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Opened 5 years ago
Closed 5 years ago
#3732 closed defect (duplicate)
Ribbon pick: index is out of bounds for axis
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | 0.94 |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Darwin-19.5.0-x86_64-i386-64bit ChimeraX Version: 0.94 (2020-04-10) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.94.dev202004100405 (2020-04-10) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/phakawat/Documents/Thesis/fourth_meeting/complex_1000.pdb format > PDB File not found: /Users/phakawat/Documents/Thesis/fourth_meeting/complex_1000.pdb > open /Users/phakawat/Documents/Thesis/fourth_meeting/complex_1000.pdb format > PDB File not found: /Users/phakawat/Documents/Thesis/fourth_meeting/complex_1000.pdb > open /Users/phakawat/Documents/Thesis/fourth_meeting/complex_1000.pdb format > PDB Summary of feedback from opening /Users/phakawat/Documents/Thesis/fourth_meeting/complex_1000.pdb --- warnings | Duplicate atom serial number found: 16912 Duplicate atom serial number found: 16913 Duplicate atom serial number found: 16914 Duplicate atom serial number found: 16915 Duplicate atom serial number found: 16916 1617 messages similar to the above omitted Chain information for complex_1000.pdb #1 --- Chain | Description A B C D E | No description available L N P | No description available > hide atoms > show cartoons > select #1/n #1/a #1/b 12891 atoms, 13085 bonds, 1 model selected > hide sel cartoons > select #1/b 6176 atoms, 6262 bonds, 1 model selected > show sel cartoons > select #1/n 541 atoms, 563 bonds, 1 model selected > show sel cartoons > select #1/a 6174 atoms, 6260 bonds, 1 model selected > show sel cartoons > select #1/a 6174 atoms, 6260 bonds, 1 model selected > hide sel cartoons > select #1/n 541 atoms, 563 bonds, 1 model selected > hide sel cartoons > select #1/l #1/d #1/e 12892 atoms, 13085 bonds, 1 model selected > hide sel cartoons Expected an objects specifier or a keyword > color sel #56c596ff > select #1/b 6176 atoms, 6262 bonds, 1 model selected > color sel #7be495ff > color sel #56c596ff > select #1/c 6173 atoms, 6259 bonds, 1 model selected > color sel #7be495ff > select #1/l 541 atoms, 562 bonds, 1 model selected > select #1/p 541 atoms, 563 bonds, 1 model selected > color sel #8000ffff > select clear > set bgColor white > lighting soft > select #1/b:149,186-192 146 atoms, 148 bonds, 1 model selected > style sel stick Changed 146 atom styles > show sel atoms > select H 15429 atoms, 1 model selected > delete atoms sel > delete bonds sel > color byhetero > select clear > select #1/p:22-32 Nothing 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/updateloop.py", line 139, in _redraw_timer_callback self.session.ui.mouse_modes.mouse_pause_tracking() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 362, in mouse_pause_tracking self._mouse_pause() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause m.pause(self._mouse_pause_position) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py", line 623, in pause p = picked_object(x, y, self.view) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object exclude = exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 617, in picked_object_on_segment p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 986, in first_intercept p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children p = d.first_intercept(cxyz1, cxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 586, in first_intercept ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 620, in _position_intercepts p = d.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] IndexError: index 853 is out of bounds for axis 0 with size 835 IndexError: index 853 is out of bounds for axis 0 with size 835 File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] 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/updateloop.py", line 139, in _redraw_timer_callback self.session.ui.mouse_modes.mouse_pause_tracking() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 362, in mouse_pause_tracking self._mouse_pause() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause m.pause(self._mouse_pause_position) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py", line 623, in pause p = picked_object(x, y, self.view) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object exclude = exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 617, in picked_object_on_segment p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 986, in first_intercept p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children p = d.first_intercept(cxyz1, cxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 586, in first_intercept ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 620, in _position_intercepts p = d.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] IndexError: index 853 is out of bounds for axis 0 with size 835 IndexError: index 853 is out of bounds for axis 0 with size 835 File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] 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/updateloop.py", line 139, in _redraw_timer_callback self.session.ui.mouse_modes.mouse_pause_tracking() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 362, in mouse_pause_tracking self._mouse_pause() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause m.pause(self._mouse_pause_position) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py", line 623, in pause p = picked_object(x, y, self.view) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object exclude = exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 617, in picked_object_on_segment p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 986, in first_intercept p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children p = d.first_intercept(cxyz1, cxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 586, in first_intercept ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 620, in _position_intercepts p = d.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] IndexError: index 853 is out of bounds for axis 0 with size 835 IndexError: index 853 is out of bounds for axis 0 with size 835 File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] 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/updateloop.py", line 139, in _redraw_timer_callback self.session.ui.mouse_modes.mouse_pause_tracking() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 362, in mouse_pause_tracking self._mouse_pause() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause m.pause(self._mouse_pause_position) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py", line 623, in pause p = picked_object(x, y, self.view) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object exclude = exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 617, in picked_object_on_segment p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 986, in first_intercept p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children p = d.first_intercept(cxyz1, cxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 586, in first_intercept ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 620, in _position_intercepts p = d.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] IndexError: index 853 is out of bounds for axis 0 with size 835 IndexError: index 853 is out of bounds for axis 0 with size 835 File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] 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/updateloop.py", line 139, in _redraw_timer_callback self.session.ui.mouse_modes.mouse_pause_tracking() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 362, in mouse_pause_tracking self._mouse_pause() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause m.pause(self._mouse_pause_position) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py", line 623, in pause p = picked_object(x, y, self.view) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object exclude = exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 617, in picked_object_on_segment p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 986, in first_intercept p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children p = d.first_intercept(cxyz1, cxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 586, in first_intercept ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 620, in _position_intercepts p = d.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] IndexError: index 853 is out of bounds for axis 0 with size 835 IndexError: index 853 is out of bounds for axis 0 with size 835 File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] 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/updateloop.py", line 139, in _redraw_timer_callback self.session.ui.mouse_modes.mouse_pause_tracking() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 362, in mouse_pause_tracking self._mouse_pause() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause m.pause(self._mouse_pause_position) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py", line 623, in pause p = picked_object(x, y, self.view) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object exclude = exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 617, in picked_object_on_segment p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 986, in first_intercept p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children p = d.first_intercept(cxyz1, cxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 586, in first_intercept ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 620, in _position_intercepts p = d.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] IndexError: index 853 is out of bounds for axis 0 with size 835 IndexError: index 853 is out of bounds for axis 0 with size 835 File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] 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/updateloop.py", line 139, in _redraw_timer_callback self.session.ui.mouse_modes.mouse_pause_tracking() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 362, in mouse_pause_tracking self._mouse_pause() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause m.pause(self._mouse_pause_position) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py", line 623, in pause p = picked_object(x, y, self.view) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object exclude = exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 617, in picked_object_on_segment p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 986, in first_intercept p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children p = d.first_intercept(cxyz1, cxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 586, in first_intercept ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 620, in _position_intercepts p = d.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] IndexError: index 853 is out of bounds for axis 0 with size 835 IndexError: index 853 is out of bounds for axis 0 with size 835 File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] 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/updateloop.py", line 139, in _redraw_timer_callback self.session.ui.mouse_modes.mouse_pause_tracking() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 362, in mouse_pause_tracking self._mouse_pause() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause m.pause(self._mouse_pause_position) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py", line 623, in pause p = picked_object(x, y, self.view) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object exclude = exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 617, in picked_object_on_segment p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 986, in first_intercept p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children p = d.first_intercept(cxyz1, cxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 586, in first_intercept ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 620, in _position_intercepts p = d.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] IndexError: index 853 is out of bounds for axis 0 with size 835 IndexError: index 853 is out of bounds for axis 0 with size 835 File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] 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/updateloop.py", line 139, in _redraw_timer_callback self.session.ui.mouse_modes.mouse_pause_tracking() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 362, in mouse_pause_tracking self._mouse_pause() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause m.pause(self._mouse_pause_position) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py", line 623, in pause p = picked_object(x, y, self.view) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object exclude = exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 617, in picked_object_on_segment p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 986, in first_intercept p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children p = d.first_intercept(cxyz1, cxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 586, in first_intercept ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 620, in _position_intercepts p = d.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] IndexError: index 853 is out of bounds for axis 0 with size 835 IndexError: index 853 is out of bounds for axis 0 with size 835 File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] 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/updateloop.py", line 139, in _redraw_timer_callback self.session.ui.mouse_modes.mouse_pause_tracking() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 362, in mouse_pause_tracking self._mouse_pause() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause m.pause(self._mouse_pause_position) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py", line 623, in pause p = picked_object(x, y, self.view) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object exclude = exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 617, in picked_object_on_segment p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 986, in first_intercept p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children p = d.first_intercept(cxyz1, cxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 586, in first_intercept ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 620, in _position_intercepts p = d.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] IndexError: index 853 is out of bounds for axis 0 with size 835 IndexError: index 853 is out of bounds for axis 0 with size 835 File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] 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/updateloop.py", line 139, in _redraw_timer_callback self.session.ui.mouse_modes.mouse_pause_tracking() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 362, in mouse_pause_tracking self._mouse_pause() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause m.pause(self._mouse_pause_position) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py", line 623, in pause p = picked_object(x, y, self.view) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object exclude = exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 617, in picked_object_on_segment p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 986, in first_intercept p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children p = d.first_intercept(cxyz1, cxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 586, in first_intercept ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 620, in _position_intercepts p = d.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] IndexError: index 853 is out of bounds for axis 0 with size 835 IndexError: index 853 is out of bounds for axis 0 with size 835 File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] 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/updateloop.py", line 139, in _redraw_timer_callback self.session.ui.mouse_modes.mouse_pause_tracking() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 362, in mouse_pause_tracking self._mouse_pause() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause m.pause(self._mouse_pause_position) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py", line 623, in pause p = picked_object(x, y, self.view) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object exclude = exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 617, in picked_object_on_segment p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 986, in first_intercept p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children p = d.first_intercept(cxyz1, cxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 586, in first_intercept ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 620, in _position_intercepts p = d.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] IndexError: index 853 is out of bounds for axis 0 with size 835 IndexError: index 853 is out of bounds for axis 0 with size 835 File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] 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/updateloop.py", line 139, in _redraw_timer_callback self.session.ui.mouse_modes.mouse_pause_tracking() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 362, in mouse_pause_tracking self._mouse_pause() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause m.pause(self._mouse_pause_position) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py", line 623, in pause p = picked_object(x, y, self.view) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object exclude = exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 617, in picked_object_on_segment p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 986, in first_intercept p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children p = d.first_intercept(cxyz1, cxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 586, in first_intercept ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 620, in _position_intercepts p = d.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] IndexError: index 853 is out of bounds for axis 0 with size 835 IndexError: index 853 is out of bounds for axis 0 with size 835 File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] 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/updateloop.py", line 139, in _redraw_timer_callback self.session.ui.mouse_modes.mouse_pause_tracking() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 362, in mouse_pause_tracking self._mouse_pause() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause m.pause(self._mouse_pause_position) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py", line 623, in pause p = picked_object(x, y, self.view) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object exclude = exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 617, in picked_object_on_segment p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 986, in first_intercept p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children p = d.first_intercept(cxyz1, cxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 586, in first_intercept ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 620, in _position_intercepts p = d.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] IndexError: index 853 is out of bounds for axis 0 with size 835 IndexError: index 853 is out of bounds for axis 0 with size 835 File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] 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/updateloop.py", line 139, in _redraw_timer_callback self.session.ui.mouse_modes.mouse_pause_tracking() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 362, in mouse_pause_tracking self._mouse_pause() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause m.pause(self._mouse_pause_position) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py", line 623, in pause p = picked_object(x, y, self.view) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object exclude = exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 617, in picked_object_on_segment p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 986, in first_intercept p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children p = d.first_intercept(cxyz1, cxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 586, in first_intercept ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 620, in _position_intercepts p = d.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] IndexError: index 853 is out of bounds for axis 0 with size 835 IndexError: index 853 is out of bounds for axis 0 with size 835 File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] 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/updateloop.py", line 139, in _redraw_timer_callback self.session.ui.mouse_modes.mouse_pause_tracking() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 362, in mouse_pause_tracking self._mouse_pause() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause m.pause(self._mouse_pause_position) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py", line 623, in pause p = picked_object(x, y, self.view) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object exclude = exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 617, in picked_object_on_segment p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 986, in first_intercept p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children p = d.first_intercept(cxyz1, cxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 586, in first_intercept ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 620, in _position_intercepts p = d.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] IndexError: index 853 is out of bounds for axis 0 with size 835 IndexError: index 853 is out of bounds for axis 0 with size 835 File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] 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/updateloop.py", line 139, in _redraw_timer_callback self.session.ui.mouse_modes.mouse_pause_tracking() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 362, in mouse_pause_tracking self._mouse_pause() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause m.pause(self._mouse_pause_position) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py", line 623, in pause p = picked_object(x, y, self.view) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object exclude = exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 617, in picked_object_on_segment p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 986, in first_intercept p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children p = d.first_intercept(cxyz1, cxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 586, in first_intercept ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 620, in _position_intercepts p = d.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] IndexError: index 853 is out of bounds for axis 0 with size 835 IndexError: index 853 is out of bounds for axis 0 with size 835 File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] 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/updateloop.py", line 139, in _redraw_timer_callback self.session.ui.mouse_modes.mouse_pause_tracking() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 362, in mouse_pause_tracking self._mouse_pause() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause m.pause(self._mouse_pause_position) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py", line 623, in pause p = picked_object(x, y, self.view) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object exclude = exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 617, in picked_object_on_segment p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 986, in first_intercept p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children p = d.first_intercept(cxyz1, cxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 586, in first_intercept ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 620, in _position_intercepts p = d.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] IndexError: index 853 is out of bounds for axis 0 with size 835 IndexError: index 853 is out of bounds for axis 0 with size 835 File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] 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/updateloop.py", line 139, in _redraw_timer_callback self.session.ui.mouse_modes.mouse_pause_tracking() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 362, in mouse_pause_tracking self._mouse_pause() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause m.pause(self._mouse_pause_position) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py", line 623, in pause p = picked_object(x, y, self.view) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object exclude = exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 617, in picked_object_on_segment p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 986, in first_intercept p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children p = d.first_intercept(cxyz1, cxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 586, in first_intercept ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 620, in _position_intercepts p = d.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] IndexError: index 853 is out of bounds for axis 0 with size 835 IndexError: index 853 is out of bounds for axis 0 with size 835 File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] 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/updateloop.py", line 139, in _redraw_timer_callback self.session.ui.mouse_modes.mouse_pause_tracking() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 362, in mouse_pause_tracking self._mouse_pause() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause m.pause(self._mouse_pause_position) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py", line 623, in pause p = picked_object(x, y, self.view) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object exclude = exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 617, in picked_object_on_segment p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 986, in first_intercept p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children p = d.first_intercept(cxyz1, cxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 586, in first_intercept ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 620, in _position_intercepts p = d.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] IndexError: index 853 is out of bounds for axis 0 with size 835 IndexError: index 853 is out of bounds for axis 0 with size 835 File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] 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/updateloop.py", line 139, in _redraw_timer_callback self.session.ui.mouse_modes.mouse_pause_tracking() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 362, in mouse_pause_tracking self._mouse_pause() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause m.pause(self._mouse_pause_position) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py", line 623, in pause p = picked_object(x, y, self.view) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object exclude = exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 617, in picked_object_on_segment p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 986, in first_intercept p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children p = d.first_intercept(cxyz1, cxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 586, in first_intercept ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 620, in _position_intercepts p = d.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] IndexError: index 853 is out of bounds for axis 0 with size 835 IndexError: index 853 is out of bounds for axis 0 with size 835 File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] 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/updateloop.py", line 139, in _redraw_timer_callback self.session.ui.mouse_modes.mouse_pause_tracking() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 362, in mouse_pause_tracking self._mouse_pause() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause m.pause(self._mouse_pause_position) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py", line 623, in pause p = picked_object(x, y, self.view) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object exclude = exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 617, in picked_object_on_segment p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 986, in first_intercept p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children p = d.first_intercept(cxyz1, cxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 586, in first_intercept ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 620, in _position_intercepts p = d.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] IndexError: index 853 is out of bounds for axis 0 with size 835 IndexError: index 853 is out of bounds for axis 0 with size 835 File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] 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/updateloop.py", line 139, in _redraw_timer_callback self.session.ui.mouse_modes.mouse_pause_tracking() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 362, in mouse_pause_tracking self._mouse_pause() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause m.pause(self._mouse_pause_position) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py", line 623, in pause p = picked_object(x, y, self.view) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object exclude = exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 617, in picked_object_on_segment p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 986, in first_intercept p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children p = d.first_intercept(cxyz1, cxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 586, in first_intercept ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 620, in _position_intercepts p = d.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] IndexError: index 853 is out of bounds for axis 0 with size 835 IndexError: index 853 is out of bounds for axis 0 with size 835 File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] 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/updateloop.py", line 139, in _redraw_timer_callback self.session.ui.mouse_modes.mouse_pause_tracking() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 362, in mouse_pause_tracking self._mouse_pause() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause m.pause(self._mouse_pause_position) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py", line 623, in pause p = picked_object(x, y, self.view) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object exclude = exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 617, in picked_object_on_segment p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 986, in first_intercept p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children p = d.first_intercept(cxyz1, cxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 586, in first_intercept ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 620, in _position_intercepts p = d.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] IndexError: index 853 is out of bounds for axis 0 with size 835 IndexError: index 853 is out of bounds for axis 0 with size 835 File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] 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/updateloop.py", line 139, in _redraw_timer_callback self.session.ui.mouse_modes.mouse_pause_tracking() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 362, in mouse_pause_tracking self._mouse_pause() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause m.pause(self._mouse_pause_position) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py", line 623, in pause p = picked_object(x, y, self.view) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object exclude = exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 617, in picked_object_on_segment p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 986, in first_intercept p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children p = d.first_intercept(cxyz1, cxyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 586, in first_intercept ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 620, in _position_intercepts p = d.first_intercept(xyz1, xyz2, exclude=exclude) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] IndexError: index 853 is out of bounds for axis 0 with size 835 IndexError: index 853 is out of bounds for axis 0 with size 835 File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/ribbon.py", line 675, in first_intercept r = self._residues[tranges[n-1][0]] See log for complete Python traceback. OpenGL version: 4.1 INTEL-14.6.18 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640 OpenGL vendor: Intel Inc.
Change History (2)
comment:1 by , 5 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Ribbon pick: index is out of bounds for axis |
| Version: | → 0.94 |
comment:2 by , 5 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Duplicate. Fixed months ago.