions"" > color sel gold > select #1 12006 atoms, 12093 bonds, 2 pseudobonds, 2 models selected > ~select #1 Nothing selected > save /Users/dbarrero/Desktop/Ian:bakerlab/Dad2_Hsk3.cxs > save /Users/dbarrero/Desktop/Ian:bakerlab/dad2_hsk3_decamer.jpg width 1032 > height 760 supersample 3 > select #1 12006 atoms, 12093 bonds, 2 pseudobonds, 2 models selected > select /G 1722 atoms, 1734 bonds, 2 models selected > color (#!1 & sel) dim gray > select /I 3324 atoms, 3348 bonds, 2 models selected > toolshed show ""Color Actions"" > color sel gold > select #1 12006 atoms, 12093 bonds, 2 pseudobonds, 2 models selected > ~select #1 Nothing selected Traceback (most recent call last): File ""/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 1543, in action.triggered.connect(lambda arg, cb = callback: cb()) File ""/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 111, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 122, in show_save_file_dialog _dlg.display(session, **kw) File ""/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 24, in display self._customize_dialog(session, dialog) File ""/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 86, in _customize_dialog self._format_selected(session, dialog) File ""/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 98, in _format_selected self._options_layout.addWidget(self._current_option) RuntimeError: wrapped C/C++ object of type SaveOptionsWidget has been deleted RuntimeError: wrapped C/C++ object of type SaveOptionsWidget has been deleted File ""/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 98, in _format_selected self._options_layout.addWidget(self._current_option) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 1543, in action.triggered.connect(lambda arg, cb = callback: cb()) File ""/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 111, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 122, in show_save_file_dialog _dlg.display(session, **kw) File ""/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 24, in display self._customize_dialog(session, dialog) File ""/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 86, in _customize_dialog self._format_selected(session, dialog) File ""/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 98, in _format_selected self._options_layout.addWidget(self._current_option) RuntimeError: wrapped C/C++ object of type SaveOptionsWidget has been deleted RuntimeError: wrapped C/C++ object of type SaveOptionsWidget has been deleted File ""/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/save_command/dialog.py"", line 98, in _format_selected self._options_layout.addWidget(self._current_option) See log for complete Python traceback. OpenGL version: 4.1 ATI-3.8.24 OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine OpenGL vendor: ATI Technologies Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 6-Core Intel Core i7 Processor Speed: 2.6 GHz Number of Processors: 1 Total Number of Cores: 6 L2 Cache (per Core): 256 KB L3 Cache: 12 MB Hyper-Threading Technology: Enabled Memory: 32 GB Boot ROM Version: 1037.100.362.0.0 (iBridge: 17.16.14281.0.0,0) Software: System Software Overview: System Version: macOS 10.15.4 (19E287) Kernel Version: Darwin 19.4.0 Time since boot: 16 days 13:13 Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0000 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal: Supported, feature set macOS GPUFamily2 v1 AMD Radeon Pro 5300M: Chipset Model: AMD Radeon Pro 5300M Type: GPU Bus: PCIe PCIe Lane Width: x8 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0043 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32207P1-019 Option ROM Version: 113-D32207P1-019 EFI Driver Version: 01.01.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal: Supported, feature set macOS GPUFamily2 v1 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal DELL U2720Q: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60 Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: FQYMT83 Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: No Connection Type: Thunderbolt/DisplayPort }}} " defect closed normal Input/Output duplicate all ChimeraX