Picking: numpy.linalg.LinAlgError: Singular matrix

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-13.0-arm64-arm-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
> cofr centerOfView

UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/juntaro.lab/Library/Mobile
> Documents/com~apple~CloudDocs/研究室/y+LAT1/refined013.pdb"

refined013.pdb title:  
(Q9UM01) [more info...]  
  
Chain information for refined013.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open "/Users/juntaro.lab/Library/Mobile
> Documents/com~apple~CloudDocs/研究室/y+LAT1/yLAT1_20220815.mrc"

Opened yLAT1_20220815.mrc as #2, grid size 160,160,160, pixel 1.66, shown at
level 0.248, step 1, values float32  

> open
> /Users/juntaro.lab/Downloads/cryosparc_P12_J280_005_volume_map_sharp.mrc

Opened cryosparc_P12_J280_005_volume_map_sharp.mrc as #3, grid size
160,160,160, pixel 1.66, shown at level 0.169, step 1, values float32  

Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(NoModifier)  

Mismatch between Cocoa '\x0' and Carbon 'V' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)  

Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon '\u221a' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\u25ca' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\u221a' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\u25ca' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)  

> volume style mesh meshLighting false squareMesh false

> color #005FFF transparency 20 target s

> lighting model all directional false

> style ball

Changed 7188 atom styles  

> size ballScale 0 stickRadius 0.08

Changed 7367 bond radii, 1 ball scales  

> color byelement target a

> color C #E0E000 target a

> set bgColor black

> color ~C byelement target a

> rainbow

> show atoms

> color ~C byelement target a

> color #2 #FFFFFF transparency 20 target s

> volume #2 level 0.5625

> volume #3 level 0.4531

> ui tool show "Side View"

> volume #3 level 0.3558

> volume #3 level 0.2325

> volume #2 level 0.4008

> volume #2 level 0.4354

> color #2 #FFFFFF transparency 40 target s

> color #2 #FFFFFF transparency 50 target s

> color #3 #005FFF transparency 10 target s

> volume #3 level 0.2519

[Repeated 1 time(s)]

> hide #!2 models

> volume #3 level 0.3558

> show #!2 models

> hide #!3 models

> volume #2 level 0.5047

> show #!3 models

> hide #!2 models

> volume #3 level 0.1805

> volume #3 level 0.2519

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 687, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 720, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1048, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1092, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 190, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/matrix.py", line 130, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
File "<__array_function__ internals>", line 180, in inv  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 552, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 89, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 89, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 687, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 720, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1048, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1092, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 190, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/matrix.py", line 130, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
File "<__array_function__ internals>", line 180, in inv  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 552, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 89, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 89, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 687, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 720, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1048, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1092, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 190, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/matrix.py", line 130, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
File "<__array_function__ internals>", line 180, in inv  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 552, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 89, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 89, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 687, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 720, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1048, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1092, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 190, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/matrix.py", line 130, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
File "<__array_function__ internals>", line 180, in inv  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 552, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 89, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 89, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 687, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 720, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1048, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1092, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 190, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/matrix.py", line 130, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
File "<__array_function__ internals>", line 180, in inv  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 552, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 89, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 89, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 687, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 720, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1048, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1092, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 190, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/matrix.py", line 130, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
File "<__array_function__ internals>", line 180, in inv  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 552, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 89, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 89, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 687, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 720, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1048, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1092, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 190, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/matrix.py", line 130, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
File "<__array_function__ internals>", line 180, in inv  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 552, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 89, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 89, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 687, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 720, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1048, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1092, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 190, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/matrix.py", line 130, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
File "<__array_function__ internals>", line 180, in inv  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 552, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 89, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 89, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 687, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 720, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1048, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1092, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 190, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/matrix.py", line 130, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
File "<__array_function__ internals>", line 180, in inv  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 552, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 89, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 89, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 687, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 720, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1048, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1092, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 190, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/matrix.py", line 130, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
File "<__array_function__ internals>", line 180, in inv  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 552, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 89, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 89, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 687, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 720, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1048, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1092, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 190, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/matrix.py", line 130, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
File "<__array_function__ internals>", line 180, in inv  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 552, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 89, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/numpy/linalg/linalg.py", line 89, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  

> volume #3 level 0.226

> volume #3 level 0.1676

> volume #3 level 0.08968

> ui mousemode right "map eraser"

> volume erase #3 center 138.55,130.44,149.36 radius 11.452 outside true

Opened cryosparc_P12_J280_005_volume_map_sharp.mrc copy as #5, grid size
160,160,160, pixel 1.66, shown at step 1, values float32  

> volume #5 level 0.06603

> volume #5 level 0.03765

> volume #5 level 0.02346

> ui mousemode right translate

> open
> /Users/juntaro.lab/Downloads/cryosparc_P12_J281_class_00_00125_volume_sharp.mrc

Opened cryosparc_P12_J281_class_00_00125_volume_sharp.mrc as #6, grid size
160,160,160, pixel 1.66, shown at level 0.166, step 1, values float32  

> open
> /Users/juntaro.lab/Downloads/cryosparc_P12_J281_class_01_00125_volume_sharp.mrc

Opened cryosparc_P12_J281_class_01_00125_volume_sharp.mrc as #7, grid size
160,160,160, pixel 1.66, shown at level 0.131, step 1, values float32  

> hide #!7 models

> show #!7 models

> volume #7 level 0.1121

> open
> /Users/juntaro.lab/Downloads/cryosparc_P12_J260_005_volume_map_sharp.mrc

Opened cryosparc_P12_J260_005_volume_map_sharp.mrc as #8, grid size
160,160,160, pixel 1.66, shown at level 0.167, step 1, values float32  

> open
> /Users/juntaro.lab/Downloads/cryosparc_P12_J280_005_volume_map_sharp.mrc

Opened cryosparc_P12_J280_005_volume_map_sharp.mrc as #9, grid size
160,160,160, pixel 1.66, shown at level 0.169, step 1, values float32  




OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac mini
      Model Identifier: Macmini9,1
      Model Number: MGNT3J/A
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 8419.41.10
      OS Loader Version: 8419.41.10

Software:

    System Software Overview:

      System Version: macOS 13.0 (22A380)
      Kernel Version: Darwin 22.1.0
      Time since boot: 36日 3時間 49分

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        DELL S2721D:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 75.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.19.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.5
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

[Tom Goddard]

Fixed.

The error is because a tether cone had a singular matrix because the atom radius was 0 because of setting ball scale to 0 with the command "size ballScale 0 stickRadius 0.08". I think it should not be allowed to set ball scale or atom radii to 0. The code is not designed to handle that degenerate case. So I changed the size command to require a positive ballScale value.