id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3186 Save options widgets deleted tomasiak@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Darwin-17.7.0-x86_64-i386-64bit ChimeraX Version: 1.0 (2020-05-07) Description Tried to save a map generated from a model and said that a there was a missing C++ wrapper. Log: UCSF ChimeraX version: 1.0rc202005070439 (2020-05-07) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/tomasiak/projects/ycf1/em/phenix/run1/ResolveCryoEM_4/denmod_map.ccp4 Opened denmod_map.ccp4, grid size 136,129,176, pixel 1.05, shown at level 0.371, step 1, values float32 > volume #1 level 0.177 > open /Users/tomasiak/projects/ycf1/em/coot/run2/ycf1_chimerax-coot-0.pdb Chain information for ycf1_chimerax-coot-0.pdb #2 --- Chain | Description B | No description available Drag select of 17 residues > select up 2140 atoms, 2158 bonds, 1 model selected > select up 22471 atoms, 22695 bonds, 1 model selected > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" Drag select of > toolshed show ""Fit in Map"" Fit molecule ycf1_chimerax-coot-0.pdb (#2) to map denmod_map.ccp4 (#1) using 22471 atoms average map value = 0.1486, steps = 144 shifted from previous position = 6.57 rotated from previous position = 7.7 degrees atoms outside contour = 13923, contour level = 0.17704 Position of ycf1_chimerax-coot-0.pdb (#2) relative to denmod_map.ccp4 (#1) coordinates: Matrix rotation and translation -0.99999980 -0.00054994 -0.00031318 231.01848424 -0.00055022 0.99999945 0.00088914 0.08374962 0.00031269 0.00088931 -0.99999955 229.78424368 Axis 0.00027222 -0.99999986 -0.00044311 Axis point 115.49127652 0.00000000 114.91017685 Rotation angle (degrees) 179.98207003 Shift along axis -0.12268116 > save /Users/tomasiak/projects/ycf1/em/coot/run2/ycf1_chimerax- > coot-0_resolve.pdb > show target ab > select H 11217 atoms, 1 model selected > hide sel target a Drag select of > toolshed show ""Side View"" Drag select of 1 denmod_map.ccp4 , 4 atoms, 3 residues, 2 bonds Drag select of > ui mousemode right pivot > ui mousemode right select Drag select of > hide #!2 models > hide #!1 models > show #!2 models Drag select of 1 atoms > select clear Drag select of 1 atoms > view sel Drag select of > ui mousemode right clip > show #!1 models > ui mousemode right translate > volume #1 level 0.3396 > volume #1 level 0.1083 > volume #1 level 0.202 > ui mousemode right clip > open /Users/tomasiak/projects/ycf1/em/phenix/run1/flip_987_mask.mrc Opened flip_987_mask.mrc, grid size 220,220,220, pixel 1.05, shown at level 1, step 1, values float32 > hide #!3 models > show #!3 models > volume #3 level 1 Drag select of 1 denmod_map.ccp4 , 3 flip_987_mask.mrc > select clear > volume #3 level 1 > molmap #2 6 fullMap True Expected a keyword > molmap #2 6 onGrid #1 > ui mousemode right translate Traceback (most recent call last): File ""/Applications/ChimeraX-1.0-rc-2020.05.07.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-2020.05.07.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-2020.05.07.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-2020.05.07.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-2020.05.07.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-2020.05.07.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 QLabel has been deleted RuntimeError: wrapped C/C++ object of type QLabel has been deleted File ""/Applications/ChimeraX-1.0-rc-2020.05.07.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-2020.05.07.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-2020.05.07.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-2020.05.07.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-2020.05.07.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-2020.05.07.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-2020.05.07.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 QLabel has been deleted RuntimeError: wrapped C/C++ object of type QLabel has been deleted File ""/Applications/ChimeraX-1.0-rc-2020.05.07.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-1.68.24 OpenGL renderer: AMD Radeon Pro 575 OpenGL Engine OpenGL vendor: ATI Technologies Inc.Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac18,3 Processor Name: Intel Core i7 Processor Speed: 4.2 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 8 MB Memory: 16 GB Boot ROM Version: 180.0.0.0.0 SMC Version (system): 2.41f1 Software: System Software Overview: System Version: macOS 10.13.6 (17G11023) Kernel Version: Darwin 17.7.0 Time since boot: 45 days 53 minutes Graphics/Displays: Radeon Pro 575: Chipset Model: Radeon Pro 575 Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Dynamic, Max): 4096 MB Vendor: AMD (0x1002) Device ID: 0x67df Revision ID: 0x00c4 ROM Revision: 113-D000AA-931 VBIOS Version: 113-D0001A1P-025 EFI Driver Version: 01.00.931 Metal: Supported, feature set macOS GPUFamily1 v3 Displays: iMac: Display Type: Built-In Retina LCD Resolution: 5120 x 2880 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No DELL P2715Q: Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus) UI Looks like: 2560 x 1440 @ 30 Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: X24K178B841L Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: No Connection Type: DVI or HDMI Adapter Firmware Version: 7.55 }}} " defect closed normal Input/Output duplicate all ChimeraX