Opened 2 years ago

Last modified 2 years ago

#9780 assigned defect

Draw tomogram plane: float division by zero

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

Description 

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.  
How to cite UCSF ChimeraX  

> open C:/Users/Balder/Documents/Char/Chimera/PD435/PD435_01_bin4.mrc

Opened PD435_01_bin4.mrc as #1, grid size 959,928,232, pixel 17.4,17.4,17.4,
shown at level 1.12e+03, step 4, values int16  

> volume #1 level 1354

> close session

> artiax start

Using preset: ArtiaX / Artiax Default  
Preset expands to these ChimeraX commands:

    
    
    set bgColor black
    lighting depthCue false
    camera ortho

  
Opened PD435_01_bin4.mrc as #1.1.1, grid size 959,928,232, pixel
17.4,17.4,17.4, shown at level 1.12e+03, step 1, values int16  

> artiax tomo #1.1.1 sliceDirection 0,0,1

> artiax view xy

> artiax tomo #1.1.1 slice 120

> artiax tomo #1.1.1 contrastCenter -970.50847

> artiax tomo #1.1.1 contrastWidth 4967.11525

> artiax tomo #1.1.1 contrastCenter -447.65424

> artiax tomo #1.1.1 contrastWidth 2788.55593

> artiax tomo #1.1.1 contrastCenter 75.2

> open
> C:/Users/Balder/Documents/Char/Chimera/PD435/PD435_DNAH11_class9_class19.star
> format star

Summary of feedback from opening
C:/Users/Balder/Documents/Char/Chimera/PD435/PD435_DNAH11_class9_class19.star  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Opened Particle list PD435_DNAH11_class9_class19.star with 3122 particles.  

> artiax show markers

3122 atoms, 3122 residues, atom rlnCoordinateX range 57.1 to 1.74e+03  
[Repeated 1 time(s)]

> artiax colormap #1.2.1.3 rlnCoordinateX palette redgreen minValue 57.1386
> maxValue 1738.53 transparency 0.0

3122 atoms, 3122 residues, atom rlnCoordinateX range 57.1 to 1.74e+03  
[Repeated 1 time(s)]

> artiax colormap #1.2.1.3 rlnCoordinateX palette redgreen minValue 57.1386
> maxValue 1738.53 transparency 0.0

> artiax particles #1.2.1 radius 40.34832

> artiax particles #1.2.1 radius 25.5906

set axis size 12.8453  
12.8453  
['.arrow', '0', '0', '0', '12.8453', '0', '0', '0.8563533333333333',
'3.425413333333333']  
set axis size 13.51611  
13.51611  
['.arrow', '0', '0', '0', '13.51611', '0', '0', '0.9010739999999999',
'3.6042959999999997']  
set axis size 14.18691  
14.18691  
['.arrow', '0', '0', '0', '14.18691', '0', '0', '0.9457939999999999',
'3.7831759999999997']  
set axis size 14.85772  
14.85772  
['.arrow', '0', '0', '0', '14.85772', '0', '0', '0.9905146666666667',
'3.9620586666666666']  
set axis size 15.52852  
15.52852  
['.arrow', '0', '0', '0', '15.52852', '0', '0', '1.0352346666666667',
'4.140938666666667']  
set axis size 16.19933  
16.19933  
['.arrow', '0', '0', '0', '16.19933', '0', '0', '1.0799553333333334',
'4.3198213333333335']  
set axis size 16.87013  
16.87013  
['.arrow', '0', '0', '0', '16.87013', '0', '0', '1.1246753333333332',
'4.498701333333333']  
set axis size 17.54094  
17.54094  
['.arrow', '0', '0', '0', '17.54094', '0', '0', '1.1693959999999999',
'4.6775839999999995']  
set axis size 16.87013  
16.87013  
['.arrow', '0', '0', '0', '16.87013', '0', '0', '1.1246753333333332',
'4.498701333333333']  
set axis size 16.19933  
16.19933  
['.arrow', '0', '0', '0', '16.19933', '0', '0', '1.0799553333333334',
'4.3198213333333335']  
set axis size 15.52852  
15.52852  
['.arrow', '0', '0', '0', '15.52852', '0', '0', '1.0352346666666667',
'4.140938666666667']  
set axis size 14.18691  
14.18691  
['.arrow', '0', '0', '0', '14.18691', '0', '0', '0.9457939999999999',
'3.7831759999999997']  
set axis size 12.1745  
12.1745  
['.arrow', '0', '0', '0', '12.1745', '0', '0', '0.8116333333333333',
'3.2465333333333333']  
set axis size 10.16208  
10.16208  
['.arrow', '0', '0', '0', '10.16208', '0', '0', '0.677472', '2.709888']  
set axis size 9.49128  
9.49128  
['.arrow', '0', '0', '0', '9.49128', '0', '0', '0.632752', '2.531008']  
set axis size 4.12483  
4.12483  
['.arrow', '0', '0', '0', '4.12483', '0', '0', '0.27498866666666666',
'1.0999546666666666']  
set axis size 0.77081  
0.77081  
['.arrow', '0', '0', '0', '0.77081', '0', '0', '0.051387333333333333',
'0.20554933333333333']  
set axis size 0.1  
0.1  
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']  
set axis size 0.77081  
0.77081  
['.arrow', '0', '0', '0', '0.77081', '0', '0', '0.051387333333333333',
'0.20554933333333333']  
set axis size 1.44161  
1.44161  
['.arrow', '0', '0', '0', '1.44161', '0', '0', '0.09610733333333334',
'0.38442933333333335']  
set axis size 2.11242  
2.11242  
['.arrow', '0', '0', '0', '2.11242', '0', '0', '0.140828', '0.563312']  
set axis size 2.78322  
2.78322  
['.arrow', '0', '0', '0', '2.78322', '0', '0', '0.185548', '0.742192']  
set axis size 3.45403  
3.45403  
['.arrow', '0', '0', '0', '3.45403', '0', '0', '0.23026866666666665',
'0.9210746666666666']  
set axis size 4.12483  
4.12483  
['.arrow', '0', '0', '0', '4.12483', '0', '0', '0.27498866666666666',
'1.0999546666666666']  
set axis size 4.79564  
4.79564  
['.arrow', '0', '0', '0', '4.79564', '0', '0', '0.3197093333333333',
'1.2788373333333332']  
set axis size 5.46644  
5.46644  
['.arrow', '0', '0', '0', '5.46644', '0', '0', '0.3644293333333334',
'1.4577173333333335']  
set axis size 6.13725  
6.13725  
['.arrow', '0', '0', '0', '6.13725', '0', '0', '0.40915', '1.6366']  
set axis size 6.80805  
6.80805  
['.arrow', '0', '0', '0', '6.80805', '0', '0', '0.45387', '1.81548']  
set axis size 7.47886  
7.47886  
['.arrow', '0', '0', '0', '7.47886', '0', '0', '0.4985906666666667',
'1.9943626666666667']  
set axis size 8.14966  
8.14966  
['.arrow', '0', '0', '0', '8.14966', '0', '0', '0.5433106666666667',
'2.173242666666667']  
set axis size 8.82047  
8.82047  
['.arrow', '0', '0', '0', '8.82047', '0', '0', '0.5880313333333334',
'2.3521253333333334']  
set axis size 9.49128  
9.49128  
['.arrow', '0', '0', '0', '9.49128', '0', '0', '0.632752', '2.531008']  
set axis size 10.16208  
10.16208  
['.arrow', '0', '0', '0', '10.16208', '0', '0', '0.677472', '2.709888']  
set axis size 10.83289  
10.83289  
['.arrow', '0', '0', '0', '10.83289', '0', '0', '0.7221926666666667',
'2.888770666666667']  
set axis size 11.50369  
11.50369  
['.arrow', '0', '0', '0', '11.50369', '0', '0', '0.7669126666666667',
'3.0676506666666667']  
set axis size 12.1745  
12.1745  
['.arrow', '0', '0', '0', '12.1745', '0', '0', '0.8116333333333333',
'3.2465333333333333']  
set axis size 12.1745  
12.1745  
['.arrow', '0', '0', '0', '12.1745', '0', '0', '0.8116333333333333',
'3.2465333333333333']  

> artiax particles #1.2.1 axesSize 12.1745

> artiax particles #1.2.1 radius 8.82047

3122 atoms, 3122 residues, atom rlnClassNumber range 9 to 19  
[Repeated 1 time(s)]

> artiax colormap #1.2.1.3 rlnClassNumber palette redgreen minValue 9.0
> maxValue 19.0 transparency 0.0

> ui mousemode right select

> select /M:40@M

1 atom, 1 residue, 1 model selected  

> select /M:112@M

1 atom, 1 residue, 1 model selected  

> select clear

Drag select of axes, 197 of 3122 instances, 197 atoms  

> select clear

Opened PD435_01_bin4.mrc as #1.1.1, grid size 959,928,232, pixel
17.4,17.4,17.4, shown at level 1.12e+03, step 1, values int16  

> artiax tomo #1.1.1 sliceDirection 0,0,1

> artiax view xy

> artiax particles #1.2.1 radius 14.18691

> artiax tomo #1.1.1 slice 107

> artiax tomo #1.1.1 contrastCenter 598.05424

An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
float division by zero  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 73, in draw_new_frame  
view.draw(check_for_changes = False)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 177, in draw  
self._draw_scene(camera, drawings)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 254, in _draw_scene  
draw_transparent(r, transparent_drawings)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1543, in draw_transparent  
r.draw_transparent(  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 1252, in draw_transparent  
draw()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1545, in <lambda>  
lambda: _draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1551, in _draw_multiple  
d.draw(renderer, draw_pass)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\image3d.py", line 791, in draw  
self._draw_planes(renderer, draw_pass, dtransp, pd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\image3d.py", line 811, in _draw_planes  
drawing.draw(r, draw_pass)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 764, in draw  
self.draw_self(renderer, draw_pass)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 775, in draw_self  
self._draw_geometry(renderer, transparent_only = any_opaque)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 815, in _draw_geometry  
r.set_colormap(cmap, self.colormap_range, t)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 1026, in set_colormap  
p.set_vector2('colormap_range', (s*v0, 1/(s*(v1-v0))))  
ZeroDivisionError: float division by zero  
  

> artiax tomo #1.1.1 contrastWidth 522.85424

> artiax tomo #1.1.1 contrastWidth 2788.55593

> artiax tomo #1.1.1 contrastCenter -4369.06102

> artiax tomo #1.1.1 contrastCenter -12734.72881

> artiax tomo #1.1.1 contrastCenter -2016.21695

Opened PD435_01_bin4.mrc as #1.1.1, grid size 959,928,232, pixel
17.4,17.4,17.4, shown at level 1.12e+03, step 1, values int16  

> artiax tomo #1.1.1 sliceDirection 0,0,1

> artiax view xy

> artiax tomo #1.1.1 contrastCenter -4804.77288

> artiax tomo #1.1.1 contrastCenter -2451.92881

> hide #!1.1.1 models

> show #!1.1.1 models

> artiax tomo #1.1.1 contrastWidth 3921.40678

> artiax tomo #1.1.1 contrastCenter -883.3661

> close session

> artiax start

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Using preset: ArtiaX / Artiax Default  
Preset expands to these ChimeraX commands:

    
    
    set bgColor black
    lighting depthCue false
    camera ortho

  
Opened PD435_01_bin4.mrc as #1.1.1, grid size 959,928,232, pixel
17.4,17.4,17.4, shown at level 1.12e+03, step 1, values int16  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  

> artiax tomo #1.1.1 sliceDirection 0,0,1

> artiax view xy

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "C:\Users\Balder\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\artiax\widgets\ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 Core Profile Context 23.5.2.230523
OpenGL renderer: AMD Radeon RX 7900 XT
OpenGL vendor: ATI Technologies Inc.

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

Manufacturer: System manufacturer
Model: System Product Name
OS: Microsoft Windows 10 Home (Build 19045)
Memory: 137,369,681,920
MaxProcessMemory: 137,438,953,344
CPU: 12 AMD Ryzen 5 1600 Six-Core Processor            
OSLanguage: en-US

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: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-ArtiaX: 0.3
    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-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-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    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
    geomdl: 5.3.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    pandas: 1.5.3
    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
    starfile: 0.4.11
    superqt: 0.4.1
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    WMI: 1.5.1
    zipp: 3.11.0

Change History (2)

comment:1 by Eric Pettersen, 2 years ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Draw tomogram plane: float division by zero

Could be ArtiaX specific

comment:2 by Tom Goddard, 2 years ago

Cc: Tom Goddard added
Owner: changed from Tom Goddard to Utz Ermel

Appears that ArtiaX command "artiax tomo #1.1.1 contrastCenter 598.05424" or a preceding command set the Drawing.colormap_range = (rmin, rmax) with rmin = rmax which generates this error. The colormap range cannot be an interval of 0 size.

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