id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3019 FitMap's map button updating after tool closed chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Darwin-18.7.0-x86_64-i386-64bit ChimeraX Version: 0.93 (2020-03-17) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.93 (2020-03-17) © 2016-2020 Regents of the University of California. All rights reserved. > open /Users/odonnjp06/Desktop/02april20/Figure4/figure4_color_helix.cxs > format session Log from Thu Apr 2 17:56:15 2020UCSF ChimeraX version: 0.93 (2020-03-17) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/odonnjp06/Desktop/02april20/TMDregion_sidechains.pdb Chain information for TMDregion_sidechains.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available H | No description available > set bgColor white > hide atoms > show surfaces > mlp Map values for surface ""TMDregion_sidechains.pdb_B SES surface"": minimum -28.15, mean -8.271, maximum 5.67 Map values for surface ""TMDregion_sidechains.pdb_H SES surface"": minimum -26.25, mean -8.895, maximum 5.281 Map values for surface ""TMDregion_sidechains.pdb_A SES surface"": minimum -24.51, mean 2.183, maximum 23.48 Map values for surface ""TMDregion_sidechains.pdb_C SES surface"": minimum -22.27, mean 1.172, maximum 23.63 Map values for surface ""TMDregion_sidechains.pdb_D SES surface"": minimum -28.68, mean 1.58, maximum 23.41 Map values for surface ""TMDregion_sidechains.pdb_E SES surface"": minimum -28.08, mean 1.081, maximum 23.61 > close #1 > open /Users/odonnjp06/Desktop/02april20/TMDregion_sidechains.pdb Chain information for TMDregion_sidechains.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 H | No description available > hide atoms > show surfaces > mlp Map values for surface ""TMDregion_sidechains.pdb_B SES surface"": minimum -28.15, mean -8.271, maximum 5.67 Map values for surface ""TMDregion_sidechains.pdb_H SES surface"": minimum -26.25, mean -8.895, maximum 5.281 Map values for surface ""TMDregion_sidechains.pdb_A SES surface"": minimum -24.51, mean 2.183, maximum 23.48 Map values for surface ""TMDregion_sidechains.pdb_C SES surface"": minimum -22.27, mean 1.172, maximum 23.63 Map values for surface ""TMDregion_sidechains.pdb_D SES surface"": minimum -28.68, mean 1.58, maximum 23.41 Map values for surface ""TMDregion_sidechains.pdb_E SES surface"": minimum -28.08, mean 1.081, maximum 23.61 Map values for surface ""TMDregion_sidechains.pdb_F SES surface"": minimum -28.45, mean -9.607, maximum 15.68 > close #1 > open /Users/odonnjp06/Desktop/02april20/EMC_sidechains.pdb Chain information for EMC_sidechains.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | 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 > hide atoms > show surfaces > mlp Map values for surface ""EMC_sidechains.pdb_B SES surface"": minimum -29.97, mean -2.561, maximum 24.98 Map values for surface ""EMC_sidechains.pdb_H SES surface"": minimum -28.72, mean -3.455, maximum 22.28 Map values for surface ""EMC_sidechains.pdb_A SES surface"": minimum -24.51, mean 2.183, maximum 23.48 Map values for surface ""EMC_sidechains.pdb_C SES surface"": minimum -22.27, mean 1.172, maximum 23.63 Map values for surface ""EMC_sidechains.pdb_D SES surface"": minimum -28.68, mean 1.58, maximum 23.41 Map values for surface ""EMC_sidechains.pdb_E SES surface"": minimum -28.08, mean 1.081, maximum 23.61 Map values for surface ""EMC_sidechains.pdb_G SES surface"": minimum -22.11, mean 4.355, maximum 21.21 Map values for surface ""EMC_sidechains.pdb_K SES surface"": minimum -29.9, mean -3.411, maximum 26.26 Map values for surface ""EMC_sidechains.pdb_L SES surface"": minimum -23.7, mean 1.704, maximum 24.28 Map values for surface ""EMC_sidechains.pdb_I SES surface"": minimum -24.68, mean -2.057, maximum 30.35 Map values for surface ""EMC_sidechains.pdb_J SES surface"": minimum -21.84, mean 2.181, maximum 23.27 > hide #1.12 models > show #1.12 models > hide #1.12 models > show #1.12 models > select #1.12 586 atoms, 1 model selected > ~select #1.12 1 model selected > select #1.11 7217 atoms, 1 model selected > ~select #1.11 1 model selected > select #1.10 505 atoms, 1 model selected > ~select #1.10 1 model selected > open /Users/odonnjp06/Desktop/cryosparc_P1_J425__localfilter_flip.mrc Opened cryosparc_P1_J425__localfilter_flip.mrc, grid size 224,224,224, pixel 1.38, shown at level 0.148, step 1, values float32 > hide #!2 models > toolshed show ""Side View"" > lighting simple > hide #!1 models > show #!2 models > volume #2 level 0.2198 > show #!1 models > volume #2 level 0.1719 > open /Users/odonnjp06/Desktop/01april20/EMC-coot-3.pdb Summary of feedback from opening /Users/odonnjp06/Desktop/01april20/EMC- coot-3.pdb --- warnings | End residue of secondary structure not found: HELIX 9 9 LEU G 161 PRO G 180 1 20 End residue of secondary structure not found: HELIX 53 53 SER D 127 SER D 153 1 27 Start residue of secondary structure not found: HELIX 54 54 ALA D 161 ALA D 166 1 6 Chain information for EMC-coot-3.pdb #3 --- 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 > hide atoms > show cartoons > hide #!1 models > color #!3 bychain > open /Users/odonnjp06/Desktop/cryosparc_P1_J425__localfilter_flip.mrc Opened cryosparc_P1_J425__localfilter_flip.mrc, grid size 224,224,224, pixel 1.38, shown at level 0.148, step 1, values float32 > volume #4 color #e6e6e6 > volume #4 color #cccccc > volume #4 color #b3b3b3 > hide #!4 models > volume #4 color #cccccc > volume #4 color #ffcc99 > lighting soft > volume #4 color #b3b3b3 > volume #4 level 0.11 > volume #4 level 0.15 > volume #4 level 0.14 > volume #4 level 0.16 > volume #4 level 0.12 > volume #2 level 0.21 > volume #2 level 0.2 > volume #2 level 0.19 > volume #4 color #b3b3b37b > volume #2 color #ffcc99 > volume #2 color #ffcc997a > volume #4 level 0.14 > volume #4 level 0.16 > volume #4 level 0.15 > volume #4 level 0.14 > volume #4 level 0.13 > volume #4 level 0.14 > close #3 > open /Users/odonnjp06/Desktop/02april20/EMC_sidechains.pdb Chain information for EMC_sidechains.pdb #3 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | 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 > hide #!3 atoms > show #!3 cartoons > volume #4 level 0.15 > volume #4 level 0.16 > volume #4 level 0.155 > volume #4 level 0.15 > volume #4 level 0.145 > volume #4 level 0.16 > volume #4 level 0.15 Expected an objects specifier or a view name or a keyword > view name slice1 > volume #2 color #4c4c4c > hide #!2 models > show #!2 models > show #!4 models > hide #!4 models Missing or invalid ""surfaces"" argument: invalid surfaces specifier > surface dust #* size 10 > surface dust #* size 15 > surface dust #* size 10 > hide #!2 models > show #!2 models > view name slice2 > show #!1 models > hide #!1 models > open /Users/odonnjp06/Desktop/01april20/EMC-coot-3.pdb Summary of feedback from opening /Users/odonnjp06/Desktop/01april20/EMC- coot-3.pdb --- warnings | End residue of secondary structure not found: HELIX 9 9 LEU G 161 PRO G 180 1 20 End residue of secondary structure not found: HELIX 53 53 SER D 127 SER D 153 1 27 Start residue of secondary structure not found: HELIX 54 54 ALA D 161 ALA D 166 1 6 Chain information for EMC-coot-3.pdb #5 --- 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 > hide #!3,5 atoms > show #!3,5 cartoons > hide #!3 models > hide #!5 models > show #!5 models > surface dust #* size 12 > show #!4 models > lighting soft > lighting simple > lighting soft > graphics silhouettes true > graphics silhouettes false > hide #!2 models > hide #!4 models > view name slice3 > view name slice4 > save session /Users/odonnjp06/Desktop/02april20/Figure4/figure4_tests.cxs > includeMaps true > save image cartoon.tif format tiff width 4800 height 3409 > transparentBackground true > view list Named views: slice1, slice2, slice3, slice4 > view slice4 > view slice3 > view slice2 > view slice1 > view slice2 > view slice3 > show #!4 models > hide #!5 models > show #!3 models > hide #!3 models > show #!2 models > hide #!4 models > save image 0p19contour.tif format tiff width 4800 height 3409 > transparentBackground true > hide #!2 models > show #!4 models > save image 0p15contour.tif format tiff width 4800 height 3409 > transparentBackground true > save image 0p15_bcontour.tif format tiff width 4800 height 3409 > transparentBackground true > show #!5 models > show #!2 models > hide #!4 models > lighting simple > lighting shadows true > lighting shadows false > color #!5 bychain > volume #2 level 0.21 > hide #!5 models > show #!5 models > view slice4 > hide #!5 models > show #!5 models > dssp > save session /Users/odonnjp06/Desktop/02april20/Figure4/figure4_tests.cxs > includeMaps true > close #1 > close #5 > open /Users/odonnjp06/Desktop/01april20/EMC-coot-3-dss.pdb Chain information for EMC-coot-3-dss.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 > hide #!1 cartoons > hide #!1 surfaces > show #!1 cartoons > hide #!1 atoms > molmap #1 8 > close #5 > molmap #1/A 6 > close #5 > molmap #1/A 7 > volume subtract #5 #2 > volume subtract #2 #5 > hide #!6 models > close #7 > show #!2 models > color #1/A black > color #1/A:1-961 red > color #1/A black Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide #1/A:1-961 > hide #1/A:1-961 > hide #1/A:1-961 cartoons > show #1/A:1-961 cartoons > volume #2 level 0.19 > color #1/A wheat > hide #1/B cartoons > hide #1/H cartoons > hide #1/A:1-961 cartoons > hide #1/G:1-126 cartoons > hide #1/I cartoons Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #1/C steel blue > color #1/F teal > color #1/E firebrick > color #1/F orange > color #1/F turquoise > color #1/G orange > color #1/D orange > color #1/G olive drab > save session > /Users/odonnjp06/Desktop/02april20/Figure4/figure4_color_helix.cxs > includeMaps true opened ChimeraX session > show #!3 models > hide #!2 models > hide #!3 models > hide #!1 models > close #6 > open /Users/odonnjp06/Desktop/06april20/temp_pdbs/EMC_rb_temp-coot-0.pdb Chain information for EMC_rb_temp-coot-0.pdb #6 --- 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 H | No description available > hide #!6 atoms > show #!6 cartoons > show #!2 models > close #5 > close #3 > close #1 > close #6 > open /Users/odonnjp06/Desktop/06april20/temp_pdbs/EMC_rb_temp-coot-1.pdb Chain information for EMC_rb_temp-coot-1.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 H | No description available X | No description available Y | No description available Z | No description available > hide atoms > show cartoons > show atoms > hide atoms > hide #1.1 models > select #1/X 3540 atoms, 3616 bonds, 4 pseudobonds, 2 models selected > ui mousemode rightMode ""rotate selected models"" > toolshed show ""Fit in Map"" > hide #!1 target m > close #1 > open /Users/odonnjp06/Desktop/06april20/temp_pdbs/EMC_rb_temp-NoProp2.pdb Chain information for EMC_rb_temp-NoProp2.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 H | No description available Y | No description available Z | No description available > open /Users/odonnjp06/Desktop/06april20/temp_pdbs/EMC1prop2_chainX.pdb Chain information for EMC1prop2_chainX.pdb #3 --- Chain | Description X | No description available > hide atoms > show cartoons > hide #!2 models > show #!2 models > hide #!1 models Fit molecule EMC1prop2_chainX.pdb (#3) to map cryosparc_P1_J425__localfilter_flip.mrc (#2) using 3525 atoms average map value = 0.197, steps = 68 shifted from previous position = 1.36 rotated from previous position = 3.22 degrees atoms outside contour = 1645, contour level = 0.19 Position of EMC1prop2_chainX.pdb (#3) relative to cryosparc_P1_J425__localfilter_flip.mrc (#2) coordinates: Matrix rotation and translation 0.99845682 -0.04220857 -0.03608897 12.75129353 0.04188817 0.99907629 -0.00958889 -4.61556301 0.03646037 0.00806239 0.99930258 -6.36384757 Axis 0.15695624 -0.64511276 0.74779293 Axis point 113.35027455 297.13932046 0.00000000 Rotation angle (degrees) 3.22343973 Shift along axis 0.22011345 Fit map EMC1prop2_chainX.pdb map 5 in map cryosparc_P1_J425__localfilter_flip.mrc using 13152 points correlation = 0.7189, correlation about mean = 0.1509, overlap = 912.8 steps = 108, shift = 0.266, angle = 1.01 degrees Position of EMC1prop2_chainX.pdb map 5 (#6) relative to cryosparc_P1_J425__localfilter_flip.mrc (#2) coordinates: Matrix rotation and translation 0.99924099 -0.02795213 -0.02713144 8.87771614 0.02785457 0.99960411 -0.00396710 -3.40795558 0.02723159 0.00320836 0.99962400 -4.25952823 Axis 0.09171303 -0.69484018 0.71329226 Axis point 123.21831193 313.78634370 0.00000000 Rotation angle (degrees) 2.24193104 Shift along axis 0.14389818 Average map value = 0.1968 for 3525 atoms, 1645 outside contour Fit map EMC1prop2_chainX.pdb map 5 in map cryosparc_P1_J425__localfilter_flip.mrc using 13152 points correlation = 0.7211, correlation about mean = 0.1571, overlap = 911.6 steps = 88, shift = 1.15, angle = 3.37 degrees Position of EMC1prop2_chainX.pdb map 5 (#5) relative to cryosparc_P1_J425__localfilter_flip.mrc (#2) coordinates: Matrix rotation and translation 0.99570498 -0.08551363 -0.03548246 19.35600878 0.08506693 0.99627805 -0.01391640 -10.44143614 0.03654044 0.01083824 0.99927340 -6.27329670 Axis 0.13251270 -0.38554183 0.91312534 Axis point 128.39892265 218.56490878 0.00000000 Rotation angle (degrees) 5.35951246 Shift along axis 0.86222127 Average map value = 0.1965 for 3525 atoms, 1657 outside contour > select #3 3525 atoms, 3602 bonds, 2 pseudobonds, 2 models selected Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 300, in _model_moved xf = self._relative_position() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 311, in _relative_position fatoms = self._fit_atoms() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 249, in _fit_atoms m = self._object_menu.value File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 250, in value self._sleep_check() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 78, in _sleep_check if not self._handlers and not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ModelMenuButton has been deleted Error processing trigger ""model position changed"": RuntimeError: wrapped C/C++ object of type ModelMenuButton has been deleted File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 78, in _sleep_check if not self._handlers and not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 300, in _model_moved xf = self._relative_position() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 311, in _relative_position fatoms = self._fit_atoms() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 249, in _fit_atoms m = self._object_menu.value File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 250, in value self._sleep_check() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 78, in _sleep_check if not self._handlers and not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ModelMenuButton has been deleted Error processing trigger ""model position changed"": RuntimeError: wrapped C/C++ object of type ModelMenuButton has been deleted File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 78, in _sleep_check if not self._handlers and not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 300, in _model_moved xf = self._relative_position() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 311, in _relative_position fatoms = self._fit_atoms() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 249, in _fit_atoms m = self._object_menu.value File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 250, in value self._sleep_check() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 78, in _sleep_check if not self._handlers and not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ModelMenuButton has been deleted Error processing trigger ""model position changed"": RuntimeError: wrapped C/C++ object of type ModelMenuButton has been deleted File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 78, in _sleep_check if not self._handlers and not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 300, in _model_moved xf = self._relative_position() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 311, in _relative_position fatoms = self._fit_atoms() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 249, in _fit_atoms m = self._object_menu.value File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 250, in value self._sleep_check() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 78, in _sleep_check if not self._handlers and not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ModelMenuButton has been deleted Error processing trigger ""model position changed"": RuntimeError: wrapped C/C++ object of type ModelMenuButton has been deleted File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 78, in _sleep_check if not self._handlers and not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 300, in _model_moved xf = self._relative_position() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 311, in _relative_position fatoms = self._fit_atoms() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 249, in _fit_atoms m = self._object_menu.value File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 250, in value self._sleep_check() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 78, in _sleep_check if not self._handlers and not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ModelMenuButton has been deleted Error processing trigger ""model position changed"": RuntimeError: wrapped C/C++ object of type ModelMenuButton has been deleted File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 78, in _sleep_check if not self._handlers and not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 300, in _model_moved xf = self._relative_position() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 311, in _relative_position fatoms = self._fit_atoms() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 249, in _fit_atoms m = self._object_menu.value File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 250, in value self._sleep_check() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 78, in _sleep_check if not self._handlers and not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ModelMenuButton has been deleted Error processing trigger ""model position changed"": RuntimeError: wrapped C/C++ object of type ModelMenuButton has been deleted File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 78, in _sleep_check if not self._handlers and not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 300, in _model_moved xf = self._relative_position() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 311, in _relative_position fatoms = self._fit_atoms() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 249, in _fit_atoms m = self._object_menu.value File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 250, in value self._sleep_check() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 78, in _sleep_check if not self._handlers and not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ModelMenuButton has been deleted Error processing trigger ""model position changed"": RuntimeError: wrapped C/C++ object of type ModelMenuButton has been deleted File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 78, in _sleep_check if not self._handlers and not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 300, in _model_moved xf = self._relative_position() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 311, in _relative_position fatoms = self._fit_atoms() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 249, in _fit_atoms m = self._object_menu.value File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 250, in value self._sleep_check() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 78, in _sleep_check if not self._handlers and not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ModelMenuButton has been deleted Error processing trigger ""model position changed"": RuntimeError: wrapped C/C++ object of type ModelMenuButton has been deleted File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 78, in _sleep_check if not self._handlers and not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 300, in _model_moved xf = self._relative_position() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 311, in _relative_position fatoms = self._fit_atoms() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 249, in _fit_atoms m = self._object_menu.value File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 250, in value self._sleep_check() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 78, in _sleep_check if not self._handlers and not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ModelMenuButton has been deleted Error processing trigger ""model position changed"": RuntimeError: wrapped C/C++ object of type ModelMenuButton has been deleted File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 78, in _sleep_check if not self._handlers and not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 300, in _model_moved xf = self._relative_position() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 311, in _relative_position fatoms = self._fit_atoms() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 249, in _fit_atoms m = self._object_menu.value File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 250, in value self._sleep_check() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 78, in _sleep_check if not self._handlers and not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ModelMenuButton has been deleted Error processing trigger ""model position changed"": RuntimeError: wrapped C/C++ object of type ModelMenuButton has been deleted File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 78, in _sleep_check if not self._handlers and not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 300, in _model_moved xf = self._relative_position() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 311, in _relative_position fatoms = self._fit_atoms() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 249, in _fit_atoms m = self._object_menu.value File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 250, in value self._sleep_check() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 78, in _sleep_check if not self._handlers and not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ModelMenuButton has been deleted Error processing trigger ""model position changed"": RuntimeError: wrapped C/C++ object of type ModelMenuButton has been deleted File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 78, in _sleep_check if not self._handlers and not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 300, in _model_moved xf = self._relative_position() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 311, in _relative_position fatoms = self._fit_atoms() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/fit/fitgui.py"", line 249, in _fit_atoms m = self._object_menu.value File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 250, in value self._sleep_check() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 78, in _sleep_check if not self._handlers and not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ModelMenuButton has been deleted Error processing trigger ""model position changed"": RuntimeError: wrapped C/C++ object of type ModelMenuButton has been deleted File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 78, in _sleep_check if not self._handlers and not hasattr(self, '_recursion'): See log for complete Python traceback. OpenGL version: 4.1 INTEL-12.10.12 OpenGL renderer: Intel(R) UHD Graphics 617 OpenGL vendor: Intel Inc. }}} " defect closed normal General Controls can't reproduce Tom Goddard all ChimeraX