id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4237 Ribbons: spline normal computation for straight line mmaldo@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-18.7.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-12-23) Description I'm not sure what caused this problem. It happens when I open the file or try to select the chains. The file does open, but then chain commands are not responsive, e.g. select, color, etc. Thanks! Log: UCSF ChimeraX version: 0.91 (2019-12-23) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Volumes/cloud.mcb.ucdavis.edu/mcb_labs/letts/Model_Building/T.thermophila/SCI+III2/Maps/CIMAdistal- > focused_cryosparc_P15_J424_007_volume_map_sharp-fit.mrc Opened CIMAdistal-focused_cryosparc_P15_J424_007_volume_map_sharp-fit.mrc, grid size 600,600,600, pixel 0.835, shown at level 0.318, step 4, values float32 > open > /Volumes/cloud.mcb.ucdavis.edu/mcb_labs/letts/Model_Building/T.thermophila/SCI+III2/Initial_model/CI_Modelling/MA_fitted_J424-MA- > focused_202110210_mm-coot-10.pdb Summary of feedback from opening /Volumes/cloud.mcb.ucdavis.edu/mcb_labs/letts/Model_Building/T.thermophila/SCI+III2/Initial_model/CI_Modelling/MA_fitted_J424-MA- focused_202110210_mm-coot-10.pdb --- warning | Start residue of secondary structure not found: HELIX 57 57 THR D 90 PHE D 94 1 5 Chain information for MA_fitted_J424-MA-focused_202110210_mm-coot-10.pdb #2 --- Chain | Description | No description available 1 | No description available 2 | No description available 3 | No description available 4 | No description available 5 | No description available 6 | No description available 7 | No description available 8 | No description available 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 J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available 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 j | No description available k | No description available l | No description available m | No description available n | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available u | No description available v | No description available w | No description available x | No description available y | No description available z | No description available > hide all > show #2 cartoons Traceback (most recent call last): File ""/programs/i386-mac/chimerax/0.91/ChimeraX.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 ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2661, in _update_graphics_if_needed s[i]._update_graphics_if_needed() File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 304, in _update_graphics_if_needed self._create_ribbon_graphics() File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 773, in _create_ribbon_graphics self._use_spline_normals) File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py"", line 50, in __init__ atom_normals = self._compute_normals_from_control_points(coords) File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py"", line 246, in _compute_normals_from_control_points raise RuntimeError(""spline normal computation for straight line"") RuntimeError: spline normal computation for straight line Error processing trigger ""graphics update"": RuntimeError: spline normal computation for straight line File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py"", line 246, in _compute_normals_from_control_points raise RuntimeError(""spline normal computation for straight line"") See log for complete Python traceback. > hide #!1 models > show #!1 models > volume #1 step 1 > volume #1 level 0.404 > volume #1 level 0.3639 > preset ""initial styles"" ""space-filling (single color)"" Preset implemented in Python; no expansion to individual ChimeraX commands available. > undo > show #!1 models > lighting full > color zone #1 near #2 distance 3 > hide #!1 models > show #!1 models > color zone #1 near #2 distance 3 > view > volume #1 level 0.4499 > turn y 90 > turn y 30 > turn y -15 > movie record > turn y 2 180 > wait 180 > movie encode /Users/mmaldo/Desktop/movie2.mp4 Movie saved to /Users/mmaldo/Desktop/movie2.mp4 > hide #!1 models > show #!1 models > hide #!1 models > ui mousemode rightMode select Traceback (most recent call last): File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 477, in gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_up"") File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 402, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 56, in mouse_up mouse_drag_select(self.mouse_down_position, event, mode, self.session, self.view) File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 191, in mouse_drag_select pick = view.rectangle_intercept(sx,sy,x,y,exclude=unpickable) File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 809, in rectangle_intercept picks = self.drawing.planes_pick(planes, exclude=exclude) File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 1107, in planes_pick picks.extend(d.planes_pick(pplanes, exclude)) File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 1107, in planes_pick picks.extend(d.planes_pick(pplanes, exclude)) File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 1107, in planes_pick picks.extend(d.planes_pick(pplanes, exclude)) File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2213, in planes_pick t2r = self.parent.parent._ribbon_t2r[self] KeyError: KeyError: File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2213, in planes_pick t2r = self.parent.parent._ribbon_t2r[self] See log for complete Python traceback. Traceback (most recent call last): File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 475, in gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_down"") File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 396, in _dispatch_mouse_event lm.mouse_up(MouseEvent(event, modifiers=modifiers)) File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 56, in mouse_up mouse_drag_select(self.mouse_down_position, event, mode, self.session, self.view) File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 191, in mouse_drag_select pick = view.rectangle_intercept(sx,sy,x,y,exclude=unpickable) File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 809, in rectangle_intercept picks = self.drawing.planes_pick(planes, exclude=exclude) File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 1107, in planes_pick picks.extend(d.planes_pick(pplanes, exclude)) File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 1107, in planes_pick picks.extend(d.planes_pick(pplanes, exclude)) File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 1107, in planes_pick picks.extend(d.planes_pick(pplanes, exclude)) File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2213, in planes_pick t2r = self.parent.parent._ribbon_t2r[self] KeyError: KeyError: File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2213, in planes_pick t2r = self.parent.parent._ribbon_t2r[self] See log for complete Python traceback. Traceback (most recent call last): File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 477, in gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_up"") File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 402, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 56, in mouse_up mouse_drag_select(self.mouse_down_position, event, mode, self.session, self.view) File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 191, in mouse_drag_select pick = view.rectangle_intercept(sx,sy,x,y,exclude=unpickable) File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 809, in rectangle_intercept picks = self.drawing.planes_pick(planes, exclude=exclude) File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 1107, in planes_pick picks.extend(d.planes_pick(pplanes, exclude)) File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 1107, in planes_pick picks.extend(d.planes_pick(pplanes, exclude)) File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 1107, in planes_pick picks.extend(d.planes_pick(pplanes, exclude)) File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2213, in planes_pick t2r = self.parent.parent._ribbon_t2r[self] KeyError: KeyError: File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2213, in planes_pick t2r = self.parent.parent._ribbon_t2r[self] See log for complete Python traceback. OpenGL version: 4.1 NVIDIA-12.0.24 355.11.10.50.10.103 OpenGL renderer: NVIDIA GeForce GT 750M OpenGL Engine OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Depiction not a bug all ChimeraX