id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
2305	Picking: index out of bounds	Tristan Croll	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        Linux-3.10.0-957.12.2.el7.x86_64-x86_64-with-centos-7.6.1810-Core
ChimeraX Version: 0.91 (2019-08-06)
Description
Won't copy the entire log because it's huge (result of a 3-day continuous run), but I just encountered the below traceback using the swapaa mousemode. First time I've seen it.

swapaa mousemode /AB:111 GLN
Traceback (most recent call last):   File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/mouse_modes/mousemodes.py"", line 460, in <lambda>     gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_up"")   File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/mouse_modes/mousemodes.py"", line 387, in _dispatch_mouse_event     f(MouseEvent(event, modifiers=modifiers))   File ""/home/tic20/.local/share/ChimeraX/0.91/site-packages/chimerax/isolde/mousemodes.py"", line 60, in mouse_up     self.mouse_select(event, mode, self.session, self.view)   File ""/home/tic20/.local/share/ChimeraX/0.91/site-packages/chimerax/isolde/mousemodes.py"", line 67, in mouse_select     pick = view.first_intercept(x, y, self._pick_exclude)   File ""/opt/UCSF/ChimeraX-daily/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 ""/opt/UCSF/ChimeraX-daily/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 ""/opt/UCSF/ChimeraX-daily/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 ""/opt/UCSF/ChimeraX-daily/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 ""/opt/UCSF/ChimeraX-daily/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 ""/opt/UCSF/ChimeraX-daily/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 ""/opt/UCSF/ChimeraX-daily/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 ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/atomic/structure.py"", line 1728, in _position_intercepts     p = d.first_intercept(xyz1, xyz2, exclude=exclude)   File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/atomic/structure.py"", line 2060, in first_intercept     atom = self.visible_atoms[anum]   File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/atomic/molarray.py"", line 155, in __getitem__     v = self._object_class.c_ptr_to_py_inst(self._pointers[i]) IndexError: index 1562 is out of bounds for axis 0 with size 1562 IndexError: index 1562 is out of bounds for axis 0 with size 1562 File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/atomic/molarray.py"", line 155, in __getitem__ v = self._object_class.c_ptr_to_py_inst(self._pointers[i]) See log for complete Python traceback. 

OpenGL version: 3.3.0 NVIDIA 415.27
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

}}}
"	defect	closed	normal		Graphics		fixed						all	ChimeraX