Opened 7 years ago

Closed 7 years ago

#1718 closed defect (duplicate)

self._positions is None

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics Version: 0.8
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-18.2.0-x86_64-i386-64bit
ChimeraX Version: 0.8 (2018-12-17)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.8 (2018-12-17)  
How to cite UCSF ChimeraX  
Updating list of available bundles failed: 'list' object has no attribute
'split'  

> open /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_utp.pdb

Summary of feedback from opening
/Users/lijuanyin/project/kre33_90S/figures/figure1/c5_utp.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
3723 messages similar to the above omitted  
  
Chain information for c5_utp.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E I | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
X | No description available  
Y | No description available  
Z | No description available  
  

> open /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_ribo.pdb

Chain information for c5_ribo.pdb #2  
---  
Chain | Description  
1 | No description available  
2 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N d | No description available  
O | No description available  
P | No description available  
Q | No description available  
R S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
e g | No description available  
f | No description available  
h | No description available  
i | No description available  
j m | No description available  
k | No description available  
l | No description available  
n | No description available  
o | No description available  
p | No description available  
  

> open
/Users/lijuanyin/project/kre33_90S/job028_class3d_job026_8c/c5_and_c146ofc2/second_refine/post_2/postprocess_masked.mrc

Opened postprocess_masked.mrc, grid size 480,480,480, pixel 1.08, shown at
level 0.0347, step 2, values float32  

> open /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_map.mrc

Opened kre33_map.mrc, grid size 480,480,480, pixel 1.08, shown at level
-2.76e-05, step 2, values float32  

> color #3 light gray

> volume #3 transparency 0.75

> volume #3 step 1 level 0.04

> volume #4 step 1 level 0.01

> surface dust #1-8 size 5

> set bgColor white

> lighting soft

> color #1 #2 light gray

> color #2/R forest green

> color #2/S cyan

> color #2/W cornflower blue

> color #2/Y hot pink

> color #2/Z tomato

> hide #1 #2 target a

> show #2/R /S /W /Z /Y target r

> windowsize 600 800

> set silhouettes true

> color zone #4 near #2 #1 distance 6

> view matrix camera
0.88647,-0.27586,-0.37157,21.602,-0.30963,0.24319,-0.91923,-306,0.34394,0.92993,0.13017,328.02

> save /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_position.png
supersample 3

> hide #1 #2 target r

> show #2/R:790 target a

> style #2/R:786 :797 :885 : 889 :890 :802 :794 stick

Changed 63 atom styles  

> color #2/R@N* blue

> color #2/R@O* red

> windowsize 600 600

Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/graphics.py", line 80, in resizeEvent  
v.draw(check_for_changes = False)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/view.py", line 159, in draw  
self._draw_scene(camera, drawings)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/view.py", line 213, in _draw_scene  
draw_depth(r, opaque_drawings)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 1379, in draw_depth  
draw_opaque(r, drawings)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 1360, in draw_opaque  
_draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 1371, in _draw_multiple  
d.draw(renderer, draw_pass)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 684, in draw  
if not self.display:  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 311, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 311, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  

> set silhouettes true

> close

> open /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_utp.pdb

Summary of feedback from opening
/Users/lijuanyin/project/kre33_90S/figures/figure1/c5_utp.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
3723 messages similar to the above omitted  
  
Chain information for c5_utp.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E I | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
X | No description available  
Y | No description available  
Z | No description available  
  

> open /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_ribo.pdb

Chain information for c5_ribo.pdb #2  
---  
Chain | Description  
1 | No description available  
2 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N d | No description available  
O | No description available  
P | No description available  
Q | No description available  
R S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
e g | No description available  
f | No description available  
h | No description available  
i | No description available  
j m | No description available  
k | No description available  
l | No description available  
n | No description available  
o | No description available  
p | No description available  
  

> open
/Users/lijuanyin/project/kre33_90S/job028_class3d_job026_8c/c5_and_c146ofc2/second_refine/post_2/postprocess_masked.mrc

Opened postprocess_masked.mrc, grid size 480,480,480, pixel 1.08, shown at
level 0.0347, step 2, values float32  

> open /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_map.mrc

Opened kre33_map.mrc, grid size 480,480,480, pixel 1.08, shown at level
-2.76e-05, step 2, values float32  

> color #3 light gray

> volume #3 transparency 0.75

> volume #3 step 1 level 0.04

> volume #4 step 1 level 0.01

> surface dust #1-8 size 5

> set bgColor white

> lighting soft

> color #1 #2 light gray

> color #2/R forest green

> color #2/S cyan

> color #2/W cornflower blue

> color #2/Y hot pink

> color #2/Z tomato

> hide #1 #2 target a

> show #2/R /S /W /Z /Y target r

> windowsize 600 800

> set silhouettes true

> color zone #4 near #2 #1 distance 6

> view matrix camera
0.88647,-0.27586,-0.37157,21.602,-0.30963,0.24319,-0.91923,-306,0.34394,0.92993,0.13017,328.02

> save /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_position.png
supersample 3

> hide #1 #2 target r

> show #2/R:790 target a

> style #2/R:786 :797 :885 : 889 :890 :802 :794 stick

Changed 63 atom styles  

> color #2/R@N* blue

> color #2/R@O* red

> windowsize 600 600

Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/graphics.py", line 80, in resizeEvent  
v.draw(check_for_changes = False)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/view.py", line 159, in draw  
self._draw_scene(camera, drawings)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/view.py", line 213, in _draw_scene  
draw_depth(r, opaque_drawings)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 1379, in draw_depth  
draw_opaque(r, drawings)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 1360, in draw_opaque  
_draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 1371, in _draw_multiple  
d.draw(renderer, draw_pass)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 684, in draw  
if not self.display:  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 311, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 311, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.4.9
OpenGL renderer: AMD Radeon Pro 455 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (2)

comment:1 by Eric Pettersen, 7 years ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → self._positions is None
Version: → 0.8

comment:2 by Tom Goddard, 7 years ago

Resolution: → duplicate
Status: assigned → closed

Duplicate of #1717.

Window resize causes error when ribbon changed since last redraw and shadows are shown. Error occurs because bounds() calculation causes graphics update, which causes ribbon recompute which deletes ribbon drawing that is part of the draw tree.

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