Opened 7 years ago

Closed 7 years ago

#1477 closed defect (can't reproduce)

Volume Viewer: wrapped C/C++ object of type QFrame has been deleted

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

Description 

The following bug report has been submitted:
Platform:        Linux-4.4.0-112-generic-x86_64-with-debian-stretch-sid
ChimeraX Version: 0.7 (2018-08-07)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.7 (2018-08-07)  
OpenGL version: 3.3.0 NVIDIA 390.87  
OpenGL renderer: Quadro K2200/PCIe/SSE2  
OpenGL vendor: NVIDIA Corporation  
How to cite UCSF ChimeraX  

open /home/szhu/Desktop/PAK-motor/FlgG-PAK/AVG/FlgG0116.cxs

opened ChimeraX session  

save session /home/szhu/Desktop/PAK-motor/FlgG-PAK/AVG/motor-FlgG.cxs

Session file format is not finalized, and thus might not be restorable in
other versions of ChimeraX.  

open /home/szhu/Desktop/PAK-motor/FlgG-PAK/AVG/ribo-hide-dust.mrc

Opened ribo-hide-dust.mrc, grid size 959,927,400, pixel 11,11,11, shown at
step 1, values float32  

view orient cofr false

view orient cofr false

view orient cofr false

ui mousemode rightMode translate selected models

open /home/szhu/Desktop/PAK-motor/FlgG-PAK/AVG/motor-FlgG.cxs

opened ChimeraX session  

open /home/szhu/Desktop/PAK-motor/FlgG-PAK/AVG/motor-FlgG.cxs

opened ChimeraX session  

help group

No help found for 'group'  

open /home/szhu/Desktop/PAK-motor/FlgG-PAK/AVG/ribo-hide-dust.mrc

Opened ribo-hide-dust.mrc, grid size 959,927,400, pixel 11,11,11, shown at
step 1, values float32  

view cofr false

hide dust

Expected one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds',
'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

help

dust

Unknown command: dust  

help help:user

didn't expected commands hrefs to be to tools/sequenceviewer.html on line 239  

open /home/szhu/Desktop/PAK-motor/FlgG-PAK/AVG/REAL-OMIM-eman1.mrc

Opened REAL-OMIM-eman1.mrc, grid size 959,927,400, pixel 11,11,11, shown at
step 1, values float32  

ui mousemode rightMode rotate and select

ui mousemode rightMode translate selected models

ui mousemode rightMode rotate and select

ui mousemode rightMode rotate and select

ui mousemode rightMode rotate and select

ui mousemode rightMode rotate selected models

ui mousemode rightMode rotate selected models

ui mousemode rightMode rotate selected models

lighting soft

lighting shadows true intensity 0.5

lighting soft

lighting full

lighting soft

ui mousemode rightMode translate selected models

ui mousemode rightMode rotate and select

ui mousemode rightMode rotate and select

ui mousemode rightMode rotate and select

ui mousemode rightMode rotate and select

ui mousemode rightMode rotate and select

ui mousemode rightMode rotate and select

ui mousemode rightMode rotate and select

ui mousemode rightMode rotate and select

ui mousemode rightMode rotate and select

ui mousemode rightMode rotate and select

ui mousemode rightMode rotate and select

ui mousemode rightMode rotate and select

ui mousemode rightMode rotate and select

ui mousemode rightMode rotate and select

ui mousemode rightMode rotate and select

ui mousemode rightMode rotate and select

ui mousemode rightMode rotate and select

ui mousemode rightMode translate selected models

ui mousemode rightMode translate selected models

ui mousemode rightMode rotate selected models

ui mousemode rightMode rotate selected models

ui mousemode rightMode rotate selected models

show target m

show target m

hide target m

show target m

toolshed show "Mouse Modes for Right Button"

ui mousemode rightMode translate selected models

ui mousemode rightMode rotate and select

ui mousemode rightMode rotate selected models

QXcbConnection: XCB error: 148 (Unknown), sequence: 56319, resource id: 0,
major code: 140 (Unknown), minor code: 20  

ui mousemode rightMode translate selected models

help help:user

surface dust #5 size 5

surface dust #5 size 15

surface dust #5 size 100

surface dust #5 size 150

surface dust #5 size 100

surface dust #5 size 150

surface dust #5 size 200

ui mousemode rightMode translate selected models

surface dust #6 size 150

surface dust #5 size 250

save session /home/szhu/Desktop/PAK-motor/FlgG-PAK/AVG/OMIM-ribo-motor.cxs

Session file format is not finalized, and thus might not be restorable in
other versions of ChimeraX.  

view orient cofr false

ui mousemode rightMode translate selected models

ui mousemode rightMode rotate and select

ui mousemode rightMode translate selected models

ui mousemode rightMode rotate selected models

Opened C-ring.lp30.mrc, grid size 100,100,100, pixel 11, shown at level 0.267,
step 1, values float32  

ui mousemode rightMode translate selected models

ui mousemode rightMode rotate selected models

Opened C-ring.lp30.mrc, grid size 100,100,100, pixel 11, shown at level 0.267,
step 1, values float32  

No model specified for saving map  

Opened C-ring.lp30.mrc, grid size 100,100,100, pixel 11, shown at level 0.267,
step 1, values float32  

help help:user

Traceback (most recent call last):  
  File "/home/szhu/chimerax/lib/python3.6/site-packages/chimerax/ui/gui.py",
line 1147, in <lambda>  
    dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)  
  File "/home/szhu/chimerax/lib/python3.6/site-packages/chimerax/ui/gui.py",
line 485, in close_request  
    tool_instance.delete()  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 124, in delete  
    super().delete()  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/core/tools.py", line 176, in delete  
    self.session.tools.remove([self])  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/core/tools.py", line 368, in remove  
    del self._tool_instances[tid]  
KeyError: 11  
  

KeyError: 11  
  
File "/home/szhu/chimerax/lib/python3.6/site-packages/chimerax/core/tools.py",
line 368, in remove  
del self._tool_instances[tid]  
  
See log for complete Python traceback.  
  
If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and
describe what you were doing and include a copy of the contents of the log.
Don't include any data you wish to remain private since a publicly viewable
bug report will be created.  

ui mousemode rightMode translate selected models

save #8,9 MM.mrc

Expected a models specifier or a keyword  

save #9 TT.mrc

Expected a models specifier or a keyword  

save # 9 TT.mrc

Expected a models specifier or a keyword  

save #9.1,9.2 TT.mrc

Expected a models specifier or a keyword  

save TT.mrc #9

Cannot write multiple volumes using format mrc  

save map TT.mrc #9

Cannot write multiple volumes using format mrc  

save #9 tt.mrc

Expected a models specifier or a keyword  

save model #9 tt.mrc

Expected a keyword  

save TT.mrc models #9

Cannot write multiple volumes using format mrc  

save TT.mrc models #9.1

ui mousemode rightMode translate selected models

ui mousemode rightMode rotate selected models

Opened C-ring.lp30.mrc, grid size 100,100,100, pixel 11, shown at level 0.267,
step 1, values float32  

ui mousemode rightMode translate selected models

Opened C-ring.lp30.mrc, grid size 100,100,100, pixel 11, shown at level 0.267,
step 1, values float32  
Traceback (most recent call last):  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 1847, in <lambda>  
    sm.addAction(style, lambda s=style: self.representation_changed_cb(s))  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 2351, in
representation_changed_cb  
    self.set_map_style(v, style)  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 2374, in set_map_style  
    maximum_intensity_projection = False)  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume.py", line 320, in set_parameters  
    self.call_change_callbacks('rendering options changed')  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume.py", line 156, in call_change_callbacks  
    cb(self, ct)  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 268, in data_region_changed  
    tp.update_panel_widgets(v, activate = False)  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 1633, in update_panel_widgets  
    hp.update_threshold_gui(message_cb = None)  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 2509, in update_threshold_gui  
    self.update_histogram(read_matrix, message_cb)  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 2591, in update_histogram  
    self.update_timer = timer = QTimer(self.frame)  
RuntimeError: wrapped C/C++ object of type QFrame has been deleted  
  

RuntimeError: wrapped C/C++ object of type QFrame has been deleted  
  
File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 2591, in update_histogram  
self.update_timer = timer = QTimer(self.frame)  
  
See log for complete Python traceback.  
  
If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and
describe what you were doing and include a copy of the contents of the log.
Don't include any data you wish to remain private since a publicly viewable
bug report will be created.  

Traceback (most recent call last):  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 1847, in <lambda>  
    sm.addAction(style, lambda s=style: self.representation_changed_cb(s))  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 2351, in
representation_changed_cb  
    self.set_map_style(v, style)  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 2370, in set_map_style  
    v.show(representation = style, show = v.shown())  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume.py", line 627, in show  
    self.set_representation(representation)  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume.py", line 594, in set_representation  
    self.call_change_callbacks('representation changed')  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume.py", line 156, in call_change_callbacks  
    cb(self, ct)  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 251, in data_region_changed  
    tp.update_panel_widgets(v, activate = False)  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 1633, in update_panel_widgets  
    hp.update_threshold_gui(message_cb = None)  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 2509, in update_threshold_gui  
    self.update_histogram(read_matrix, message_cb)  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 2591, in update_histogram  
    self.update_timer = timer = QTimer(self.frame)  
RuntimeError: wrapped C/C++ object of type QFrame has been deleted  
  

RuntimeError: wrapped C/C++ object of type QFrame has been deleted  
  
File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 2591, in update_histogram  
self.update_timer = timer = QTimer(self.frame)  
  
See log for complete Python traceback.  
  
If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and
describe what you were doing and include a copy of the contents of the log.
Don't include any data you wish to remain private since a publicly viewable
bug report will be created.  

Traceback (most recent call last):  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 1847, in <lambda>  
    sm.addAction(style, lambda s=style: self.representation_changed_cb(s))  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 2351, in
representation_changed_cb  
    self.set_map_style(v, style)  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 2385, in set_map_style  
    show_outline_box = True)  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume.py", line 320, in set_parameters  
    self.call_change_callbacks('rendering options changed')  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume.py", line 156, in call_change_callbacks  
    cb(self, ct)  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 268, in data_region_changed  
    tp.update_panel_widgets(v, activate = False)  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 1633, in update_panel_widgets  
    hp.update_threshold_gui(message_cb = None)  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 2509, in update_threshold_gui  
    self.update_histogram(read_matrix, message_cb)  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 2591, in update_histogram  
    self.update_timer = timer = QTimer(self.frame)  
RuntimeError: wrapped C/C++ object of type QFrame has been deleted  
  

RuntimeError: wrapped C/C++ object of type QFrame has been deleted  
  
File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 2591, in update_histogram  
self.update_timer = timer = QTimer(self.frame)  
  
See log for complete Python traceback.  
  
If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and
describe what you were doing and include a copy of the contents of the log.
Don't include any data you wish to remain private since a publicly viewable
bug report will be created.  

ui mousemode rightMode rotate selected models

ui mousemode rightMode translate selected models

ui mousemode rightMode translate selected models

ui mousemode rightMode rotate selected models

ui mousemode rightMode translate selected models

ui mousemode rightMode rotate selected models

ui mousemode rightMode translate selected models

ui mousemode rightMode translate selected models

ui mousemode rightMode translate selected models

ui mousemode rightMode translate selected models

ui mousemode rightMode rotate selected models

ui mousemode rightMode translate selected models

ui mousemode rightMode rotate selected models

ui mousemode rightMode translate selected models

ui mousemode rightMode translate selected models

close #11

ui mousemode rightMode translate selected models

ui mousemode rightMode rotate selected models

ui mousemode rightMode translate selected models

ui mousemode rightMode rotate selected models

ui mousemode rightMode translate selected models

close #7

Opened C-ring.lp30.mrc, grid size 100,100,100, pixel 11, shown at level 0.267,
step 1, values float32  

ui mousemode rightMode translate selected models

ui mousemode rightMode rotate selected models

Opened C-ring.lp30.mrc, grid size 100,100,100, pixel 11, shown at level 0.267,
step 1, values float32  

ui mousemode rightMode translate selected models

ui mousemode rightMode rotate selected models

ui mousemode rightMode translate selected models

ui mousemode rightMode rotate selected models

ui mousemode rightMode translate selected models

view orient cofr false

ui mousemode rightMode translate selected models

ui mousemode rightMode rotate selected models

ui mousemode rightMode translate selected models

ui mousemode rightMode rotate selected models

ui mousemode rightMode translate selected models

ui mousemode rightMode rotate selected models

ui mousemode rightMode translate selected models

ui mousemode rightMode rotate selected models

view orient cofr false

ui mousemode rightMode translate selected models

ui mousemode rightMode rotate selected models

ui mousemode rightMode translate selected models

ui mousemode rightMode translate selected models

view orient cofr false

ui mousemode rightMode translate selected models

ui mousemode rightMode rotate selected models

ui mousemode rightMode translate selected models

ui mousemode rightMode rotate selected models

ui mousemode rightMode translate selected models

view orient cofr false

ui mousemode rightMode translate selected models

ui mousemode rightMode rotate selected models

surface dust #5 size 250

surface dust #5 size 300

surface dust #5 size 330

surface dust #5 size 300

surface dust #5 size 350

view cofr false

view orient cofr false

set silhouettes true

set silhouettes false

set silhouettes true

set silhouettes false

set silhouettes true

set silhouettes false

set silhouettes true

set silhouettes false

lighting flat

lighting flat

set silhouettes false

lighting flat

lighting full

lighting full

lighting full

set silhouettes false

lighting soft

lighting shadows true intensity 0.5

lighting simple

lighting soft

lighting soft

lighting flat

lighting soft

set silhouettes false

help help:credits.html

lighting gentle

lighting soft

lighting gentle

lighting soft

save ~/Desktop/PAKFleNFlgG-A019.png width 600 height 600 supersample 3
transparentBackground true

view orient cofr false

save ~/Desktop/PAKFleNFlgG-A019-1.png width 600 height 600 supersample 3
transparentBackground true

view orient cofr false

view orient cofr false

view orient cofr false

view orient cofr false

toolshed show Shell

/home/szhu/chimerax/lib/python3.6/site-packages/IPython/core/history.py:226:
UserWarning: IPython History requires SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  

show selAtoms

style selAtoms stick

Changed 0 atom styles  

view cofr false

view orient cofr false

help help:user/tools/graphics.html

view initial

view orient

view orient

view initial

view orient cofr false

view cofr false

view cofr false

view orient cofr false

Traceback (most recent call last):  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 1847, in <lambda>  
    sm.addAction(style, lambda s=style: self.representation_changed_cb(s))  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 2351, in
representation_changed_cb  
    self.set_map_style(v, style)  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 2370, in set_map_style  
    v.show(representation = style, show = v.shown())  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume.py", line 627, in show  
    self.set_representation(representation)  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume.py", line 594, in set_representation  
    self.call_change_callbacks('representation changed')  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume.py", line 156, in call_change_callbacks  
    cb(self, ct)  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 251, in data_region_changed  
    tp.update_panel_widgets(v, activate = False)  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 1633, in update_panel_widgets  
    hp.update_threshold_gui(message_cb = None)  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 2509, in update_threshold_gui  
    self.update_histogram(read_matrix, message_cb)  
  File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 2591, in update_histogram  
    self.update_timer = timer = QTimer(self.frame)  
RuntimeError: wrapped C/C++ object of type QFrame has been deleted  
  

RuntimeError: wrapped C/C++ object of type QFrame has been deleted  
  
File "/home/szhu/chimerax/lib/python3.6/site-
packages/chimerax/map/volume_viewer.py", line 2591, in update_histogram  
self.update_timer = timer = QTimer(self.frame)  
  
See log for complete Python traceback.  
  
If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and
describe what you were doing and include a copy of the contents of the log.
Don't include any data you wish to remain private since a publicly viewable
bug report will be created.  




OpenGL version: 3.3.0 NVIDIA 390.87
OpenGL renderer: Quadro K2200/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (3)

comment:1 by Eric Pettersen, 7 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Volume Viewer: wrapped C/C++ object of type QFrame has been deleted

comment:2 by Eric Pettersen, 7 years ago

There was an earlier error deleting/removing the Volume Viewer tool for the list of tool instances, so this may be a "core" error that needs reassignment...

comment:3 by Tom Goddard, 7 years ago

Resolution: → can't reproduce
Status: assigned → closed

Appears to be a Toolshed bug in ChimeraX 0.7. User clicked close button on window frame of Volume Viewer panel, gui was deleted, but tool manager threw an error and apparently left the deleted volume viewer in the list of tools, so next time a volume was opened it got reused and caused further errors because all the GUI elements had been deleted.

Could not reproduce this in current ChimeraX daily. Not worth investigating cause in old (August 2018) ChimeraX.

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