id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2288 traceback interactively moving clip plane after coloring by map value and playing with cap subdiv Elaine Meng Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-17.7.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-08-03) Description I was messing around with right-mouse clip translate/rotate while the cap was colored by map value. Maybe significant that this traceback occurred after a mouseclick made the molecular surface no longer clipped but subsequent mousing re-clipped it (cap was no longer colored, which I expect... only the traceback was unexpected). Probably doesn't matter which data, but was 3eeb after deleting chain A and opening attached dx file of ESP for chain B. Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' UCSF ChimeraX version: 0.91 (2019-08-03) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 3mhc format mmCIF fromDatabase pdb 3mhc title: Crystal structure of human cabonic anhydrase II in adduct with an adamantyl analogue of acetazolamide in a novel hydrophobic binding pocket [more info...] Chain information for 3mhc #1 --- Chain | Description A | Carbonic anhydrase 2 Non-standard residues in 3mhc #1 --- ARZ — (3S,5S,7S)-N-(5-sulfamoyl-1,3,4-thiadiazol-2-yl)tricyclo[3.3.1.1~3,7~]decane-1-carboxamide (5-(1-adamantylcarboxamido)-1,3,4-thiadiazole-2-sulfonamide) ZN — zinc ion > surface > molmap protein 6 Expected a keyword > surface close #1 > toolshed show ""Side View"" > color sample #2 map #2 Map values for surface ""surface"": minimum 0.09594, mean 0.09594, maximum 0.09594 Map values for surface ""cap near"": minimum 0.08372, mean 0.2245, maximum 0.6163 > surface cap subdivision 2 > surface cap subdivision 2.0 Clip caps on, offset 0.01 Clip caps on, offset 0.01 > surface cap subdivision 3 > surface cap subdivision 3.0 Clip caps on, offset 0.01 Clip caps on, offset 0.01 > surface cap subdivision 5 > surface cap subdivision 5.0 Clip caps on, offset 0.01 Clip caps on, offset 0.01 > surface cap subdivision 1 > surface cap subdivision 1.0 Clip caps on, offset 0.01 Clip caps on, offset 0.01 > hide #!2 models > surface > color sample #1 map #2 Map values for surface ""3mhc_A SES surface"": minimum 0.05977, mean 0.206, maximum 0.3934 Map values for surface ""cap near"": minimum 0.08004, mean 0.3183, maximum 0.6074 > surface cap subdivision 2 > surface cap subdivision 2.0 Clip caps on, offset 0.01 Clip caps on, offset 0.01 > surface cap subdivision 4 > surface cap subdivision 4.0 Clip caps on, offset 0.01 Clip caps on, offset 0.01 > surface cap subdivision 1 > surface cap subdivision 1.0 Clip caps on, offset 0.01 Clip caps on, offset 0.01 > hide cartoons > surface cap subdivision 1 Clip caps on, offset 0.01 > surface cap subdivision 2 > surface cap subdivision 2.0 Clip caps on, offset 0.01 Clip caps on, offset 0.01 > surface cap subdivision 1 > surface cap subdivision 1.0 Clip caps on, offset 0.01 Clip caps on, offset 0.01 > surface cap subdivision .5 > surface cap subdivision 0.5 Clip caps on, offset 0.01 Clip caps on, offset 0.01 > surface cap subdivision 5 > surface cap subdivision 5.0 Clip caps on, offset 0.01 Clip caps on, offset 0.01 > surface cap subdivision 1 > surface cap subdivision 1.0 Clip caps on, offset 0.01 Clip caps on, offset 0.01 > surface cap subdivision 2 > surface cap subdivision 2.0 Clip caps on, offset 0.01 Clip caps on, offset 0.01 > surface close #1 > surface #1 > color sample #1 map #2 palette lipophilicity Map values for surface ""3mhc_A SES surface"": minimum 0.05977, mean 0.206, maximum 0.3934 Map values for surface ""cap near"": minimum 0.07418, mean 0.3598, maximum 0.6423 > surface cap subdivision 5 > surface cap subdivision 5.0 Clip caps on, offset 0.01 Clip caps on, offset 0.01 > surface cap subdivision 1 > surface cap subdivision 1.0 Clip caps on, offset 0.01 Clip caps on, offset 0.01 > close > open /Users/meng/Desktop/chidata/3eebB.dx Opened 3eebB.dx, grid size 129,129,129, pixel 0.555,0.529,0.48, shown at level -45.7,45.7, step 1, values float32 > open 3eeb 3eeb title: Structure of the V. cholerae RTX cysteine protease domain [more info...] Chain information for 3eeb #2 --- Chain | Description A B | RTX toxin RtxA Non-standard residues in 3eeb #2 --- IHP — inositol hexakisphosphate NA — sodium ion 3eeb mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > delete /a > surface > hide #1 > color sample #2 map #1 Map values for surface ""3eeb_B SES surface"": minimum -138.4, mean 1.503, maximum 144.4 Map values for surface ""cap near"": minimum -246.1, mean 11.78, maximum 273 > ui mousemode rightMode ""clip rotate"" > color sample #2 map #1 Map values for surface ""3eeb_B SES surface"": minimum -138.4, mean 1.503, maximum 144.4 Map values for surface ""cap front"": minimum -326.8, mean 5.751, maximum 227.2 > help color Missing or invalid ""surfaces"" argument: invalid surfaces specifier > color sample #2 map #1 palette -10,red:0,white:10,blue Map values for surface ""3eeb_B SES surface"": minimum -138.4, mean 1.503, maximum 144.4 Map values for surface ""cap front"": minimum -316.8, mean 8.885, maximum 365.9 > color sample #2 map #1 palette -50,red:0,white:50,blue Map values for surface ""3eeb_B SES surface"": minimum -138.4, mean 1.503, maximum 144.4 Map values for surface ""cap front"": minimum -316.8, mean 8.885, maximum 365.9 > lighting soft > surface cap subdivision 2 > surface cap subdivision 2.0 Clip caps on, offset 0.01 Clip caps on, offset 0.01 > surface cap subdivision 1 > surface cap subdivision 1.0 Clip caps on, offset 0.01 Clip caps on, offset 0.01 > surface cap subdivision 2 > surface cap subdivision 2.0 Clip caps on, offset 0.01 Clip caps on, offset 0.01 > surface cap subdivision 3 > surface cap subdivision 3.0 Clip caps on, offset 0.01 Clip caps on, offset 0.01 > surface cap subdivision 5 > surface cap subdivision 5.0 Clip caps on, offset 0.01 Clip caps on, offset 0.01 > hide cartoons > ui mousemode rightMode clip > ui mousemode rightMode ""clip rotate"" > style ligand ball Changed 36 atom styles Traceback (most recent call last): File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 459, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 387, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 643, in mouse_drag self.clip_rotate(axis, angle) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 668, in clip_rotate r = rotation(scene_axis, angle, v.center_of_rotation) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 640, in _get_cofr cofr = self._compute_center_of_rotation() File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 667, in _compute_center_of_rotation p = self._front_center_cofr() File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 722, in _front_center_cofr cr = self._front_center_point() # Can be None File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 728, in _front_center_point exclude=lambda d: hasattr(d, 'no_cofr') and d.no_cofr) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 743, in first_intercept p = self.first_intercept_on_segment(xyz1, xyz2, exclude=exclude, beyond=beyond) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 757, in first_intercept_on_segment p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 986, in first_intercept p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2, exclude=exclude) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 1002, in first_intercept_children p = d.first_intercept(cxyz1, cxyz2, exclude=exclude) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1695, in first_intercept ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1728, in _position_intercepts p = d.first_intercept(xyz1, xyz2, exclude=exclude) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 456, in first_intercept v = self.triangles[t,0] IndexError: index 175018 is out of bounds for axis 0 with size 166250 IndexError: index 175018 is out of bounds for axis 0 with size 166250 File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 456, in first_intercept v = self.triangles[t,0] See log for complete Python traceback. Traceback (most recent call last): File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 459, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 387, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 643, in mouse_drag self.clip_rotate(axis, angle) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 668, in clip_rotate r = rotation(scene_axis, angle, v.center_of_rotation) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 640, in _get_cofr cofr = self._compute_center_of_rotation() File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 667, in _compute_center_of_rotation p = self._front_center_cofr() File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 722, in _front_center_cofr cr = self._front_center_point() # Can be None File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 728, in _front_center_point exclude=lambda d: hasattr(d, 'no_cofr') and d.no_cofr) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 743, in first_intercept p = self.first_intercept_on_segment(xyz1, xyz2, exclude=exclude, beyond=beyond) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 757, in first_intercept_on_segment p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 986, in first_intercept p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2, exclude=exclude) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 1002, in first_intercept_children p = d.first_intercept(cxyz1, cxyz2, exclude=exclude) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1695, in first_intercept ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1728, in _position_intercepts p = d.first_intercept(xyz1, xyz2, exclude=exclude) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 456, in first_intercept v = self.triangles[t,0] IndexError: index 185459 is out of bounds for axis 0 with size 166250 IndexError: index 185459 is out of bounds for axis 0 with size 166250 File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molsurf.py"", line 456, in first_intercept v = self.triangles[t,0] See log for complete Python traceback. OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102 OpenGL renderer: NVIDIA GeForce GTX 675MX OpenGL Engine OpenGL vendor: NVIDIA Corporation File attachment: 3eebB.dx }}} [attachment:""3eebB.dx""] " defect closed minor Surface fixed all ChimeraX