id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2374 ISOLDE: multiple different errors chimerax-bug-report@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Linux-4.15.0-54-generic-x86_64-with-debian-buster-sid ChimeraX Version: 0.9 (2019-06-06) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.9 (2019-06-06) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > toolshed show ViewDockX No suitable models found for ViewDockX > open /net/rossmann/home/wang83/Desktop/cryosparc_VH7D_emptyNK/shlth_1_rsr3-coot-3.pdb Summary of feedback from opening /net/rossmann/home/wang83/Desktop/cryosparc_VH7D_emptyNK/shlth_1_rsr3-coot-3.pdb --- warnings | Ignored bad PDB record found on line 47 GEOMETRY RESTRAINTS LIBRARY: CDL v1.2 Ignored bad PDB record found on line 48 DEVIATIONS FROM IDEAL VALUES. Ignored bad PDB record found on line 49 BOND : 0.006 0.072 7064 Ignored bad PDB record found on line 50 ANGLE : 1.617 53.274 12727 Ignored bad PDB record found on line 51 CHIRALITY : 0.063 0.479 593 16 messages similar to the above omitted Start residue of secondary structure not found: HELIX 1 1 ALA 83 PHE 90 1 8 Start residue of secondary structure not found: HELIX 2 2 GLN 95 ASN 101 1 7 Start residue of secondary structure not found: HELIX 3 3 PHE 103 PHE 104 1 2 Start residue of secondary structure not found: HELIX 4 4 ILE 147 LEU 150 1 4 Start residue of secondary structure not found: HELIX 6 6 ILE 260 VAL 267 1 8 13 messages similar to the above omitted End residue of secondary structure not found: SHEET 1 D 2 ALA 152 ILE 160 0 Start residue of secondary structure not found: SHEET 2 D 2 VAL 170 PHE 175 -1 Start residue of secondary structure not found: SHEET 1 E 2 ALA 196 SER 199 0 Start residue of secondary structure not found: SHEET 2 E 2 LYS 206 SER 209 -1 Start residue of secondary structure not found: SHEET 1 F 2 TYR 298 PHE 301 0 Start residue of secondary structure not found: SHEET 2 F 2 ARG 326 LEU 329 1 6 messages similar to the above omitted End residue of secondary structure not found: HELIX 6 6 ILE 229 ALA 231 1 3 Start residue of secondary structure not found: HELIX 7 7 LEU 257 VAL 267 1 11 Start residue of secondary structure not found: HELIX 8 8 ASP 280 ALA 292 1 13 Start residue of secondary structure not found: HELIX 9 9 THR 303 TYR 305 1 3 Start residue of secondary structure not found: HELIX 10 10 PRO 313 LYS 318 1 6 Start residue of secondary structure not found: HELIX 11 11 ARG 335 TYR 341 1 7 14 messages similar to the above omitted Chain information for shlth_1_rsr3-coot-3.pdb #1 --- Chain | Description | No description available > open /net/rossmann/home/wang83/Desktop/cryosparc_VH7D_emptyNK/x1_shlth2.mrc Opened x1_shlth2.mrc, grid size 60,72,56, pixel 1.62,1.62,1.62, shown at level 2.71, step 1, values float32 > toolshed show ViewDockX No suitable models found for ViewDockX > select #1 7159 atoms, 7170 bonds selected > toolshed show ViewDockX No suitable models found for ViewDockX > toolshed show ISOLDE > set selectionWidth 4 Chain information for shlth_1_rsr3-coot-3.pdb --- Chain | Description 1.3/ | No description available Done loading forcefield /net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/molobject.py:1720: RuntimeWarning: divide by zero encountered in double_scalars self.global_k = scaling_constant/ref_g Bad residue number: 1 Excluding residue Bad residue number: 1 Excluding residue Bad residue number: 1 Excluding residue Bad residue number: 1 Excluding residue Bad residue number: 1 Excluding residue Bad residue number: 1 Excluding residue Bad residue number: 1 Excluding residue Bad residue number: 1 Excluding residue Bad residue number: 1 Excluding residue Bad residue number: 1 Excluding residue Bad residue number: 1 Excluding residue Bad residue number: 1 Excluding residue Bad residue number: 1 Excluding residue Bad residue number: 1 Excluding residue Bad residue number: 1 Doing nothing > style selAtoms stick Changed 7159 atom styles > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode select > ui mousemode rightMode rotate Bad residue number: 1 Doing nothing > toolshed show ViewDockX No suitable models found for ViewDockX > select #1.3 7159 atoms, 7170 bonds, 10 models selected > toolshed show ViewDockX No suitable models found for ViewDockX > preset cartoons/nucleotides ribbons/slabs Changed 0 atom styles Preset expands to these ChimeraX commands: surf hide; style (protein|nucleic|solvent) & @@draw_mode=0 stick; cartoon; cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20; cartoon style ~(nucleic|strand) x round; cartoon style (nucleic|strand) x rect; nucleotides tube/slab shape box > preset ""initial styles"" cartoon Preset implemented in Python; no expansion to individual ChimeraX commands available. > toolshed show ""Basic Actions"" > open /net/rossmann/home/wang83/Desktop/cryosparc_VH7D_emptyNK/x1_shlth2.mrc Opened x1_shlth2.mrc, grid size 60,72,56, pixel 1.62,1.62,1.62, shown at level 2.71, step 1, values float32 > toolshed show ViewDockX No suitable models found for ViewDockX > hide #!2 models > hide #!2.1 models > show #!2 models > show #!2.1 models > select 7159 atoms, 7170 bonds, 18 models selected > select clear > select 7159 atoms, 7170 bonds, 18 models selected > select clear > color selAtoms bychain > select #1.3 7159 atoms, 7170 bonds, 10 models selected > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""rotate selected models"" > select clear > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""rotate selected models"" > select #1.3 7159 atoms, 7170 bonds, 10 models selected > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""rotate selected models"" > toolshed show ViewDockX No suitable models found for ViewDockX > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode pivot > ui mousemode rightMode ""rotate selected models"" > select #1.3 7159 atoms, 7170 bonds, 10 models selected > fitmap #1 inMap #2 Fit molecule shlth_1_rsr3-coot-3.pdb (#1.3) to map x1_shlth2.mrc (#2) using 7159 atoms average map value = 1.49, steps = 160 shifted from previous position = 8.82 rotated from previous position = 41.3 degrees atoms outside contour = 5245, contour level = 2.443 Position of shlth_1_rsr3-coot-3.pdb (#1.3) relative to x1_shlth2.mrc (#2) coordinates: Matrix rotation and translation 0.99999717 0.00108140 -0.00211750 -16.30497335 -0.00106877 0.99998170 0.00595530 30.58341123 0.00212390 -0.00595302 0.99998003 -46.80005943 Axis -0.92869285 -0.33077367 -0.16768534 Axis point 0.00000000 -7479.22200823 -5873.52545832 Rotation angle (degrees) 0.36734513 Shift along axis 12.87380853 > fitmap #1 inMap #2 Fit molecule shlth_1_rsr3-coot-3.pdb (#1.3) to map x1_shlth2.mrc (#2) using 7159 atoms average map value = 1.49, steps = 112 shifted from previous position = 2.08 rotated from previous position = 13.5 degrees atoms outside contour = 3904, contour level = 1.2605 Position of shlth_1_rsr3-coot-3.pdb (#1.3) relative to x1_shlth2.mrc (#2) coordinates: Matrix rotation and translation 0.99999733 0.00103974 -0.00206562 -16.30158009 -0.00102773 0.99998262 0.00580558 30.57565674 0.00207162 -0.00580344 0.99998101 -46.81007184 Axis -0.92898752 -0.33107437 -0.16544469 Axis point 0.00000000 -7682.30388464 -6017.57961543 Rotation angle (degrees) 0.35799862 Shift along axis 12.76562638 > ui mousemode rightMode zoom > select #1.3 7159 atoms, 7170 bonds, 10 models selected > select #1.3 7159 atoms, 7170 bonds, 10 models selected > select #1.3 7159 atoms, 7170 bonds, 10 models selected > select #1.3 7159 atoms, 7170 bonds, 10 models selected > select #1 7159 atoms, 7170 bonds, 16 models selected > select #1.3 7159 atoms, 7170 bonds, 10 models selected > select #1.3 7159 atoms, 7170 bonds, 10 models selected > select #1 7159 atoms, 7170 bonds, 16 models selected > select #1 7159 atoms, 7170 bonds, 16 models selected > select #1 7159 atoms, 7170 bonds, 16 models selected > select #1 7159 atoms, 7170 bonds, 16 models selected > select clear > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models Bad residue number: 1 Doing nothing Bad residue number: 1 Excluding residue Bad residue number: 1 Excluding residue Bad residue number: 1 Excluding residue Bad residue number: 1 Excluding residue Bad residue number: 1 Excluding residue Bad residue number: 2 Excluding residue Bad residue number: 2 Excluding residue Bad residue number: 26 Excluding residue Bad residue number: 47 Excluding residue Bad residue number: 47 Excluding residue Bad residue number: 47 Excluding residue Bad residue number: 49 Excluding residue Bad residue number: 49 Excluding residue Bad residue number: 49 Excluding residue Bad residue number: 49 Excluding residue Bad residue number: 49 Excluding residue Bad residue number: 50 Excluding residue Bad residue number: 50 Excluding residue Bad residue number: 138 Excluding residue Bad residue number: 138 Excluding residue Bad residue number: 138 Excluding residue Bad residue number: 141 Excluding residue Bad residue number: 141 Excluding residue Bad residue number: 142 Excluding residue Bad residue number: 149 Excluding residue Bad residue number: 75 Excluding residue Bad residue number: 202 Excluding residue Bad residue number: 222 Excluding residue Bad residue number: 241 Excluding residue > hide #!2 models Traceback (most recent call last): File ""/apps/chimerax/0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 445, in gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_down"") File ""/apps/chimerax/0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 374, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/tugging.py"", line 103, in mouse_down pick = picking.pick_closest_to_line(self.session, x, y, self._atoms, 0.5) File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/picking.py"", line 25, in pick_closest_to_line length = numpy.linalg.norm(xyz2-xyz1) TypeError: unsupported operand type(s) for -: 'NoneType' and 'NoneType' TypeError: unsupported operand type(s) for -: 'NoneType' and 'NoneType' File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/picking.py"", line 25, in pick_closest_to_line length = numpy.linalg.norm(xyz2-xyz1) See log for complete Python traceback. Traceback (most recent call last): File ""/apps/chimerax/0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 445, in gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_down"") File ""/apps/chimerax/0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 374, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/tugging.py"", line 103, in mouse_down pick = picking.pick_closest_to_line(self.session, x, y, self._atoms, 0.5) File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/picking.py"", line 25, in pick_closest_to_line length = numpy.linalg.norm(xyz2-xyz1) TypeError: unsupported operand type(s) for -: 'NoneType' and 'NoneType' TypeError: unsupported operand type(s) for -: 'NoneType' and 'NoneType' File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/picking.py"", line 25, in pick_closest_to_line length = numpy.linalg.norm(xyz2-xyz1) See log for complete Python traceback. > hide #!2 models > show #!2 models > select #2 4 models selected > ~select #2 Nothing selected > ~select #1 Nothing selected > select #1 7159 atoms, 7170 bonds, 16 models selected Exception ignored in: Traceback (most recent call last): File ""/apps/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 2393, in __del__ % self.shader_variable_name) RuntimeError: OpenGL buffer ""None"" was not deleted before core.graphics.Buffer destroyed > select #1 7159 atoms, 7170 bonds, 16 models selected Exception ignored in: Traceback (most recent call last): File ""/apps/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 2393, in __del__ % self.shader_variable_name) RuntimeError: OpenGL buffer ""None"" was not deleted before core.graphics.Buffer destroyed Traceback (most recent call last): File ""/apps/chimerax/0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 445, in gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_down"") File ""/apps/chimerax/0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 374, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/tugging.py"", line 103, in mouse_down pick = picking.pick_closest_to_line(self.session, x, y, self._atoms, 0.5) File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/picking.py"", line 25, in pick_closest_to_line length = numpy.linalg.norm(xyz2-xyz1) TypeError: unsupported operand type(s) for -: 'NoneType' and 'NoneType' TypeError: unsupported operand type(s) for -: 'NoneType' and 'NoneType' File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/picking.py"", line 25, in pick_closest_to_line length = numpy.linalg.norm(xyz2-xyz1) See log for complete Python traceback. > select #1.1 6 models selected > select #1.2 2 models selected > select #1.3 7159 atoms, 7170 bonds, 10 models selected QWidget::repaint: Recursive repaint detected > clipper spotlight radius 11.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 10.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 9.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 10.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 11.00 Setting spotlight mode for model 1.3 to True > select #1.2 2 models selected > select #1.3 7159 atoms, 7170 bonds, 10 models selected > show #1.3 target m > show selAtoms ribbons > fitmap #1 inMap #2 Fit molecule shlth_1_rsr3-coot-3.pdb (#1.3) to map x1_shlth2.mrc (#2) using 7159 atoms average map value = 1.48, steps = 60 shifted from previous position = 0.0168 rotated from previous position = 0.00891 degrees atoms outside contour = 3392, contour level = 0.8534 Position of shlth_1_rsr3-coot-3.pdb (#1.3) relative to x1_shlth2.mrc (#2) coordinates: Matrix rotation and translation 0.99999699 0.00109272 -0.00219547 -16.30879867 -0.00108011 0.99998295 0.00573836 30.58324907 0.00220170 -0.00573597 0.99998113 -46.83312006 Axis -0.91951761 -0.35237497 -0.17412421 Axis point 0.00000000 -7769.05475207 -6112.55687240 Rotation angle (degrees) 0.35748923 Shift along axis 12.37423620 > fitmap #1 inMap #2 Fit molecule shlth_1_rsr3-coot-3.pdb (#1.3) to map x1_shlth2.mrc (#2) using 7159 atoms average map value = 1.48, steps = 48 shifted from previous position = 0.00955 rotated from previous position = 0.0104 degrees atoms outside contour = 3391, contour level = 0.8534 Position of shlth_1_rsr3-coot-3.pdb (#1.3) relative to x1_shlth2.mrc (#2) coordinates: Matrix rotation and translation 0.99999706 0.00116182 -0.00212953 -16.32220427 -0.00114991 0.99998374 0.00558507 30.58776689 0.00213598 -0.00558261 0.99998214 -46.84164871 Axis -0.91718540 -0.35032051 -0.18985912 Axis point 0.00000000 -7923.24146483 -6324.48234943 Rotation angle (degrees) 0.34881982 Shift along axis 13.14827934 > toolshed show ViewDockX No suitable models found for ViewDockX > toolshed show ""Model Panel"" > preset ""initial styles"" cartoon Preset implemented in Python; no expansion to individual ChimeraX commands available. > toolshed show ""Modeller Comparative"" > toolshed show ISOLDE > set selectionWidth 4 Done loading forcefield > select #2 4 models selected Traceback (most recent call last): File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/isolde.py"", line 2647, in _start_sim_or_toggle_pause self.start_sim() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/isolde.py"", line 2664, in start_sim main_sel = self._last_main_sel = self._get_main_sim_selection() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/isolde.py"", line 2811, in _get_main_sim_selection raise TypeError('You must select at least one atom from the current ' TypeError: You must select at least one atom from the current working model prior to starting a simulation! TypeError: You must select at least one atom from the current working model prior to starting a simulation! File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/isolde.py"", line 2811, in _get_main_sim_selection raise TypeError('You must select at least one atom from the current ' See log for complete Python traceback. > select #1.3 7159 atoms, 7170 bonds, 10 models selected Traceback (most recent call last): File ""/apps/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 273, in _model_changed_cb self.update_scatter() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 370, in update_scatter if not self.visible: File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 281, in visible return self.parent.isVisible() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted Error processing trigger ""changes"": wrapped C/C++ object of type QVBoxLayout has been deleted: RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() See log for complete Python traceback. Traceback (most recent call last): File ""/apps/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 273, in _model_changed_cb self.update_scatter() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 370, in update_scatter if not self.visible: File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 281, in visible return self.parent.isVisible() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted Error processing trigger ""changes"": wrapped C/C++ object of type QVBoxLayout has been deleted: RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() See log for complete Python traceback. Traceback (most recent call last): File ""/apps/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 273, in _model_changed_cb self.update_scatter() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 370, in update_scatter if not self.visible: File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 281, in visible return self.parent.isVisible() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted Error processing trigger ""changes"": wrapped C/C++ object of type QVBoxLayout has been deleted: RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() See log for complete Python traceback. Traceback (most recent call last): File ""/apps/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 273, in _model_changed_cb self.update_scatter() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 370, in update_scatter if not self.visible: File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 281, in visible return self.parent.isVisible() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted Error processing trigger ""changes"": wrapped C/C++ object of type QVBoxLayout has been deleted: RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() See log for complete Python traceback. Traceback (most recent call last): File ""/apps/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 273, in _model_changed_cb self.update_scatter() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 370, in update_scatter if not self.visible: File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 281, in visible return self.parent.isVisible() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted Error processing trigger ""changes"": wrapped C/C++ object of type QVBoxLayout has been deleted: RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() See log for complete Python traceback. Traceback (most recent call last): File ""/apps/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 273, in _model_changed_cb self.update_scatter() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 370, in update_scatter if not self.visible: File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 281, in visible return self.parent.isVisible() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted Error processing trigger ""changes"": wrapped C/C++ object of type QVBoxLayout has been deleted: RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() See log for complete Python traceback. Traceback (most recent call last): File ""/apps/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 273, in _model_changed_cb self.update_scatter() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 370, in update_scatter if not self.visible: File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 281, in visible return self.parent.isVisible() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted Error processing trigger ""changes"": wrapped C/C++ object of type QVBoxLayout has been deleted: RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() See log for complete Python traceback. Traceback (most recent call last): File ""/apps/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 273, in _model_changed_cb self.update_scatter() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 370, in update_scatter if not self.visible: File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 281, in visible return self.parent.isVisible() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted Error processing trigger ""changes"": wrapped C/C++ object of type QVBoxLayout has been deleted: RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() See log for complete Python traceback. Traceback (most recent call last): File ""/apps/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 273, in _model_changed_cb self.update_scatter() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 370, in update_scatter if not self.visible: File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 281, in visible return self.parent.isVisible() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted Error processing trigger ""changes"": wrapped C/C++ object of type QVBoxLayout has been deleted: RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() See log for complete Python traceback. Traceback (most recent call last): File ""/apps/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 273, in _model_changed_cb self.update_scatter() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 370, in update_scatter if not self.visible: File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 281, in visible return self.parent.isVisible() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted Error processing trigger ""changes"": wrapped C/C++ object of type QVBoxLayout has been deleted: RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() See log for complete Python traceback. Traceback (most recent call last): File ""/apps/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 273, in _model_changed_cb self.update_scatter() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 370, in update_scatter if not self.visible: File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 281, in visible return self.parent.isVisible() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted Error processing trigger ""changes"": wrapped C/C++ object of type QVBoxLayout has been deleted: RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() See log for complete Python traceback. Traceback (most recent call last): File ""/apps/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 273, in _model_changed_cb self.update_scatter() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 370, in update_scatter if not self.visible: File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 281, in visible return self.parent.isVisible() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted Error processing trigger ""changes"": wrapped C/C++ object of type QVBoxLayout has been deleted: RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() See log for complete Python traceback. Traceback (most recent call last): File ""/apps/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 273, in _model_changed_cb self.update_scatter() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 370, in update_scatter if not self.visible: File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 281, in visible return self.parent.isVisible() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted Error processing trigger ""changes"": wrapped C/C++ object of type QVBoxLayout has been deleted: RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() See log for complete Python traceback. Traceback (most recent call last): File ""/apps/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 273, in _model_changed_cb self.update_scatter() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 370, in update_scatter if not self.visible: File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 281, in visible return self.parent.isVisible() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted Error processing trigger ""changes"": wrapped C/C++ object of type QVBoxLayout has been deleted: RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() See log for complete Python traceback. Traceback (most recent call last): File ""/apps/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 273, in _model_changed_cb self.update_scatter() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 370, in update_scatter if not self.visible: File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 281, in visible return self.parent.isVisible() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted Error processing trigger ""changes"": wrapped C/C++ object of type QVBoxLayout has been deleted: RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() See log for complete Python traceback. Traceback (most recent call last): File ""/apps/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 273, in _model_changed_cb self.update_scatter() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 370, in update_scatter if not self.visible: File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 281, in visible return self.parent.isVisible() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted Error processing trigger ""changes"": wrapped C/C++ object of type QVBoxLayout has been deleted: RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() See log for complete Python traceback. Traceback (most recent call last): File ""/apps/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 273, in _model_changed_cb self.update_scatter() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 370, in update_scatter if not self.visible: File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 281, in visible return self.parent.isVisible() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted Error processing trigger ""changes"": wrapped C/C++ object of type QVBoxLayout has been deleted: RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() See log for complete Python traceback. Traceback (most recent call last): File ""/apps/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 273, in _model_changed_cb self.update_scatter() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 370, in update_scatter if not self.visible: File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 281, in visible return self.parent.isVisible() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted Error processing trigger ""changes"": wrapped C/C++ object of type QVBoxLayout has been deleted: RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() See log for complete Python traceback. Traceback (most recent call last): File ""/apps/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 273, in _model_changed_cb self.update_scatter() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 370, in update_scatter if not self.visible: File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 281, in visible return self.parent.isVisible() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted Error processing trigger ""changes"": wrapped C/C++ object of type QVBoxLayout has been deleted: RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() See log for complete Python traceback. Traceback (most recent call last): File ""/apps/chimerax/0.9/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 273, in _model_changed_cb self.update_scatter() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 370, in update_scatter if not self.visible: File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 281, in visible return self.parent.isVisible() File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted Error processing trigger ""changes"": wrapped C/C++ object of type QVBoxLayout has been deleted: RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted File ""/net/rossmann/home/wang83/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/validation/ramaplot.py"", line 277, in parent return self.container.parentWidget() See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 390.77 OpenGL renderer: GeForce GTX 1060 6GB/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Third Party fixed all ChimeraX