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Opened 10 months ago
Closed 10 months ago
#16585 closed defect (duplicate)
Volume Viewer after session restore: wrapped C/C++ object of type QScrollArea has been deleted
| Reported by: | 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: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/jingyu/Desktop/Image
> processing/RNA_granules_with_spermine_nuclease/Non_uniform_refinement/After_3DVA_2nd_join/Chimera_session_to_make_figures/RNA_granules_ChimeraX_session_to_generate_figures.cxs"
Traceback (most recent call last):
File "/Applications/ChimeraX-1.4
1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/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
Populating font family aliases took 359 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/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 "/Applications/ChimeraX-1.4
1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/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 "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Opened
Non_uniform_refine_with_mask_motion_80S_with_AP_PE_tRNA_2ndjoin_J166.mrc as
#3, grid size 448,448,448, pixel 1.09, shown at step 1, values float32
Traceback (most recent call last):
File "/Applications/ChimeraX-1.4
1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/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 "/Users/jingyu/Library/Application Support/ChimeraX/1.4/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 "/Applications/ChimeraX-1.4
1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/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 "/Users/jingyu/Library/Application Support/ChimeraX/1.4/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 "/Applications/ChimeraX-1.4
1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/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 "/Users/jingyu/Library/Application Support/ChimeraX/1.4/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 "/Applications/ChimeraX-1.4
1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/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 "/Users/jingyu/Library/Application Support/ChimeraX/1.4/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 "/Applications/ChimeraX-1.4
1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/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 "/Users/jingyu/Library/Application Support/ChimeraX/1.4/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 "/Applications/ChimeraX-1.4
1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/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 "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Opened 80S_with_AP_PE_tRNA_J166_background.mrc as #6.1, grid size 448,448,448,
pixel 1.09, shown at level 0.0872, step 1, values float32
Opened 80S_with_AP_PE_tRNA_J166_AP_tRNA.mrc as #6.2, grid size 448,448,448,
pixel 1.09, shown at level 0.0655, step 1, values float32
Opened 80S_with_AP_PE_tRNA_J166_PE_tRNA.mrc as #6.3, grid size 448,448,448,
pixel 1.09, shown at level 0.071, step 1, values float32
Traceback (most recent call last):
File "/Applications/ChimeraX-1.4
1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/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 "/Users/jingyu/Library/Application Support/ChimeraX/1.4/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 "/Applications/ChimeraX-1.4
1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/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 "/Users/jingyu/Library/Application Support/ChimeraX/1.4/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 "/Applications/ChimeraX-1.4
1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/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 "/Users/jingyu/Library/Application Support/ChimeraX/1.4/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 "/Applications/ChimeraX-1.4
1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/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 "/Users/jingyu/Library/Application Support/ChimeraX/1.4/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 "/Applications/ChimeraX-1.4
1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/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 "/Users/jingyu/Library/Application Support/ChimeraX/1.4/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 "/Applications/ChimeraX-1.4
1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/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 "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Opened
Non_uniform_refine_with_mask_motion_80S_with_PP_EE_tRNA_2ndjoin_J169.mrc as
#1, grid size 448,448,448, pixel 1.09, shown at level 0.0853, step 1, values
float32
Traceback (most recent call last):
File "/Applications/ChimeraX-1.4
1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/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 "/Users/jingyu/Library/Application Support/ChimeraX/1.4/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 "/Applications/ChimeraX-1.4
1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/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 "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Opened 80S_with_PP_EE_tRNA_J169_background.mrc as #9.1, grid size 448,448,448,
pixel 1.09, shown at level 0.0853, step 1, values float32
Opened 80S_with_PP_EE_tRNA_J169_PP_tRNA.mrc as #9.2, grid size 448,448,448,
pixel 1.09, shown at level 0.0715, step 1, values float32
Opened 80S_with_PP_EE_tRNA_J169_EE_tRNA.mrc as #9.3, grid size 448,448,448,
pixel 1.09, shown at level 0.0775, step 1, values float32
Traceback (most recent call last):
File "/Applications/ChimeraX-1.4
1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/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 "/Users/jingyu/Library/Application Support/ChimeraX/1.4/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 "/Applications/ChimeraX-1.4
1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/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 "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Log from Wed Jan 8 17:54:40 2025You can double click a model's Name or ID in
the model panel to edit those fields
Using preset: ArtiaX / Artiax Default
Preset expands to these ChimeraX commands:
set bgColor black
lighting depthCue false
camera ortho
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/jingyu/Desktop/Image
> processing/RNA_granules_with_spermine_nuclease/PDB atomic model/6HCJ.pdb"
Summary of feedback from opening /Users/jingyu/Desktop/Image
processing/RNA_granules_with_spermine_nuclease/PDB atomic model/6HCJ.pdb
---
warnings | Bad residue range for secondary structure: HELIX 210 210 ILE M 123
ARG M 132 1 10
Bad residue range for secondary structure: SHEET 192 192 1 ARG C 78 VAL C 79 0
Bad residue range for secondary structure: SHEET 213 213 1 PHE F 210 LYS F 211
0
Bad residue range for secondary structure: SHEET 257 257 1 LEU N 36 ALA N 39 0
Bad residue range for secondary structure: SHEET 284 284 1 ARG S 83 TYR S 84 0
3 messages similar to the above omitted
Chain information for 6HCJ.pdb #2
---
Chain | Description
1 | No description available
3 | No description available
5 | No description available
7 | No description available
8 | No description available
A | 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 | 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
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
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 | No description available
o | No description available
p | No description available
q | No description available
r | No description available
t | No description available
u | No description available
v | No description available
w | No description available
> open "/Users/jingyu/Desktop/Image
> processing/RNA_granules_with_spermine_nuclease/Non_uniform_refinement/After_3DVA_2nd_join/Non_uniform_refine_with_mask_motion_80S_with_AP_PE_tRNA_2ndjoin_J166.mrc"
Opened
Non_uniform_refine_with_mask_motion_80S_with_AP_PE_tRNA_2ndjoin_J166.mrc as
#3, grid size 448,448,448, pixel 1.09, shown at level 0.0872, step 2, values
float32
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> nucleotides atoms
> style nucleic stick
Changed 124380 atom styles
> nucleotides atoms
> style nucleic stick
Changed 124380 atom styles
> style ball
Changed 219683 atom styles
> show cartoons
> hide atoms
> hide surfaces
> show surfaces
[Repeated 1 time(s)]
> hide surfaces
> fitmap #2 inMap #3
Fit molecule 6HCJ.pdb (#2) to map
Non_uniform_refine_with_mask_motion_80S_with_AP_PE_tRNA_2ndjoin_J166.mrc (#3)
using 219683 atoms
average map value = 0.1191, steps = 820
shifted from previous position = 45.2
rotated from previous position = 53.2 degrees
atoms outside contour = 92945, contour level = 0.087155
Position of 6HCJ.pdb (#2) relative to
Non_uniform_refine_with_mask_motion_80S_with_AP_PE_tRNA_2ndjoin_J166.mrc (#3)
coordinates:
Matrix rotation and translation
0.66048689 -0.47659661 0.58018337 81.06264542
0.22194354 0.86211185 0.45552631 -106.15828368
-0.71728525 -0.17210120 0.67519112 327.24886199
Axis -0.39186181 0.81007985 0.43613640
Axis point 404.71349596 0.00000000 80.25187988
Rotation angle (degrees) 53.20920616
Shift along axis 24.96310077
> volume #3 step 1
> select /q
1580 atoms, 1764 bonds, 2 pseudobonds, 75 residues, 3 models selected
> color (#!2 & sel) red
> select add /3
3184 atoms, 3559 bonds, 2 pseudobonds, 150 residues, 4 models selected
> color (#!2 & sel) yellow
> select clear
> select add /q
1580 atoms, 1764 bonds, 2 pseudobonds, 75 residues, 3 models selected
> color (#!2 & sel) red
> select add /3
3184 atoms, 3559 bonds, 2 pseudobonds, 150 residues, 4 models selected
> select ~sel
216499 atoms, 232194 bonds, 450 pseudobonds, 17796 residues, 9 models selected
> hide sel cartoons
> select clear
> select add #2
219683 atoms, 235753 bonds, 452 pseudobonds, 17946 residues, 3 models selected
> ui tool show "Color Zone"
> color zone #3 near #2 distance 6.54
> color #2 #ff0000fe
> color #2 #747474fe
> color single #3
> select clear
[Repeated 1 time(s)]
> select add /3
1604 atoms, 1795 bonds, 75 residues, 1 model selected
> color (#!2 & sel) yellow
> select add /q
3184 atoms, 3559 bonds, 2 pseudobonds, 150 residues, 4 models selected
> color (#!2 & sel) red
> select clear
> select add /3
1604 atoms, 1795 bonds, 75 residues, 1 model selected
> color (#!2 & sel) yellow
> select add /q
3184 atoms, 3559 bonds, 2 pseudobonds, 150 residues, 4 models selected
> color zone #3 near #2 distance 6.54
> hide #!1 models
> hide #!3 models
> show #!3 models
> hide #3.1 models
> show #3.1 models
> volume splitbyzone #3
Opened
Non_uniform_refine_with_mask_motion_80S_with_AP_PE_tRNA_2ndjoin_J166.mrc 0 as
#4.1, grid size 448,448,448, pixel 1.09, shown at level 0.0872, step 1, values
float32
Opened
Non_uniform_refine_with_mask_motion_80S_with_AP_PE_tRNA_2ndjoin_J166.mrc 1 as
#4.2, grid size 448,448,448, pixel 1.09, shown at level 0.0872, step 1, values
float32
Opened
Non_uniform_refine_with_mask_motion_80S_with_AP_PE_tRNA_2ndjoin_J166.mrc 2 as
#4.3, grid size 448,448,448, pixel 1.09, shown at level 0.0872, step 1, values
float32
Opened
Non_uniform_refine_with_mask_motion_80S_with_AP_PE_tRNA_2ndjoin_J166.mrc 3 as
#4.4, grid size 448,448,448, pixel 1.09, shown at level 0.0872, step 1, values
float32
> volume #4.2 color #747474fe
> close #4.3
> close #4.4
> close #4.2
> close #4.1
> color zone #3 near sel distance 6.54
> volume splitbyzone #3
Opened
Non_uniform_refine_with_mask_motion_80S_with_AP_PE_tRNA_2ndjoin_J166.mrc 0 as
#5.1, grid size 448,448,448, pixel 1.09, shown at level 0.0872, step 1, values
float32
Opened
Non_uniform_refine_with_mask_motion_80S_with_AP_PE_tRNA_2ndjoin_J166.mrc 1 as
#5.2, grid size 448,448,448, pixel 1.09, shown at level 0.0872, step 1, values
float32
Opened
Non_uniform_refine_with_mask_motion_80S_with_AP_PE_tRNA_2ndjoin_J166.mrc 2 as
#5.3, grid size 448,448,448, pixel 1.09, shown at level 0.0872, step 1, values
float32
> volume #5.1 color #b2b2b2
> close #5.2
> close #5.1
> close #5.3
> color zone #3 near sel distance 5
[Repeated 1 time(s)]
> color zone #3 near sel distance 4.65
> color zone #3 near sel distance 2.25
> select clear
> volume splitbyzone #3
Opened
Non_uniform_refine_with_mask_motion_80S_with_AP_PE_tRNA_2ndjoin_J166.mrc 0 as
#6.1, grid size 448,448,448, pixel 1.09, shown at level 0.0872, step 1, values
float32
Opened
Non_uniform_refine_with_mask_motion_80S_with_AP_PE_tRNA_2ndjoin_J166.mrc 1 as
#6.2, grid size 448,448,448, pixel 1.09, shown at level 0.0872, step 1, values
float32
Opened
Non_uniform_refine_with_mask_motion_80S_with_AP_PE_tRNA_2ndjoin_J166.mrc 2 as
#6.3, grid size 448,448,448, pixel 1.09, shown at level 0.0872, step 1, values
float32
> volume #6.1 color #b2b2b25b
> volume #6.1 color #b2b2b240
> volume #6.3 level 0.06968
> set bgColor white
> volume #6.1 color #b2b2b24e
> volume #6.1 color #8a8a8a4e
> volume #6.1 color #42799c4e
> volume #6.1 color #792e9c4e
> volume #6.1 color #aaa0b24e
> volume #6.1 color #acadb24e
> surface dust #6.1 size 10.9
> surface dust #6.2 size 10.9
> surface dust #6.3 size 10.9
> volume #6.3 level 0.07103
> volume #6.2 level 0.0777
> ui tool show "Side View"
> open "/Users/jingyu/Desktop/Image
> processing/RNA_granules_with_spermine_nuclease/PDB atomic
> model/7B7D_with_AA_PP_tRNA_Yeast.pdb"
Summary of feedback from opening /Users/jingyu/Desktop/Image
processing/RNA_granules_with_spermine_nuclease/PDB atomic
model/7B7D_with_AA_PP_tRNA_Yeast.pdb
---
warnings | Bad residue range for secondary structure: HELIX 162 162 PRO L 32
ASN L 43 1 12
Bad residue range for secondary structure: HELIX 169 169 LEU L 235 LEU L 238 1
4
Bad residue range for secondary structure: HELIX 171 171 GLU L 252 TRP L 262 1
11
Bad residue range for secondary structure: HELIX 181 181 TRP L 95 LYS L 112 1
18
Bad residue range for secondary structure: HELIX 188 188 LYS L 262 TYR L 272 1
11
123 messages similar to the above omitted
Chain information for 7B7D_with_AA_PP_tRNA_Yeast.pdb #7
---
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
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
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
d | No description available
e | No description available
f | No description available
g | No description available
> show cartoons
> hide atoms
> show cartoons
> hide cartoons
> select add #7
211144 atoms, 226602 bonds, 8 pseudobonds, 17543 residues, 2 models selected
> show sel cartoons
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 3 maps.
> select subtract #7
Nothing selected
> select add #7
211144 atoms, 226602 bonds, 8 pseudobonds, 17543 residues, 2 models selected
> hide #4 models
> show #4 models
> hide #4 models
Must specify one map, got 0
> hide #5 models
> show #5 models
> hide #5 models
> show #4 models
> hide #4 models
> show #5 models
> show #4 models
> hide #!6 models
> show #!6 models
> hide #5 models
> show #5 models
> hide #4 models
> hide #5 models
> show #4 models
> hide #4 models
> show #5 models
Must specify one map, got 0
> fitmap #4 #7
Missing required "in_map" argument
> fitmap #7 inMap map #4
Invalid "inMap" argument: invalid density map specifier
Must specify one map, got 0
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,11.94,0,1,0,-28.208,0,0,1,74.021
> ui mousemode right translate
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 3 maps.
> hide #!2 models
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 3 maps.
> hide #1.1 models
> hide #1.2 models
> hide #1.3 models
> hide #5 models
> hide #3.1 models
> hide #!6.3 models
> hide #!6.1 models
> hide #!6 models
> hide #!6.2 models
> show #!6 models
> hide #!6 models
> show #5 models
> hide #5 models
> show #!3 models
> fitmap #7 inMap #3
Fit molecule 7B7D_with_AA_PP_tRNA_Yeast.pdb (#7) to map
Non_uniform_refine_with_mask_motion_80S_with_AP_PE_tRNA_2ndjoin_J166.mrc (#3)
using 211144 atoms
average map value = 0.03655, steps = 268
shifted from previous position = 40.6
rotated from previous position = 17 degrees
atoms outside contour = 180570, contour level = 0.087155
Position of 7B7D_with_AA_PP_tRNA_Yeast.pdb (#7) relative to
Non_uniform_refine_with_mask_motion_80S_with_AP_PE_tRNA_2ndjoin_J166.mrc (#3)
coordinates:
Matrix rotation and translation
0.95665448 -0.11176365 0.26892581 -5.30843045
0.10597110 0.99371701 0.03600886 -22.99448463
-0.27126063 -0.00594967 0.96248754 126.84964945
Axis -0.07185583 0.92509298 0.37288031
Axis point 420.20747920 0.00000000 80.41210659
Rotation angle (degrees) 16.97553379
Shift along axis 26.40914175
> show #4 models
> show #5 models
> show #!6 models
> show #!6.1 models
> hide #!6.1 models
> show #!6.1 models
> show #!6.2 models
> show #!6.3 models
> ui mousemode right translate
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.8112,-0.58431,0.023157,193.97,0.46556,0.66928,0.57906,-122.24,-0.35385,-0.45895,0.81496,288.68
> view matrix models
> #7,0.69958,-0.58893,0.40466,149.67,0.37681,0.78523,0.49136,-115.5,-0.60713,-0.19126,0.77124,285.73
> ui mousemode right translate
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 4 maps.
> hide #!6.3 models
> hide #!6.2 models
> hide #4 models
> hide #5 models
> hide #!6 models
> hide #!6.1 models
> show #!6.1 models
> hide #!6.1 models
> show #!6.1 models
> hide #!6.1 models
> hide #!3 models
> show #!6.1 models
> fitmap #7 inMap #6.1
Fit molecule 7B7D_with_AA_PP_tRNA_Yeast.pdb (#7) to map
Non_uniform_refine_with_mask_motion_80S_with_AP_PE_tRNA_2ndjoin_J166.mrc 0
(#6.1) using 211144 atoms
average map value = 0.06635, steps = 336
shifted from previous position = 20.5
rotated from previous position = 14.2 degrees
atoms outside contour = 145497, contour level = 0.087155
Position of 7B7D_with_AA_PP_tRNA_Yeast.pdb (#7) relative to
Non_uniform_refine_with_mask_motion_80S_with_AP_PE_tRNA_2ndjoin_J166.mrc 0
(#6.1) coordinates:
Matrix rotation and translation
0.66314716 -0.44509162 0.60177179 73.44374604
0.24052136 0.88806043 0.39178839 -93.40549654
-0.70879144 -0.11507439 0.69596880 291.17573299
Axis -0.32418346 0.83822079 0.43850997
Axis point 365.48572818 0.00000000 68.76130687
Rotation angle (degrees) 51.42136030
Shift along axis 25.57978682
> hide #!6 models
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select add #7/S
211144 atoms, 226602 bonds, 8 pseudobonds, 17543 residues, 2 models selected
> hide #!7 models
> show #!7 models
> select clear
> select add #7/S
5267 atoms, 5688 bonds, 408 residues, 1 model selected
> select ~sel
425560 atoms, 456667 bonds, 460 pseudobonds, 35081 residues, 20 models
selected
> hide sel & #!7 cartoons
Drag select of 258 residues
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> hide sel surfaces
> hide sel cartoons
> select clear
Drag select of 76 residues
> select subtract #7/S:76
1584 atoms, 74 residues, 1 model selected
> select add #7/S:76
1635 atoms, 54 bonds, 77 residues, 1 model selected
> select subtract #7/S:76
1584 atoms, 74 residues, 1 model selected
> select add #7/S:76
1635 atoms, 54 bonds, 77 residues, 1 model selected
> color sel cornflower blue
> show #!6.2 models
> show #!6.3 models
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> hide #!6 models
Drag select of 75 residues
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> color sel purple
> show #4 models
> hide #4 models
> select add #4
1605 atoms, 75 residues, 2 models selected
> select subtract #4
1605 atoms, 75 residues, 1 model selected
> show #4 models
> show #5 models
> show #!6 models
> hide #!6 models
> hide #4 models
> hide #5 models
> hide #!6.1 models
> show #!6 models
> hide #!6 models
> show #5 models
> hide #5 models
> show #!6 models
> hide #!6 models
> select clear
> open "/Users/jingyu/Desktop/Image
> processing/RNA_granules_with_spermine_nuclease/PDB atomic
> model/6GZ5_PP_EE.pdb"
Summary of feedback from opening /Users/jingyu/Desktop/Image
processing/RNA_granules_with_spermine_nuclease/PDB atomic model/6GZ5_PP_EE.pdb
---
warnings | Bad residue range for secondary structure: HELIX 19 19 ILE B 35 LYS
B 44 1 10
Bad residue range for secondary structure: HELIX 23 23 LEU B 22 ASP B 27 1 6
Bad residue range for secondary structure: HELIX 30 30 GLU B 102 TYR B 115 1
14
Bad residue range for secondary structure: HELIX 34 34 LYS B 72 ASN B 83 1 12
Bad residue range for secondary structure: HELIX 36 36 ALA B 27 ILE B 30 1 4
212 messages similar to the above omitted
Chain information for 6GZ5_PP_EE.pdb #8
---
Chain | Description
A | No description available
A | No description available
B | No description available
B | No description available
C | No description available
> hide #!7-8 cartoons
> show #!7-8 cartoons
> hide #!7-8 cartoons
> select add #8
225601 atoms, 241677 bonds, 390 pseudobonds, 18791 residues, 3 models selected
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> show sel cartoons
> hide sel surfaces
> hide sel atoms
> show #5 models
> show #!6 models
> hide #!6 models
> hide #5 models
> show #!6.1 models
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.088881,-0.3221,-0.94253,476.72,-0.78823,0.55575,-0.26425,350.95,0.60892,0.76642,-0.20449,-113.99
> view matrix models
> #8,0.6852,0.42985,0.58799,-139.6,-0.50525,0.86198,-0.041362,164.72,-0.52461,-0.26874,0.80781,229.93
> view matrix models
> #8,0.3288,0.59348,0.73462,-120.89,-0.90399,0.4229,0.06295,351.15,-0.27331,-0.68479,0.67555,296.72
> view matrix models
> #8,0.39129,0.59089,0.70551,-130.02,-0.84163,0.53986,0.014631,315.97,-0.37223,-0.5995,0.70855,293.45
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.39129,0.59089,0.70551,-142.63,-0.84163,0.53986,0.014631,301.47,-0.37223,-0.5995,0.70855,336.28
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.63525,0.48462,0.60133,-156.15,-0.59672,0.80229,-0.016191,182.57,-0.49029,-0.34854,0.79883,285.89
> ui mousemode right translate
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 3 maps.
> hide #!6.2 models
> hide #!6.3 models
> hide #!7 models
> fitmap #8 inMap #6.1
Fit molecule 6GZ5_PP_EE.pdb (#8) to map
Non_uniform_refine_with_mask_motion_80S_with_AP_PE_tRNA_2ndjoin_J166.mrc 0
(#6.1) using 225601 atoms
average map value = 0.03556, steps = 224
shifted from previous position = 15.3
rotated from previous position = 7.99 degrees
atoms outside contour = 193239, contour level = 0.087155
Position of 6GZ5_PP_EE.pdb (#8) relative to
Non_uniform_refine_with_mask_motion_80S_with_AP_PE_tRNA_2ndjoin_J166.mrc 0
(#6.1) coordinates:
Matrix rotation and translation
0.64652269 0.36540689 0.66969111 -136.96262044
-0.54108501 0.83846207 0.06487158 156.62437355
-0.53780609 -0.40430079 0.73980094 328.46516282
Axis -0.29673661 0.76370359 -0.57332731
Axis point 379.06905347 0.00000000 417.03081910
Rotation angle (degrees) 52.23727512
Shift along axis -28.06162740
> select clear
> ui tool show "Side View"
> view
> ui mousemode right "rotate selected models"
[Repeated 1 time(s)]
> ui mousemode right "translate selected models"
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right "rotate selected models"
> select add #8
225601 atoms, 241677 bonds, 390 pseudobonds, 18791 residues, 3 models selected
> view matrix models
> #8,0.58791,0.34808,0.73021,-129.68,-0.51453,0.85745,0.0055299,156.5,-0.6242,-0.37897,0.6832,353.71
> ui mousemode right "move picked models"
> view matrix models
> #8,0.58791,0.34808,0.73021,-157.29,-0.51453,0.85745,0.0055299,85.938,-0.6242,-0.37897,0.6832,526.27
> view matrix models
> #8,0.58791,0.34808,0.73021,-139.48,-0.51453,0.85745,0.0055299,110.05,-0.6242,-0.37897,0.6832,530.23
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.58791,0.34808,0.73021,-129.93,-0.51453,0.85745,0.0055299,124.8,-0.6242,-0.37897,0.6832,522.5
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.87732,0.10649,-0.46794,509.03,0.15991,-0.85448,-0.49426,478.75,-0.45249,-0.50845,0.73262,503.71
> view matrix models
> #8,-0.68184,0.58243,0.44256,173.98,0.21887,-0.41485,0.88317,98.984,0.69799,0.69905,0.15539,31.947
> view matrix models
> #8,-0.87091,-0.23919,0.4293,426.28,0.40201,0.15569,0.9023,-90.655,-0.28266,0.95841,-0.03943,242.13
> view matrix models
> #8,-0.66872,-0.66775,0.32699,502.53,0.68519,-0.38273,0.6197,26.736,-0.28866,0.63845,0.71348,182.86
> view matrix models
> #8,-0.07152,-0.83819,0.54066,359.95,0.82581,0.25424,0.50338,-143.85,-0.55939,0.48249,0.67401,294.7
> view matrix models
> #8,-0.48287,-0.60734,0.63085,385.83,0.30082,0.56152,0.77085,-142.31,-0.8224,0.56199,-0.088436,480.77
> view matrix models
> #8,0.0070435,-0.1858,0.98256,96.733,0.036355,0.98198,0.18543,-73.437,-0.99931,0.034415,0.013671,635.67
> view matrix models
> #8,0.47194,-0.059633,0.87961,-28.38,-0.19901,0.96475,0.17218,-9.505,-0.85888,-0.25631,0.44344,593.71
> close #8
> open "/Users/jingyu/Desktop/Image
> processing/RNA_granules_with_spermine_nuclease/PDB atomic model/6R5Q.pdb"
Summary of feedback from opening /Users/jingyu/Desktop/Image
processing/RNA_granules_with_spermine_nuclease/PDB atomic model/6R5Q.pdb
---
warnings | Bad residue range for secondary structure: HELIX 277 277 ASP Q 108
LYS Q 132 1 25
Bad residue range for secondary structure: HELIX 294 294 LYS I 25 ILE I 33 1 9
Bad residue range for secondary structure: HELIX 296 296 THR I 60 ASN I 73 1
14
Bad residue range for secondary structure: HELIX 322 322 ARG O 80 GLY O 95 1
16
Bad residue range for secondary structure: SHEET 311 311 1 VAL C 62 TRP C 67 0
2 messages similar to the above omitted
Chain information for 6R5Q.pdb #8
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
8 | No description available
9 | 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
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
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
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 | 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
w | No description available
x | No description available
y | No description available
z | No description available
> hide #!8 atoms
> show #!8 cartoons
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> ui mousemode right "rotate selected models"
> select add #8
215870 atoms, 231583 bonds, 446 pseudobonds, 17690 residues, 3 models selected
> view matrix models
> #8,0.18639,-0.13313,0.97341,49.451,-0.89011,0.39653,0.22467,323.71,-0.4159,-0.90832,-0.044591,520.12
> view matrix models
> #8,0.45949,0.45621,0.76206,-123.88,-0.75532,0.65213,0.065027,257.19,-0.46729,-0.60548,0.64423,329.54
> fitmap #8 inMap #6.1
Fit molecule 6R5Q.pdb (#8) to map
Non_uniform_refine_with_mask_motion_80S_with_AP_PE_tRNA_2ndjoin_J166.mrc 0
(#6.1) using 215870 atoms
average map value = 0.03694, steps = 328
shifted from previous position = 46.3
rotated from previous position = 13.6 degrees
atoms outside contour = 184075, contour level = 0.087155
Position of 6R5Q.pdb (#8) relative to
Non_uniform_refine_with_mask_motion_80S_with_AP_PE_tRNA_2ndjoin_J166.mrc 0
(#6.1) coordinates:
Matrix rotation and translation
0.50814197 0.34537361 0.78899226 -119.84752075
-0.58914419 0.80761247 0.02590755 189.82333876
-0.62825222 -0.47799492 0.61385665 390.53416891
Axis -0.28455794 0.80032981 -0.52773002
Axis point 366.51425613 0.00000000 387.62367020
Rotation angle (degrees) 62.30236166
Shift along axis -20.07176318
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.80104,0.59061,0.097605,-123.43,-0.57873,0.80574,-0.12595,215.94,-0.15303,0.044407,0.98722,76.454
> view matrix models
> #8,0.37953,-0.56508,0.73256,147.97,0.062922,0.80573,0.58893,-71.972,-0.92304,-0.17742,0.34135,437.75
> view matrix models
> #8,0.43723,0.10287,0.89345,-61.805,-0.38885,0.9174,0.08466,103.16,-0.81094,-0.38443,0.44112,443.55
> view matrix models
> #8,0.59845,-0.6471,0.47235,163.63,0.52968,0.76192,0.37272,-133.96,-0.60108,0.027138,0.79873,224.16
> view matrix models
> #8,0.4383,-0.56174,0.70167,138.65,0.41858,0.8184,0.39373,-124.99,-0.79542,0.12113,0.59383,285.84
> fitmap #8 inMap #6.1
Fit molecule 6R5Q.pdb (#8) to map
Non_uniform_refine_with_mask_motion_80S_with_AP_PE_tRNA_2ndjoin_J166.mrc 0
(#6.1) using 215870 atoms
average map value = 0.06864, steps = 284
shifted from previous position = 11.8
rotated from previous position = 19 degrees
atoms outside contour = 146772, contour level = 0.087155
Position of 6R5Q.pdb (#8) relative to
Non_uniform_refine_with_mask_motion_80S_with_AP_PE_tRNA_2ndjoin_J166.mrc 0
(#6.1) coordinates:
Matrix rotation and translation
0.66289420 -0.48831455 0.56755632 85.93453813
0.23271488 0.85487655 0.46371312 -108.88563150
-0.71162846 -0.17531393 0.68033077 325.59217058
Axis -0.39903724 0.79878052 0.45024322
Axis point 408.52208961 0.00000000 73.42613733
Rotation angle (degrees) 53.19805624
Shift along axis 25.32886314
> ui mousemode right translate
> select add #8/3
215870 atoms, 231583 bonds, 446 pseudobonds, 17690 residues, 3 models selected
> color (#!8 & sel) yellow
> select clear
> select add #8/3
1597 atoms, 1784 bonds, 1 pseudobond, 75 residues, 2 models selected
> select ~sel
645100 atoms, 692154 bonds, 905 pseudobonds, 53104 residues, 23 models
selected
> select clear
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> hide #!6 models
> ui tool show "Side View"
> view orient
[Repeated 2 time(s)]
> select #8/3
1597 atoms, 1784 bonds, 1 pseudobond, 75 residues, 2 models selected
> select ~sel
645100 atoms, 692154 bonds, 905 pseudobonds, 53104 residues, 23 models
selected
> hide sel & #!8 cartoons
> show #!6 models
> select clear
> show #!6.2 models
> show #!6.3 models
> show #!7 models
> hide #!7 models
> show #!7 models
> select add #7
211144 atoms, 226602 bonds, 8 pseudobonds, 17543 residues, 2 models selected
> hide #!6 models
> hide #!6.1 models
Drag select of 75 residues, 1 pseudobonds
> color (#!8 & sel) cyan
> select add #6.1
1597 atoms, 1 pseudobond, 75 residues, 4 models selected
> select add #6.2
1597 atoms, 1 pseudobond, 75 residues, 6 models selected
> select add #6.3
1597 atoms, 1 pseudobond, 75 residues, 8 models selected
> show #!6.1 models
> select subtract #6.1
1597 atoms, 1 pseudobond, 75 residues, 6 models selected
> select subtract #6.2
1597 atoms, 1 pseudobond, 75 residues, 4 models selected
> select subtract #6.3
1597 atoms, 1 pseudobond, 75 residues, 2 models selected
> select clear
> hide #!6 models
> hide #!6.1 models
> hide #!6.3 models
> hide #!6.2 models
> show #!6.3 models
> show #!6.2 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> show #!7-8 cartoons
> select #7/S
5267 atoms, 5688 bonds, 408 residues, 1 model selected
> select ~sel
641430 atoms, 688250 bonds, 906 pseudobonds, 52771 residues, 23 models
selected
> select subtract #1
641430 atoms, 688250 bonds, 906 pseudobonds, 52771 residues, 72 models
selected
> select subtract #2
421747 atoms, 452497 bonds, 454 pseudobonds, 34825 residues, 69 models
selected
> select subtract #3
421747 atoms, 452497 bonds, 454 pseudobonds, 34825 residues, 14 models
selected
> select add #3.1
421747 atoms, 452497 bonds, 454 pseudobonds, 34825 residues, 15 models
selected
> select subtract #4
421747 atoms, 452497 bonds, 454 pseudobonds, 34825 residues, 14 models
selected
> select subtract #3.1
421747 atoms, 452497 bonds, 454 pseudobonds, 34825 residues, 13 models
selected
> select add #3
421747 atoms, 452497 bonds, 454 pseudobonds, 34825 residues, 15 models
selected
> select subtract #5
421747 atoms, 452497 bonds, 454 pseudobonds, 34825 residues, 14 models
selected
> select subtract #3.1
421747 atoms, 452497 bonds, 454 pseudobonds, 34825 residues, 13 models
selected
> select add #3
421747 atoms, 452497 bonds, 454 pseudobonds, 34825 residues, 14 models
selected
> select subtract #3
421747 atoms, 452497 bonds, 454 pseudobonds, 34825 residues, 12 models
selected
> select subtract #6
421747 atoms, 452497 bonds, 454 pseudobonds, 34825 residues, 5 models selected
> select subtract #8
205877 atoms, 220914 bonds, 8 pseudobonds, 17135 residues, 2 models selected
> hide sel cartoons
> show #!6.1 models
> hide #!6.1 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> select add #8
421747 atoms, 452497 bonds, 454 pseudobonds, 34825 residues, 5 models selected
> select subtract #8
205877 atoms, 220914 bonds, 8 pseudobonds, 17135 residues, 2 models selected
> select add #7
211144 atoms, 226602 bonds, 8 pseudobonds, 17543 residues, 2 models selected
> select add #8
427014 atoms, 458185 bonds, 454 pseudobonds, 35233 residues, 5 models selected
> select subtract #7
215870 atoms, 231583 bonds, 446 pseudobonds, 17690 residues, 3 models selected
> select #8/3
1597 atoms, 1784 bonds, 1 pseudobond, 75 residues, 2 models selected
> select ~sel
645100 atoms, 692154 bonds, 905 pseudobonds, 53104 residues, 23 models
selected
> select ~sel
1597 atoms, 1784 bonds, 1 pseudobond, 75 residues, 2 models selected
> select
646697 atoms, 693938 bonds, 906 pseudobonds, 53179 residues, 23 models
selected
> select subtract #1
646697 atoms, 693938 bonds, 906 pseudobonds, 53179 residues, 72 models
selected
> select subtract #2
427014 atoms, 458185 bonds, 454 pseudobonds, 35233 residues, 69 models
selected
> select subtract #3
427014 atoms, 458185 bonds, 454 pseudobonds, 35233 residues, 14 models
selected
> select add #3.1
427014 atoms, 458185 bonds, 454 pseudobonds, 35233 residues, 15 models
selected
> select subtract #3.1
427014 atoms, 458185 bonds, 454 pseudobonds, 35233 residues, 14 models
selected
> select subtract #4
427014 atoms, 458185 bonds, 454 pseudobonds, 35233 residues, 13 models
selected
> select subtract #5
427014 atoms, 458185 bonds, 454 pseudobonds, 35233 residues, 12 models
selected
> select subtract #6
427014 atoms, 458185 bonds, 454 pseudobonds, 35233 residues, 5 models selected
> select add #6.1
427014 atoms, 458185 bonds, 454 pseudobonds, 35233 residues, 7 models selected
> select subtract #7
215870 atoms, 231583 bonds, 446 pseudobonds, 17690 residues, 5 models selected
> select subtract #6.1
215870 atoms, 231583 bonds, 446 pseudobonds, 17690 residues, 3 models selected
> select ~sel
430827 atoms, 462355 bonds, 460 pseudobonds, 35489 residues, 20 models
selected
> select subtract #1
430827 atoms, 462355 bonds, 460 pseudobonds, 35489 residues, 69 models
selected
> select subtract #2
211144 atoms, 226602 bonds, 8 pseudobonds, 17543 residues, 66 models selected
> select subtract #3
211144 atoms, 226602 bonds, 8 pseudobonds, 17543 residues, 11 models selected
> select subtract #4
211144 atoms, 226602 bonds, 8 pseudobonds, 17543 residues, 10 models selected
> select subtract #5
211144 atoms, 226602 bonds, 8 pseudobonds, 17543 residues, 9 models selected
> select subtract #6
211144 atoms, 226602 bonds, 8 pseudobonds, 17543 residues, 2 models selected
> select add #6.1
211144 atoms, 226602 bonds, 8 pseudobonds, 17543 residues, 4 models selected
> select subtract #6.1
211144 atoms, 226602 bonds, 8 pseudobonds, 17543 residues, 2 models selected
> select subtract #7
Nothing selected
> select add #8
215870 atoms, 231583 bonds, 446 pseudobonds, 17690 residues, 3 models selected
> select subtract #8
Nothing selected
> select add #8
215870 atoms, 231583 bonds, 446 pseudobonds, 17690 residues, 3 models selected
> hide #!8 models
> show #!8 models
> hide #!8 models
Drag select of 258 residues
> hide sel cartoons
> show #!8 models
> hide #!8 models
> show #!8 models
> select #8/3
1597 atoms, 1784 bonds, 1 pseudobond, 75 residues, 2 models selected
> select ~sel
645100 atoms, 692154 bonds, 905 pseudobonds, 53104 residues, 23 models
selected
> select subtract #7
433956 atoms, 465552 bonds, 897 pseudobonds, 35561 residues, 74 models
selected
> select subtract #6.3
433956 atoms, 465552 bonds, 897 pseudobonds, 35561 residues, 72 models
selected
> select subtract #6.2
433956 atoms, 465552 bonds, 897 pseudobonds, 35561 residues, 70 models
selected
> select subtract #6.1
433956 atoms, 465552 bonds, 897 pseudobonds, 35561 residues, 68 models
selected
> select add #6
433956 atoms, 465552 bonds, 897 pseudobonds, 35561 residues, 74 models
selected
> select subtract #5
433956 atoms, 465552 bonds, 897 pseudobonds, 35561 residues, 73 models
selected
> select subtract #1
433956 atoms, 465552 bonds, 897 pseudobonds, 35561 residues, 69 models
selected
> select subtract #2
214273 atoms, 229799 bonds, 445 pseudobonds, 17615 residues, 66 models
selected
> select subtract #3
214273 atoms, 229799 bonds, 445 pseudobonds, 17615 residues, 11 models
selected
> select add #3.1
214273 atoms, 229799 bonds, 445 pseudobonds, 17615 residues, 12 models
selected
> select add #3
214273 atoms, 229799 bonds, 445 pseudobonds, 17615 residues, 13 models
selected
> select subtract #3.1
214273 atoms, 229799 bonds, 445 pseudobonds, 17615 residues, 12 models
selected
> select add #3
214273 atoms, 229799 bonds, 445 pseudobonds, 17615 residues, 13 models
selected
> select subtract #3
214273 atoms, 229799 bonds, 445 pseudobonds, 17615 residues, 11 models
selected
> select subtract #4
214273 atoms, 229799 bonds, 445 pseudobonds, 17615 residues, 10 models
selected
> select subtract #6
214273 atoms, 229799 bonds, 445 pseudobonds, 17615 residues, 3 models selected
> select add #6.1
214273 atoms, 229799 bonds, 445 pseudobonds, 17615 residues, 5 models selected
> select subtract #6.1
214273 atoms, 229799 bonds, 445 pseudobonds, 17615 residues, 3 models selected
> hide sel cartoons
> delete atoms (#!8 & sel)
> delete bonds (#!8 & sel)
> volume #6.2 level 0.06546
> lighting full
> lighting soft
> lighting full
[Repeated 1 time(s)]
> lighting soft
> lighting simple
> lighting full
> lighting soft
> lighting full
> lighting soft
> lighting full
[Repeated 1 time(s)]
> lighting soft
[Repeated 1 time(s)]
> volume #6.1 color #acadb2
[Repeated 1 time(s)]
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> lighting full
> lighting soft
> lighting full
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> lighting full
> volume #6.1 color #acadb2
> volume #6.1 color #a1abbf
> hide #!6 models
> show #!6 models
> hide #!8 models
> hide #!7 models
> save "/Users/jingyu/Desktop/Image
> processing/RNA_granules_with_spermine_nuclease/Non_uniform_refinement/After_3DVA_2nd_join/Chimera_session_to_make_figures/ChimeraX_session_to_make_figures.cxs"
> includeMaps true
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class
return f(class_name)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'ArtiaX'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x7fae4431f130>: Unknown class name 'ArtiaX'
Populating font family aliases took 328 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.
ValueError: error processing: 'models' -> : Unknown class name 'ArtiaX'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class
return f(class_name)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'ArtiaX'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x7fae4431f130>: Unknown class name 'ArtiaX'
ValueError: error processing: 'models' -> : Unknown class name 'ArtiaX'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save "/Users/jingyu/Desktop/Image
> processing/RNA_granules_with_spermine_nuclease/Non_uniform_refinement/After_3DVA_2nd_join/Chimera_session_to_make_figures/ChimeraX_session_to_make_figures.cxs"
> includeMaps true
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class
return f(class_name)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'ArtiaX'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x7fae4431f130>: Unknown class name 'ArtiaX'
ValueError: error processing: 'models' -> : Unknown class name 'ArtiaX'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class
return f(class_name)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'ArtiaX'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x7fae4431f130>: Unknown class name 'ArtiaX'
ValueError: error processing: 'models' -> : Unknown class name 'ArtiaX'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save "/Users/jingyu/Desktop/Image
> processing/RNA_granules_with_spermine_nuclease/Non_uniform_refinement/After_3DVA_2nd_join/Chimera_session_to_make_figures/adsfadsf.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class
return f(class_name)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'ArtiaX'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x7fae4431f130>: Unknown class name 'ArtiaX'
ValueError: error processing: 'models' -> : Unknown class name 'ArtiaX'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class
return f(class_name)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'ArtiaX'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x7fae4431f130>: Unknown class name 'ArtiaX'
ValueError: error processing: 'models' -> : Unknown class name 'ArtiaX'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> save "/Users/jingyu/Desktop/Image
> processing/RNA_granules_with_spermine_nuclease/Non_uniform_refinement/After_3DVA_2nd_join/adfadf.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class
return f(class_name)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'ArtiaX'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x7fae4431f130>: Unknown class name 'ArtiaX'
ValueError: error processing: 'models' -> : Unknown class name 'ArtiaX'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class
return f(class_name)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'ArtiaX'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x7fae4431f130>: Unknown class name 'ArtiaX'
ValueError: error processing: 'models' -> : Unknown class name 'ArtiaX'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> close #1
> hide #2.3 models
> show #2.3 models
> hide #2.55 models
> show #2.55 models
> open "/Users/jingyu/Desktop/Image
> processing/RNA_granules_with_spermine_nuclease/Non_uniform_refinement/After_3DVA_2nd_join/Non_uniform_refine_with_mask_motion_80S_with_PP_EE_tRNA_2ndjoin_J169.mrc"
Opened
Non_uniform_refine_with_mask_motion_80S_with_PP_EE_tRNA_2ndjoin_J169.mrc as
#1, grid size 448,448,448, pixel 1.09, shown at level 0.0967, step 2, values
float32
> hide #!6.1 models
> hide #!6 models
> hide #!6.2 models
> hide #!6.3 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> volume #1 step 1
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> volume #1 level 0.08535
> show #!7 models
> hide #!7 models
> show #!6.3 models
> hide #!6.3 models
> show #!8 models
> show #!6.1 models
> hide #!6.1 models
> show #!6.2 models
> hide #!6.2 models
> show #!7 models
> hide #!8 models
> show #!8 models
> hide #!1 models
Drag select of 75 residues
> hide sel cartoons
> show #!1 models
> hide #!6 models
> show #!6 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select clear
Drag select of 150 residues, 1 pseudobonds
> select add #1
3203 atoms, 1 pseudobond, 150 residues, 5 models selected
> select subtract #1
3203 atoms, 1 pseudobond, 150 residues, 3 models selected
> show #!1 models
> ui tool show "Color Zone"
> color zone #1 near sel distance 6.54
> color zone #1 near sel distance 6.1
> color zone #1 near sel distance 4.43
> volume splitbyzone #1
Opened
Non_uniform_refine_with_mask_motion_80S_with_PP_EE_tRNA_2ndjoin_J169.mrc 0 as
#9.1, grid size 448,448,448, pixel 1.09, shown at level 0.0853, step 1, values
float32
Opened
Non_uniform_refine_with_mask_motion_80S_with_PP_EE_tRNA_2ndjoin_J169.mrc 1 as
#9.2, grid size 448,448,448, pixel 1.09, shown at level 0.0853, step 1, values
float32
Opened
Non_uniform_refine_with_mask_motion_80S_with_PP_EE_tRNA_2ndjoin_J169.mrc 2 as
#9.3, grid size 448,448,448, pixel 1.09, shown at level 0.0853, step 1, values
float32
> hide #!7 models
> show #!7 models
> hide #!9.1 models
> show #!9.1 models
> hide #!9.1 models
> select clear
> select add #8
1597 atoms, 1784 bonds, 1 pseudobond, 75 residues, 2 models selected
> select add #7
212741 atoms, 228386 bonds, 9 pseudobonds, 17618 residues, 4 models selected
> select add #2
432424 atoms, 464139 bonds, 461 pseudobonds, 35564 residues, 7 models selected
> show #!2 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> select subtract #7
221280 atoms, 237537 bonds, 453 pseudobonds, 18021 residues, 58 models
selected
> select add #7
432424 atoms, 464139 bonds, 461 pseudobonds, 35564 residues, 60 models
selected
> select clear
> show #!6.2 models
> hide #!6.2 models
> select #7/2
37739 atoms, 42211 bonds, 2 pseudobonds, 1771 residues, 2 models selected
> show sel cartoons
> hide sel cartoons
> select #7/S
5267 atoms, 5688 bonds, 408 residues, 1 model selected
> show sel cartoons
> select clear
Drag select of 258 residues
[Repeated 2 time(s)]
> delete atoms sel
> delete bonds sel
> lighting full
[Repeated 1 time(s)]
> lighting soft
[Repeated 1 time(s)]
> lighting full
> volume #9.2 level 0.07147
> volume #9.3 level 0.07752
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> hide #!7 models
> color #7.1 #e5fee9 models transparency 0
> hide #!6 models
> color #6.3 #99fe3bfe models
> hide #!9.1 models
> show #!9.1 models
> color #9.1 #ffffb228 models
> color #9.1 #ffffb2 models transparency 0
> color #9.1 #fcf4ff models transparency 0
> color #9.1 #edfff6 models transparency 0
> color #9.1 #ecfff6 models transparency 0
> color #9.1 #c9daff models transparency 0
> lighting full
[Repeated 1 time(s)]
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> lighting soft
> lighting full
> select add #8
1597 atoms, 1784 bonds, 1 pseudobond, 75 residues, 2 models selected
> select subtract #8
Nothing selected
> select add #8
1597 atoms, 1784 bonds, 1 pseudobond, 75 residues, 2 models selected
> select subtract #8
Nothing selected
> select add #8
1597 atoms, 1784 bonds, 1 pseudobond, 75 residues, 2 models selected
> select add #7
210685 atoms, 226289 bonds, 9 pseudobonds, 17360 residues, 4 models selected
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> hide #!2 models
> select subtract #7
1597 atoms, 1784 bonds, 1 pseudobond, 75 residues, 2 models selected
> select subtract #7.1
1597 atoms, 1784 bonds, 1 pseudobond, 75 residues, 2 models selected
> select subtract #8
Nothing selected
> select subtract #8.1
Nothing selected
> select add #8.2
1 pseudobond, 1 model selected
> show #!7 models
> select subtract #8.1
1 pseudobond, 1 model selected
> select subtract #8.2
Nothing selected
> select subtract #8.1
Nothing selected
> save "/Users/jingyu/Desktop/Image
> processing/RNA_granules_with_spermine_nuclease/Non_uniform_refinement/After_3DVA_2nd_join/Chimera_session_to_make_figures/80S_with_AP_PE_tRNA_J166_background.mrc"
> models #6.1
> hide #!7 models
> hide #7.1 models
> hide #!9 models
> hide #8.1 models
> show #8.1 models
> show #!9 models
> hide #!9 models
> show #!6.2 models
> hide #!6.2 models
> show #!6.3 models
> hide #!6.3 models
> show #!6.3 models
> save "/Users/jingyu/Desktop/Image
> processing/RNA_granules_with_spermine_nuclease/Non_uniform_refinement/After_3DVA_2nd_join/Chimera_session_to_make_figures/80S_with_AP_PE_tRNA_J166_AP_tRNA.mrc"
> models #6.2
> save "/Users/jingyu/Desktop/Image
> processing/RNA_granules_with_spermine_nuclease/Non_uniform_refinement/After_3DVA_2nd_join/Chimera_session_to_make_figures/80S_with_AP_PE_tRNA_J166_PE_tRNA.mrc"
> models #6.3
> hide #!6.3 models
> show #!6.3 models
> hide #!6.3 models
> show #!9 models
> hide #!9.1 models
> show #!9.1 models
> save "/Users/jingyu/Desktop/Image
> processing/RNA_granules_with_spermine_nuclease/Non_uniform_refinement/After_3DVA_2nd_join/Chimera_session_to_make_figures/80S_with_PP_EE_tRNA_J169_background.mrc"
> models #9.1
> save "/Users/jingyu/Desktop/Image
> processing/RNA_granules_with_spermine_nuclease/Non_uniform_refinement/After_3DVA_2nd_join/Chimera_session_to_make_figures/80S_with_PP_EE_tRNA_J169_PP_tRNA.mrc"
> models #9.2
> save "/Users/jingyu/Desktop/Image
> processing/RNA_granules_with_spermine_nuclease/Non_uniform_refinement/After_3DVA_2nd_join/Chimera_session_to_make_figures/80S_with_PP_EE_tRNA_J169_EE_tRNA.mrc"
> models #9.3
> save "/Users/jingyu/Desktop/Image
> processing/RNA_granules_with_spermine_nuclease/Non_uniform_refinement/After_3DVA_2nd_join/Chimera_session_to_make_figures/ChimeraX_session_to_generate_figures.cxs"
——— End of log from Wed Jan 8 17:54:40 2025 ———
opened ChimeraX session
Traceback (most recent call last):
File "/Applications/ChimeraX-1.4
1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 1530, in <lambda>
QTimer.singleShot(200, lambda f=f: f.setMinimumHeight(50))
RuntimeError: wrapped C/C++ object of type QScrollArea has been deleted
RuntimeError: wrapped C/C++ object of type QScrollArea has been deleted
File "/Applications/ChimeraX-1.4
1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 1530, in
QTimer.singleShot(200, lambda f=f: f.setMinimumHeight(50))
See log for complete Python traceback.
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon R9 M395 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac17,1
Processor Name: Quad-Core Intel Core i7
Processor Speed: 4 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 522.0.0.0.0
OS Loader Version: 540.120.3~37
SMC Version (system): 2.34f3
Software:
System Software Overview:
System Version: macOS 12.7.1 (21G920)
Kernel Version: Darwin 21.6.0
Time since boot: 72 days 22:37
Graphics/Displays:
AMD Radeon R9 M395:
Chipset Model: AMD Radeon R9 M395
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 2 GB
Vendor: AMD (0x1002)
Device ID: 0x6920
Revision ID: 0x0001
ROM Revision: 113-C905AA-799
VBIOS Version: 113-C905A1-007
EFI Driver Version: 01.00.799
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.10.8
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-ArtiaX: 0.3
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
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
ChimeraX-Label: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
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: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.0
pandas: 1.4.3
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
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
starfile: 0.4.11
suds-community: 1.0.0
superqt: 0.3.3
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
typing-extensions: 4.3.0
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 10 months ago
| Component: | Unassigned → Volume Data |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Volume Viewer after session restore: wrapped C/C++ object of type QScrollArea has been deleted |
comment:2 by , 10 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Duplicate of #7103