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#8007 closed defect (nonchimerax)

Picking: Singular matrix

Reported by:	chimerax-bug-report@…	Owned by:	Tom Goddard
Priority:	normal	Milestone:
Component:	Graphics	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Linux-5.4.0-126-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7ud4.pdb

Summary of feedback from opening 7ud4.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER VIRUS 2022-03-18 7UD4  
  
7ud4.pdb title:  
Cryo-EM structure of AAV-PHP.eB [more info...]  
  
Chain information for 7ud4.pdb #1  
---  
Chain | Description  
A | No description available  
  

> sym #1 biomt

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 738, in pause  
p = self.view.picked_object(x, y)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 802, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 834, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1037, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1054, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 636, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 661, in _position_intercepts  
xyz1, xyz2 = place.inverse() * (mxyz1, mxyz2)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 190, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/geometry/matrix.py", line 130, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
File "<__array_function__ internals>", line 5, in inv  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 545, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 88, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 88, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 738, in pause  
p = self.view.picked_object(x, y)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 802, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 834, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1037, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1054, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 636, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 661, in _position_intercepts  
xyz1, xyz2 = place.inverse() * (mxyz1, mxyz2)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 190, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/geometry/matrix.py", line 130, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
File "<__array_function__ internals>", line 5, in inv  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 545, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 88, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 88, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 738, in pause  
p = self.view.picked_object(x, y)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 802, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 834, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1037, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1054, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 636, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 661, in _position_intercepts  
xyz1, xyz2 = place.inverse() * (mxyz1, mxyz2)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 190, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/geometry/matrix.py", line 130, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
File "<__array_function__ internals>", line 5, in inv  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 545, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 88, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 88, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 738, in pause  
p = self.view.picked_object(x, y)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 802, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 834, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1037, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1054, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 636, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 661, in _position_intercepts  
xyz1, xyz2 = place.inverse() * (mxyz1, mxyz2)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 190, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/geometry/matrix.py", line 130, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
File "<__array_function__ internals>", line 5, in inv  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 545, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 88, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 88, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 738, in pause  
p = self.view.picked_object(x, y)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 802, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 834, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1037, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1054, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 636, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 661, in _position_intercepts  
xyz1, xyz2 = place.inverse() * (mxyz1, mxyz2)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 190, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/geometry/matrix.py", line 130, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
File "<__array_function__ internals>", line 5, in inv  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 545, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 88, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 88, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 738, in pause  
p = self.view.picked_object(x, y)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 802, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 834, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1037, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1054, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 636, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 661, in _position_intercepts  
xyz1, xyz2 = place.inverse() * (mxyz1, mxyz2)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 190, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/geometry/matrix.py", line 130, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
File "<__array_function__ internals>", line 5, in inv  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 545, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 88, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 88, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 738, in pause  
p = self.view.picked_object(x, y)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 802, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 834, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1037, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1054, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 636, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 661, in _position_intercepts  
xyz1, xyz2 = place.inverse() * (mxyz1, mxyz2)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 190, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/geometry/matrix.py", line 130, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
File "<__array_function__ internals>", line 5, in inv  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 545, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 88, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 88, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 470.141.03
OpenGL renderer: Quadro P2000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: PowerEdge T640
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 88 Intel(R) Xeon(R) Gold 6152 CPU @ 2.10GHz
Cache Size: 30976 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:          251Gi        16Gi       1.4Gi       414Mi       233Gi       233Gi
	Swap:         8.0Gi       136Mi       7.9Gi

Graphics:
	3b:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP106GL [Quadro P2000] [10de:1c30] (rev a1)	
	Subsystem: NVIDIA Corporation GP106GL [Quadro P2000] [10de:11b3]	
	Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component:	Unassigned → Graphics
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Picking: Singular matrix

comment:2 by Tom Goddard, 3 years ago

Resolution:	→ nonchimerax
Status:	assigned → closed

Opened 7ud4.pdb then "sym #1 biomt" then mouse over causes an error very likely because a BIOMT symmetry matrix was singular (not invertible). The PDB entry 7ud4 is not available in PDB format so I don't know where they got this 7ud4.pdb file with the bad BIOMT records. Opening the mmCIF 7ud4 and using assembly 1 symmetry (full virus capsid) all works fine. Downloading the tar file of "PDB-like files" has a PDB file that has no BIOMT remarks.

The error is caused by a bad file which is bad in an extremely rare way (singular BIOMT matrices), so I'm not going to put in code to catch this and give a saner error.

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