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#10416 assigned defect

'PickedAtomicShape' object has no attribute 'triangle_num'

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

Description (last modified by Eric Pettersen)

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

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

> open "C:\\\Users\\\Linnea\\\Desktop\\\PhD 2023\\\Writing\\\Nat
> Comm\\\SAM_orientation_bias\\\Chimerax_sharpened_maps_BILD.cxs"

Opened cryosparc_P80_J617_005_volume_map_sharp.mrc as #1, grid size
400,400,400, pixel 0.574, shown at level 0.0925, step 1, values float32  
Opened cryosparc_P80_J604_004_volume_map_sharp.mrc as #2, grid size
400,400,400, pixel 0.574, shown at level 0.0503, step 1, values float32  
Opened cryosparc_P80_J518_003_volume_map_sharp.mrc as #3, grid size
400,400,400, pixel 0.574, shown at level 0.0412, step 1, values float32  
Log from Sat Dec 30 16:20:15 2023UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "C:\\\Users\\\Linnea\\\Desktop\\\PhD 2023\\\Writing\\\Nat
> Comm\\\SAM_orientation_bias\\\Chimerax_sharpened_maps_BILD.cxs"

Opened cryosparc_P80_J617_005_volume_map_sharp.mrc as #1, grid size
400,400,400, pixel 0.574, shown at level 0.0826, step 1, values float32  
Opened cryosparc_P80_J604_004_volume_map_sharp.mrc as #2, grid size
400,400,400, pixel 0.574, shown at level 0.0503, step 1, values float32  
Opened cryosparc_P80_J518_003_volume_map_sharp.mrc as #3, grid size
400,400,400, pixel 0.574, shown at level 0.0412, step 1, values float32  
Log from Sat Dec 30 15:29:11 2023

> ui tool show "Model Panel"

> ui tool show "Side View"

> cd "C:/Users/Linnea/Desktop/PhD 2023/Writing/Data and Images"

Current working directory is: C:\Users\Linnea\Desktop\PhD 2023\Writing\Data
and Images  
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 "C:\\\Users\\\Linnea\\\Desktop\\\PhD 2023\\\Writing\\\Nat
> Comm\\\SAM_orientation_bias\\\W1_Au_Flat_NoTCEP_NoTween\\\cryosparc_P80_J617_005_volume_map_sharp.mrc"

Opened cryosparc_P80_J617_005_volume_map_sharp.mrc as #1, grid size
400,400,400, pixel 0.574, shown at level 0.0297, step 2, values float32  

> volume #1 step 1

> volume #1 level 0.06016

> open "C:/Users/Linnea/Desktop/PhD 2023/Writing/Nat
> Comm/SAM_orientation_bias/W1_Au_Flat_NoTCEP_NoTween/J617_viewing_direction_distribution_iteration_005
> (1).bild"

Opened BILD data containing 2504 objects  

> lighting soft

> color #1 #a5a5a5ff models

> set bgColor white

> graphics silhouettes true

> volume #1 level 0.08262

> rename #2 id #1

> open "C:/Users/Linnea/Desktop/PhD 2023/Writing/Nat
> Comm/SAM_orientation_bias/W2_Au_flat_PBS/cryosparc_P80_J604_004_volume_map_sharp.mrc"

Opened cryosparc_P80_J604_004_volume_map_sharp.mrc as #2, grid size
400,400,400, pixel 0.574, shown at level 0.0217, step 2, values float32  

> open "C:/Users/Linnea/Desktop/PhD 2023/Writing/Nat
> Comm/SAM_orientation_bias/W2_Au_flat_PBS/J604_viewing_direction_distribution_iteration_004.bild"

Opened BILD data containing 2733 objects  

> color #2 #a5a5a5ff models

> volume #2 step 1

> volume #2 level 0.04277

> volume #2 level 0.0503

> rename #3 id #2

> open "C:/Users/Linnea/Desktop/PhD 2023/Writing/Nat
> Comm/SAM_orientation_bias/W3_Quantfoil_noTCEP_No
> Tween/cryosparc_P80_J518_003_volume_map_sharp.mrc"

Opened cryosparc_P80_J518_003_volume_map_sharp.mrc as #3, grid size
400,400,400, pixel 0.574, shown at level 0.0194, step 2, values float32  

> open "C:/Users/Linnea/Desktop/PhD 2023/Writing/Nat
> Comm/SAM_orientation_bias/W3_Quantfoil_noTCEP_No
> Tween/J518_viewing_direction_distribution_iteration_003.bild"

Opened BILD data containing 2964 objects  

> color #3 #a5a5a5ff models

> volume #3 level 0.02684

> volume #3 step 1

> volume #3 level 0.04121

> rename #4 id #3

> hide #!3 models

> save "C:/Users/Linnea/Desktop/PhD 2023/Writing/Nat
> Comm/SAM_orientation_bias/Chimerax_sharpened_maps_BILD.cxs"

——— End of log from Sat Dec 30 15:29:11 2023 ———

opened ChimeraX session  

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!1 models

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  

> view name 1

> view name front1

> hide #!1 models

> show #!2 models

> hide #2.2 models

> show #2.2 models

> hide #2.2 models

> view name front2

> show #2.2 models

> hide #!2 models

> show #!3 models

> hide #3.2 models

> view name front3

> show #3.2 models

> view front3

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  

> view name front3

> hide #!3 models

> show #!2 models

> view front2

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  

> hide #3.2 models

> hide #2.2 models

> show #!3 models

> show #2.2 models

> show #3.2 models

> hide #!3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!3 models

> show #!2 models

> hide #!3 models

> view front2

> view name front2

> hide #!2 models

> show #!3 models

> view front3

> hide #!3 models

> show #!1 models

> view front1

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  

> view name front1

> view front1

> tunr z -90

Unknown command: tunr z -90  

> view front1

> turn y -90

> view front1

> turn y -90

> view front1

> turn y +90

> view front1

> turn y -90

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  

> view front1

> volume #1 level 0.09255

> volumeflip #1 y

Unknown command: volumeflip #1 y  

> volume flip #1 y

Expected a keyword  

> volume flip #1 axis y

Opened cryosparc_P80_J617_005_volume_map_sharp.mrc y flip as #4, grid size
400,400,400, pixel 0.574, shown at step 1, values float32  

QWindowsWindow::setGeometry: Unable to set geometry 3840x2310+0+66 (frame:
3876x2413-18-19) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 3840x1973+0+67 (frame: 3876x2076-18-18) margins: 18, 85,
18, 18 minimum size: 426x770 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=1314,
y=2413)))  

> hide #!4 models

> show #!1 models

> close #4

> save "C:/Users/Linnea/Desktop/PhD 2023/Writing/Nat
> Comm/SAM_orientation_bias/W1_Au_Flat_NoTCEP_NoTween/J617_Bild_Front.png"
> width 5000 height 3288 supersample 3 transparentBackground true

> turn y -90

> save "C:/Users/Linnea/Desktop/PhD 2023/Writing/Nat
> Comm/SAM_orientation_bias/W1_Au_Flat_NoTCEP_NoTween/J617_Bild_y-90.png"
> width 5000 height 3288 supersample 3 transparentBackground true

> hide #!1 models

> show #!2 models

> view front2

> save "C:/Users/Linnea/Desktop/PhD 2023/Writing/Nat
> Comm/SAM_orientation_bias/W2_Au_flat_PBS/J604_Bild_Front.png" width 5000
> height 3288 supersample 3 transparentBackground true

> turn y -90

> save "C:/Users/Linnea/Desktop/PhD 2023/Writing/Nat
> Comm/SAM_orientation_bias/W2_Au_flat_PBS/J604_Bild_Side.png" width 5000
> height 3288 supersample 3 transparentBackground true

> hide #!2 models

> show #!3 models

> view front3

> save "C:/Users/Linnea/Desktop/PhD 2023/Writing/Nat
> Comm/SAM_orientation_bias/W3_Quantfoil_noTCEP_No Tween/J518_Bild_Front.png"
> width 5000 height 3288 supersample 3 transparentBackground true

> turn y -90

> save "C:/Users/Linnea/Desktop/PhD 2023/Writing/Nat
> Comm/SAM_orientation_bias/W3_Quantfoil_noTCEP_No Tween/J518_Bild_Side.png"
> width 5000 height 3288 supersample 3 transparentBackground true

> hide #!3 models

> show #!3 models

> hide #3.2 models

> view front3

> turn y -90

> save "C:/Users/Linnea/Desktop/PhD 2023/Writing/Nat
> Comm/SAM_orientation_bias/Chimerax_sharpened_maps_BILD.cxs"

——— End of log from Sat Dec 30 16:20:15 2023 ———

opened ChimeraX session  

> open "C:/Users/Linnea/Desktop/PhD 2023/Writing/Nat
> Comm/SAM_orientation_bias/Final_model399/cryosparc_P80_J399_004_volume_map_sharp.mrc"

Opened cryosparc_P80_J399_004_volume_map_sharp.mrc as #4, grid size
400,400,400, pixel 0.574, shown at level 0.101, step 2, values float32  

> open "C:/Users/Linnea/Desktop/PhD 2023/Writing/Nat
> Comm/SAM_orientation_bias/Final_model399/J476_viewing_direction_distribution.bild"

Opened BILD data containing 3072 objects  

> hide #!3 models

> rename #5 id #4

> hide #4.2 models

> volume #4 step 1

> volume #4 level 0.3344

> view1

Unknown command: view1  

> view view1

Expected an objects specifier or a view name or a keyword  

> view view2

Expected an objects specifier or a view name or a keyword  

> show #4.2 models

> save "C:/Users/Linnea/Desktop/PhD 2023/Writing/Nat
> Comm/SAM_orientation_bias/Final_model399/J399_bild_front.png" width 5000
> height 3288 supersample 3 transparentBackground true

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
[a _lot_ of these deleted]

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 817, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 849, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 126, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1070, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 1121, in first_intercept  
if d.display_style == d.Mesh or hasattr(pd, 'is_transparent') and
pd.is_transparent():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
AttributeError: 'PickedAtomicShape' object has no attribute 'triangle_num'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 374, in is_transparent  
t = self.triangle_num  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.14802 Core Profile Forward-Compatible Context 21.40.52 30.0.14052.5
OpenGL renderer: AMD Radeon(TM) Graphics
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: en_CH.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: LENOVO
Model: 20XLS0CJ00
OS: Microsoft Windows 10 Education (Build 19045)
Memory: 33,099,800,576
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 PRO 5850U with Radeon Graphics     
OSLanguage: en-GB

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.9.24
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.1.3
    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-QScore: 1.0
    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
    comtypes: 1.1.10
    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
    MolecularDynamicsViewer: 1.4
    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
    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
    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
    pywin32: 303
    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
    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
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    WMI: 1.5.1
    zipp: 3.11.0

Change History (2)

comment:1 by Eric Pettersen, 22 months ago

Cc:	Greg Couch Eric Pettersen added
Component:	Unassigned → Graphics
Description:	modified (diff)
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → 'PickedAtomicShape' object has no attribute 'triangle_num'

AFAICT, happens when trying to pick and atomic shape through a transparent volume surface, but I couldn't reproduce it using 1.5 with 1bna and its EDS map.

comment:2 by Tom Goddard, 22 months ago

Cc:	Tom Goddard added; Greg Couch removed
Owner:	changed from Tom Goddard to Greg Couch

This error happens when a BILD model is made a child of a volume. The user uses the rename command to do that. The problem is a bug in BILD picked object code in the PickedAtomicShape class is_transparent() method. That class was originally in the bild bundle written by Greg who moved it to the atomic bundle in shapesdrawing.py 7 years ago. The is_transparent() method will always give an error because it accesses an undefined attribute self.triangle_num. We see this when the bild model is a child of a Volume because the Volume code calls the is_transparent() method on the picked object to allow picking through transparent layers.

Reassigning to Greg so he can fix the PickedAtomicShape.is_transparent() method.

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