Opened 5 years ago

Closed 5 years ago

#3294 closed defect (fixed)

Deleted color-blob check box still being used

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-3.10.0-1062.el7.x86_64-x86_64-with-centos-7.7.1908-Core
ChimeraX Version: 1.0rc202005200643 (2020-05-20 06:43:06 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.0rc202005200643 (2020-05-20)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open cryosparc_P23_J774__localfilter_3.1A.mrc

Opened cryosparc_P23_J774__localfilter_3.1A.mrc, grid size 240,240,240, pixel
1.09, shown at level 0.314, step 1, values float32  

> lighting soft

> set bgColor white

> set bgColor black

> set bgColor white

> open
> /home/Wulab/Desktop/WORK/YN_new/Models/Refinement/YN_v6_real_space_refined.pdb

Chain information for YN_v6_real_space_refined.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide line

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

> hide linkline

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

> volume #1 level 0.5053

> volume #1 level 0.9354

> ui tool show "Volume Viewer"

> hide #!1 models

> lighting simple

> lighting soft

> dssp

> ui tool show "Show Volume Menu"

> show #!1 models

> transparency #0 50

> transparency volume #0 50

Missing or invalid "percent" argument: Expected a number  

> transparency 50 volume #0

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> transparency 50 volume

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> hide #!2 models

> lighting soft

> lighting simple

> lighting soft

> lighting full

> lighting soft

> ui tool show "Show Volume Menu"

> ui tool show "Map Coordinates"

> show #!2 models

> hide #!2 models

> show #!2 models

> ui tool show "Fit in Map"

Fit molecule YN_v6_real_space_refined.pdb (#2) to map
cryosparc_P23_J774__localfilter_3.1A.mrc (#1) using 12240 atoms  
average map value = 1.035, steps = 40  
shifted from previous position = 0.0133  
rotated from previous position = 0.00917 degrees  
atoms outside contour = 5959, contour level = 0.93536  
  
Position of YN_v6_real_space_refined.pdb (#2) relative to
cryosparc_P23_J774__localfilter_3.1A.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999999 -0.00007659 -0.00014042 0.01594125  
0.00007659 1.00000000 -0.00000645 -0.01435875  
0.00014042 0.00000644 0.99999999 -0.02040724  
Axis 0.04028224 -0.87719486 0.47844176  
Axis point 157.17546247 0.00000000 112.51591929  
Rotation angle (degrees) 0.00917173  
Shift along axis 0.00347390  
  
Fit molecule YN_v6_real_space_refined.pdb (#2) to map
cryosparc_P23_J774__localfilter_3.1A.mrc (#1) using 12240 atoms  
average map value = 1.035, steps = 40  
shifted from previous position = 0.0015  
rotated from previous position = 0.00256 degrees  
atoms outside contour = 5959, contour level = 0.93536  
  
Position of YN_v6_real_space_refined.pdb (#2) relative to
cryosparc_P23_J774__localfilter_3.1A.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999998 -0.00005589 -0.00017985 0.01729760  
0.00005589 1.00000000 -0.00000902 -0.01096003  
0.00017985 0.00000901 0.99999998 -0.02499565  
Axis 0.04783301 -0.95386140 0.29641261  
Axis point 145.37293468 0.00000000 95.13458505  
Rotation angle (degrees) 0.01080299  
Shift along axis 0.00387272  
  
Fit molecule YN_v6_real_space_refined.pdb (#2) to map
cryosparc_P23_J774__localfilter_3.1A.mrc (#1) using 12240 atoms  
average map value = 1.035, steps = 28  
shifted from previous position = 0.0159  
rotated from previous position = 0.0128 degrees  
atoms outside contour = 5964, contour level = 0.93536  
  
Position of YN_v6_real_space_refined.pdb (#2) relative to
cryosparc_P23_J774__localfilter_3.1A.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999998 0.00014111 -0.00010095 -0.00434835  
-0.00014111 0.99999999 0.00006189 0.01340237  
0.00010096 -0.00006188 0.99999999 -0.00503460  
Axis -0.33595315 -0.54803377 -0.76602511  
Axis point 87.10366185 35.65113300 0.00000000  
Rotation angle (degrees) 0.01055440  
Shift along axis -0.00202748  
  
Fit molecule YN_v6_real_space_refined.pdb (#2) to map
cryosparc_P23_J774__localfilter_3.1A.mrc (#1) using 12240 atoms  
average map value = 1.035, steps = 36  
shifted from previous position = 0.00462  
rotated from previous position = 0.00617 degrees  
atoms outside contour = 5966, contour level = 0.93536  
  
Position of YN_v6_real_space_refined.pdb (#2) relative to
cryosparc_P23_J774__localfilter_3.1A.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999997 0.00020897 -0.00014197 -0.00332340  
-0.00020898 0.99999998 -0.00001093 0.03268535  
0.00014197 0.00001096 0.99999999 -0.01812251  
Axis 0.04328694 -0.56142860 -0.82639226  
Axis point 146.95435515 15.19709820 -0.00000000  
Rotation angle (degrees) 0.01448874  
Shift along axis -0.00351805  
  

> volume #1 level 0.7918

> hide #!1 models

> select /B

1483 atoms, 1528 bonds, 2 pseudobonds, 2 models selected  

> color (#!2 & sel) red

> color (#!2 & sel) red

> color (#!2 & sel) #cc0000ff

> color (#!2 & sel) #ef2929ff

> color (#!2 & sel) #cc0000ff

> color (#!2 & sel) #a40000ff

> color (#!2 & sel) #cc0000ff

> color (#!2 & sel) #ef2929ff

> color (#!2 & sel) #cc0000ff

> select clear

> select /B

1483 atoms, 1528 bonds, 2 pseudobonds, 2 models selected  

> color (#!2 & sel) red

> select clear

> select /B:273

10 atoms, 10 bonds, 1 model selected  

> select up

212 atoms, 218 bonds, 1 model selected  

> select up

1483 atoms, 1528 bonds, 1 model selected  

> select up

12240 atoms, 12568 bonds, 1 model selected  

> show #!1 models

> volume show

> volume hide

> volume show

> volume hide

> volume show

> volume style surface

> volume style mesh

> volume style surface

> transparency 50

> volume showOutlineBox true

> volume showOutlineBox false

> volume style surface

> transparency 0

> ui tool show "Color Actions"

> ui tool show "Volume Viewer"

> ui mousemode right "crop volume"

> ui mousemode right "crop volume"

> ui mousemode right "crop volume"

> volume #1 region 0,0,0,239,226,239

> volume #1 region 0,0,0,239,214,239

> ui tool show "Segment Map"

> volume #1 region 0,0,0,239,214,239

> ui tool show "Volume Viewer"

> show #!1 target m

> hide #!2 models

> lighting simple

> lighting soft

> ui tool show "Measure and Color Blobs"

> help help:devel

> color zone

Missing or invalid "surfaces" argument: empty atom specifier  

> color surface

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color #1 byhetero

> show #!2 models

> hide #!1 models

> show #!1 models

> select sel @< 5

12240 atoms, 12568 bonds, 10 pseudobonds, 2 models selected  

> color (#!2 & sel) byhetero

> measure blob #!1.1 triangleNumber 17617 color #0000ccff outline true

Surface cryosparc_P23_J774__localfilter_3.1A.mrc #1.1 blob:  
volume = 2356.8  
area = 3716.7  
size = 52.821 35.945 19.524  
  

> measure blob #!1.1 triangleNumber 14898 color #d78030ff outline true

Surface cryosparc_P23_J774__localfilter_3.1A.mrc #1.1 blob:  
volume = 2356.8  
area = 3716.7  
size = 52.821 35.945 19.524  
  

> hide #!2 models

> show #!2 models

> ~select #2

Nothing selected  

> select #2

12240 atoms, 12568 bonds, 10 pseudobonds, 2 models selected  

> ~select #2

Nothing selected  

> hide #!1 models

> hide #!2 models

> show #!2 models

> show #!1 models

> select clear

> hide #!1 models

> show #!1 models

> hide #!1 models

> select /B:273

10 atoms, 10 bonds, 1 model selected  

> select up

212 atoms, 218 bonds, 1 model selected  

> select up

1483 atoms, 1528 bonds, 1 model selected  

> show #!1 models

> hide #!1 models

> show #!1 models

> select sel @< 5

1823 atoms, 1819 bonds, 2 pseudobonds, 2 models selected  

> select sel @< 5

2377 atoms, 2405 bonds, 2 pseudobonds, 2 models selected  

> surface (#!2 & sel)

> surface hidePatches (#!2 & sel)

> volume showOutlineBox true

Drag select of 1 cryosparc_P23_J774__localfilter_3.1A.mrc , 60 atoms, 2
pseudobonds, 166 residues, 57 bonds  

> hide #!1 models

> show #!1 models

> hide #!2 models

Drag select of 1 cryosparc_P23_J774__localfilter_3.1A.mrc  

> select clear

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> select /B:331

9 atoms, 8 bonds, 1 model selected  

> select up

24 atoms, 23 bonds, 2 models selected  

> select up

1483 atoms, 1528 bonds, 2 models selected  

> select up

12240 atoms, 12568 bonds, 2 models selected  

> select up

12240 atoms, 12568 bonds, 10 pseudobonds, 4 models selected  

> show #!1 models

> show target m

> select #1

2 models selected  

> select #1

2 models selected  

> select #2

12240 atoms, 12568 bonds, 10 pseudobonds, 2 models selected  

> measure blob #!1.1 triangleNumber 41357 color #8582aeff outline true
> outlineColor #ff99ccff

Surface cryosparc_P23_J774__localfilter_3.1A.mrc #1.1 blob:  
volume = 19895  
area = 31106  
size = 116.88 66.958 68.363  
  

> measure blob #!1.1 triangleNumber 38447 color #e3740eff outline true
> outlineColor #ff99ccff

Surface cryosparc_P23_J774__localfilter_3.1A.mrc #1.1 blob:  
volume = 2356.8  
area = 3716.7  
size = 52.821 35.945 19.524  
  

> measure blob #!1.1 triangleNumber 123799 color #b60bb3ff outline true
> outlineColor #ff99ccff

Surface cryosparc_P23_J774__localfilter_3.1A.mrc #1.1 blob:  
volume = 19895  
area = 31106  
size = 116.88 66.958 68.363  
  

> measure blob #!1.1 triangleNumber 24951 color #db277cff outline true
> outlineColor #ff99ccff

Surface cryosparc_P23_J774__localfilter_3.1A.mrc #1.1 blob:  
volume = 2695.6  
area = 4264.4  
size = 81.296 32.693 25.125  
  

> measure blob #!1.1 triangleNumber 788 color #f93217ff outline true
> outlineColor #ff99ccff

Surface cryosparc_P23_J774__localfilter_3.1A.mrc #1.1 blob:  
volume = 1876.1  
area = 3227.4  
size = 44.94 31.663 23.662  
  

> measure blob #!1.1 triangleNumber 23460 color #fe1012ff outline true
> outlineColor #ff99ccff

Surface cryosparc_P23_J774__localfilter_3.1A.mrc #1.1 blob:  
volume = 2356.8  
area = 3716.7  
size = 52.821 35.945 19.524  
  

> measure blob #!1.1 triangleNumber 163885 color #ec0661ff outline true
> outlineColor #ff99ccff

Surface cryosparc_P23_J774__localfilter_3.1A.mrc #1.1 blob:  
volume = 6086.2  
area = 9843.1  
size = 77.907 69.893 37.387  
  

> measure blob #!1.1 triangleNumber 98492 color #71e404ff outline true
> outlineColor #ff99ccff

Surface cryosparc_P23_J774__localfilter_3.1A.mrc #1.1 blob:  
volume = 19895  
area = 31106  
size = 116.88 66.958 68.363  
  

> measure blob #!1.1 triangleNumber 15900 color #9ead64ff outline true
> outlineColor #ff99ccff

Surface cryosparc_P23_J774__localfilter_3.1A.mrc #1.1 blob:  
volume = 108.6  
area = 202.28  
size = 12.937 8.4771 6.9205  
  

> undo

> select #2

12240 atoms, 12568 bonds, 10 pseudobonds, 2 models selected  

> hide #!2 target m

> hide #!2 target m

> hide #!2 target m

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!2 models

> show #!1 models

> close #1

> close

> open
> /home/Wulab/Desktop/WORK/YN_new/Models/Refinement/cryosparc_P23_J774__localfilter_3.1A.mrc
> format mrc

Opened cryosparc_P23_J774__localfilter_3.1A.mrc, grid size 240,240,240, pixel
1.09, shown at level 0.314, step 1, values float32  

> volume #1 level 1.074

Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/pick_blobs/pickblobs.py", line 201, in mouse_down  
self._pick_blob(pick)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/pick_blobs/pickblobs.py", line 220, in _pick_blob  
if settings.color_blob:  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/pick_blobs/pickblobs.py", line 335, in color_blob  
return self._color_blob.checkState() == Qt.Checked  
RuntimeError: wrapped C/C++ object of type QCheckBox has been deleted  
  
RuntimeError: wrapped C/C++ object of type QCheckBox has been deleted  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/pick_blobs/pickblobs.py", line 335, in color_blob  
return self._color_blob.checkState() == Qt.Checked  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/pick_blobs/pickblobs.py", line 201, in mouse_down  
self._pick_blob(pick)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/pick_blobs/pickblobs.py", line 220, in _pick_blob  
if settings.color_blob:  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/pick_blobs/pickblobs.py", line 335, in color_blob  
return self._color_blob.checkState() == Qt.Checked  
RuntimeError: wrapped C/C++ object of type QCheckBox has been deleted  
  
RuntimeError: wrapped C/C++ object of type QCheckBox has been deleted  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/pick_blobs/pickblobs.py", line 335, in color_blob  
return self._color_blob.checkState() == Qt.Checked  
  
See log for complete Python traceback.  
  

> open
> /home/Wulab/Desktop/WORK/YN_new/Models/Refinement/YN_v6_real_space_refined.pdb
> format pdb

Chain information for YN_v6_real_space_refined.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> volume #1 level 0.9391

Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/pick_blobs/pickblobs.py", line 201, in mouse_down  
self._pick_blob(pick)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/pick_blobs/pickblobs.py", line 220, in _pick_blob  
if settings.color_blob:  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/pick_blobs/pickblobs.py", line 335, in color_blob  
return self._color_blob.checkState() == Qt.Checked  
RuntimeError: wrapped C/C++ object of type QCheckBox has been deleted  
  
RuntimeError: wrapped C/C++ object of type QCheckBox has been deleted  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/pick_blobs/pickblobs.py", line 335, in color_blob  
return self._color_blob.checkState() == Qt.Checked  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 430.50
OpenGL renderer: Quadro P4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision 7920 Tower
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 32 Intel(R) Xeon(R) Silver 4110 CPU @ 2.10GHz
Cache Size: 11264 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           125G        6.8G         49G        181M         68G        117G
	Swap:          4.0G          0B        4.0G

Graphics:
	73:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104GL [Quadro P4000] [10de:1bb1] (rev a1)	
	Subsystem: Dell Device [1028:11a3]	
	Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Deleted color-blob check box still being used

comment:2 by Tom Goddard, 5 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

Pick blobs mouse mode used after pick blobs gui panel was closed. Was not recreating panel.

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