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#3019 closed defect (can't reproduce)
FitMap's map button updating after tool closed
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | General Controls | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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.
Change History (3)
comment:1 by , 6 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → General Controls |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → FitMap's map button updating after tool closed |
comment:2 by , 6 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
comment:3 by , 6 years ago
Fixed.
I also could not reproduce it. But the basic problem was clearly that the Fit Map tool was closed and it did not remove the handler that updates correlation coefficient when the "Real-time correlation / average update" option has been enabled. I added code to remove that handler when the tool is closed and tested it with some debugging print statements.
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Tried a few simple things, but couldn't reproduce.