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Opened 2 months ago
Closed 2 months ago
#18493 closed defect (can't reproduce)
Deleting atoms: OSError: access violation
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26100
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> C:/Users/guynw/Desktop/WSL_Naked_mole_rat/sonicparanoid/il6/fold_il6_nmr/nmr_il6.pdb
Chain information for nmr_il6.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> open
> C:/Users/guynw/Desktop/WSL_Naked_mole_rat/sonicparanoid/il6/human_il6_1ALU.pdb
human_il6_1ALU.pdb title:
Human interleukin-6 [more info...]
Chain information for human_il6_1ALU.pdb #2
---
Chain | Description | UniProt
A | interleukin-6 | IL6_HUMAN 0-184
Non-standard residues in human_il6_1ALU.pdb #2
---
SO4 — sulfate ion
TLA — L(+)-tartaric acid
15 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open
> C:/Users/guynw/Desktop/WSL_Naked_mole_rat/sonicparanoid/il6/mouse_il6_alphafold.pdb
mouse_il6_alphafold.pdb title:
Alphafold monomer V2.0 prediction for interleukin-6 (P08505) [more info...]
Chain information for mouse_il6_alphafold.pdb #3
---
Chain | Description | UniProt
A | interleukin-6 | IL6_MOUSE 1-211
Computing secondary structure
> select add #1
1733 atoms, 1761 bonds, 218 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #1
1733 atoms, 1761 bonds, 218 residues, 1 model selected
> select subtract #1
Nothing selected
> hide #1 models
> hide #!2 models
> hide #3 models
> show #!2 models
> show #1 models
> show #3 models
> hide #!2 models
> hide #3 models
> select down
Nothing selected
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\guynw/Desktop\movie1.mp4
Movie saved to C:\Users\guynw/Desktop\movie1.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\guynw/Desktop\movie2.mp4
C:\Program Files\ChimeraX 1.10.1\bin\ffmpeg.exe -r 25 -i
C:\Users\guynw\AppData\Local\Temp\chimovie_ZWCY-%05d.ppm -vf
crop=floor(in_w/2)*2:floor(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4 -pix_fmt
yuv420p -crf 20 C:\Users\guynw/Desktop\movie2.mp4
stdout:
stderr:
An error occurred during encoding. See Reply Log for details.
Error during MPEG encoding:
\-----------------------------
Exit value: 3221225794
Error message:
stdout:
stderr:
\-----------------------------
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\guynw/Desktop\movie2.mp4
Movie saved to C:\Users\guynw/Desktop\movie2.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\guynw/Desktop\movie3.mp4
Movie saved to C:\Users\guynw/Desktop\movie3.mp4
> save C:\Users\guynw/Desktop\image1.png supersample 3
> show #1 cartoons
[Repeated 3 time(s)]
> style #1 stick
Changed 1733 atom styles
> rainbow #1
[Repeated 1 time(s)]
> color #1 byhetero
> color #1 bypolymer
[Repeated 1 time(s)]
> color #1 #ffaaffff
> color #1 #0055ffff
> color #1 cyan
> color #1 #00aa00ff
> color #1 #aaaa00ff
> color #1 #aaaa7fff
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #1 models
> show #!2 models
> show #!2 target m
[Repeated 1 time(s)]
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> open
> C:/Users/guynw/Desktop/WSL_Naked_mole_rat/sonicparanoid/il6/human_il6_4CNI.pdb
human_il6_4CNI.pdb title:
Crystal structure of the fab portion of olokizumab In complex with il- 6 [more
info...]
Chain information for human_il6_4CNI.pdb #4
---
Chain | Description | UniProt
A H | olokizumab heavy chain, fab portion |
B L | olokizumab light chain, fab portion |
C D | interleukin-6 | IL6_HUMAN 14-184
Non-standard residues in human_il6_4CNI.pdb #4
---
SO4 — sulfate ion
TAM — tris(hydroxyethyl)aminomethane
42 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #4 target m
> show #!2 models
> select add #2
1398 atoms, 1289 bonds, 1 pseudobond, 282 residues, 3 models selected
> select subtract #2
Nothing selected
> select add #2
1398 atoms, 1289 bonds, 1 pseudobond, 282 residues, 3 models selected
> select subtract #2
Nothing selected
> select add #2
1398 atoms, 1289 bonds, 1 pseudobond, 282 residues, 3 models selected
> select subtract #2
Nothing selected
> cartoon
> show #1 models
> show #3 models
> cartoon
> ui windowfill toggle
[Repeated 1 time(s)]
> cartoon #1-3
> color #1 skyblue
> color #2 orange
> color #3 lime
> matchmaker #2:26-999 to #1:26-999
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker nmr_il6.pdb, chain A (#1) with human_il6_1ALU.pdb, chain A (#2),
sequence alignment score = 437.6
RMSD between 133 pruned atom pairs is 1.042 angstroms; (across all 149 pairs:
1.692)
> matchmaker #3:26-999 to #1:26-999
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker nmr_il6.pdb, chain A (#1) with mouse_il6_alphafold.pdb, chain A
(#3), sequence alignment score = 477.2
RMSD between 144 pruned atom pairs is 0.953 angstroms; (across all 184 pairs:
10.616)
> orient #1-3
Unknown command: orient #1-3
> view #4 clip false
> combine #1,#2,#3 name IL6_superposed
Expected a keyword
> savepos il6_view
Unknown command: savepos il6_view
> hide #1 models
> hide #!2 models
> show #1 models
> show #!2 models
> hide #3 models
> hide #1 models
> show #1 models
> show #3 models
> hide #3 models
> hide #1 models
> show #1 models
> show #3 models
> open
> C:/Users/guynw/Desktop/WSL_Naked_mole_rat/sonicparanoid/il6/il6_human_v2.pdb
il6_human_v2.pdb title:
Alphafold monomer V2.0 prediction for interleukin-6 (P05231) [more info...]
Chain information for il6_human_v2.pdb #5
---
Chain | Description | UniProt
A | interleukin-6 | IL6_HUMAN 1-212
Computing secondary structure
> hide #!2 models
> rename #5 id #1
> hide #!2.1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.1 models
> hide #!2 models
> rename #3 id #2
> rename #1 id #3
> rename #2 id #4
> view #3 clip false
[Repeated 1 time(s)]
> delete atoms
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\std_commands\delete.py", line 50, in delete_atoms
atoms.delete()
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molarray.py", line 830, in delete
c_function('atom_delete',
OSError: exception: access violation writing 0x00007FFA10A99260
OSError: exception: access violation writing 0x00007FFA10A99260
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molarray.py", line 830, in delete
c_function('atom_delete',
See log for complete Python traceback.
> delete atoms
> open
> C:\Users\guynw\Desktop\WSL_Naked_mole_rat\sonicparanoid\il6\il6_human_v2.pdb
> format pdb
il6_human_v2.pdb title:
Alphafold monomer V2.0 prediction for interleukin-6 (P05231) [more info...]
Chain information for il6_human_v2.pdb #1
---
Chain | Description | UniProt
A | interleukin-6 | IL6_HUMAN 1-212
Computing secondary structure
> open
> C:/Users/guynw/Desktop/WSL_Naked_mole_rat/sonicparanoid/il6/mouse_il6_alphafold.pdb
mouse_il6_alphafold.pdb title:
Alphafold monomer V2.0 prediction for interleukin-6 (P08505) [more info...]
Chain information for mouse_il6_alphafold.pdb #2
---
Chain | Description | UniProt
A | interleukin-6 | IL6_MOUSE 1-211
Computing secondary structure
> open
> C:/Users/guynw/Desktop/WSL_Naked_mole_rat/sonicparanoid/il6/fold_il6_nmr/nmr_il6.pdb
Chain information for nmr_il6.pdb #3
---
Chain | Description
A | No description available
Computing secondary structure
> hide #3 models
> matchmaker
Missing or invalid "matchAtoms" argument: empty atom specifier
> matchmaker #1 #2 # Align NMR to human
Expected a keyword
> matchmaker #1 #3 # Align NMR to mouse
Expected a keyword
> matchmaker #1 #2
Missing required "to" argument
> matchmaker #2:26-999 to #1:26-999 matchmaker #3:26-999 to #1:26-999 orient
> #1-3
Expected a keyword
> matchmaker #2:26-999 to #1:26-999
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker il6_human_v2.pdb, chain A (#1) with mouse_il6_alphafold.pdb, chain
A (#2), sequence alignment score = 462.4
RMSD between 127 pruned atom pairs is 0.904 angstroms; (across all 184 pairs:
17.568)
> show #3 models
> matchmaker #3:26-999 to #1:26-999
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker il6_human_v2.pdb, chain A (#1) with nmr_il6.pdb, chain A (#3),
sequence alignment score = 477.9
RMSD between 147 pruned atom pairs is 1.044 angstroms; (across all 181 pairs:
8.269)
> orient #1-3
Unknown command: orient #1-3
> save C:\Users\guynw/Desktop\image2.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\guynw/Desktop\movie4.mp4
Movie saved to C:\Users\guynw/Desktop\movie4.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\guynw/Desktop\movie5.mp4
Movie saved to C:\Users\guynw/Desktop\movie5.mp4
> movie record size 3840,2160 supersample 2
> turn y 1 360
> wait 360
> movie encode output spin4k.mp4 format h264 quality highest
Movie saved to spin4k.mp4
> save C:\Users\guynw/Desktop/figure.tif width 4000 supersample 1
> hide #2 models
> hide #3 models
> save C:\Users\guynw/Desktop/il6_human.tif width 4000 supersample 1
> hide #1 models
> show #2 models
> save C:\Users\guynw/Desktop/il6_mouse.tif width 4000 supersample 1
> hide #2 models
> show #3 models
> save C:\Users\guynw/Desktop/il6_nmr.tif width 4000 supersample 1
> show #2 models
> show #1 models
> save C:\Users\guynw/Desktop/il6_human_mouse_nmr.png width 3840 supersample 2
> transparentBackground true
> hide #2 models
> hide #3 models
> save C:\Users\guynw/Desktop/il6_human.png width 3840 supersample 2
> transparentBackground true
> show #2 models
> hide #1 models
> save C:\Users\guynw/Desktop/il6_mouse.png width 3840 supersample 2
> transparentBackground true
> hide #2 models
> show #3 models
> save C:\Users\guynw/Desktop/il6_nmr.png width 3840 supersample 2
> transparentBackground true
> show #2 models
> show #1 models
> 2dlabels create figtitle text "Local resolution (Å)" xpos 0.84 ypos 0.92
> size 28 color white bgColor none outline 2
> coulombic #1 & protein key true
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for il6_human_v2.pdb_A SES surface #1.1: minimum, -11.69,
mean -0.79, maximum 12.55
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> coulombic #1 & protein key true
Coulombic values for il6_human_v2.pdb_A SES surface #1.1: minimum, -11.69,
mean -0.79, maximum 12.55
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> key delete
> undo
[Repeated 9 time(s)]
> select add #1
1663 atoms, 1691 bonds, 212 residues, 1 model selected
> select subtract #1
1 model selected
> select add #2
1712 atoms, 1741 bonds, 211 residues, 1 model selected
> select subtract #2
Nothing selected
> hide #!4 models
> 2dlabels delete figtitle
Expected 'all' or a label/arrow models specifier or a keyword
> open
> C:\Users\guynw\Desktop\WSL_Naked_mole_rat\sonicparanoid\il6\il6_human_v2.pdb
> format pdb
il6_human_v2.pdb title:
Alphafold monomer V2.0 prediction for interleukin-6 (P05231) [more info...]
Chain information for il6_human_v2.pdb #6
---
Chain | Description | UniProt
A | interleukin-6 | IL6_HUMAN 1-212
Computing secondary structure
> undo
[Repeated 5 time(s)]No undo action is available
> undo
No undo action is available
> undo
No undo action is available
> undo
No undo action is available
> undo
No undo action is available
> undo
No undo action is available
> undo
No undo action is available
> undo
No undo action is available
> undo
No undo action is available
> close session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1090, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1278, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1090, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1278, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1090, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1278, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1090, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1278, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1090, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1278, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1090, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1278, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1090, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1278, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1090, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1278, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
> open
> C:\Users\guynw\Desktop\WSL_Naked_mole_rat\sonicparanoid\il6\il6_human_v2.pdb
> format pdb
il6_human_v2.pdb title:
Alphafold monomer V2.0 prediction for interleukin-6 (P05231) [more info...]
Chain information for il6_human_v2.pdb #1
---
Chain | Description | UniProt
A | interleukin-6 | IL6_HUMAN 1-212
Computing secondary structure
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1090, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1278, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1090, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1278, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1090, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1278, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1090, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1278, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1090, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1278, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1090, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1278, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1090, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1278, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1090, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1278, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
> open
> C:/Users/guynw/Desktop/WSL_Naked_mole_rat/sonicparanoid/il6/mouse_il6_alphafold.pdb
mouse_il6_alphafold.pdb title:
Alphafold monomer V2.0 prediction for interleukin-6 (P08505) [more info...]
Chain information for mouse_il6_alphafold.pdb #2
---
Chain | Description | UniProt
A | interleukin-6 | IL6_MOUSE 1-211
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1090, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1278, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1090, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1278, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1090, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1278, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1090, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1278, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1090, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1278, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1090, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1278, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1090, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1278, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1090, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1278, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Computing secondary structure
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1090, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1278, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1090, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1278, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1090, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1278, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1090, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1278, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1090, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1278, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1090, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1278, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1090, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1278, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1090, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1278, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 96, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
OpenGL version: 3.3.0 Core Profile Context 24.30.40.08.250611
OpenGL renderer: AMD Radeon 780M Graphics
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: en_GB.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows
Manufacturer: LENOVO
Model: 21MCCTO1WW
OS: Microsoft Windows 11 Home (Build 26100)
Memory: 136,007,344,128
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 PRO 8840U w/ Radeon 780M Graphics
OSLanguage: en-GB
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2025.7.14
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.10
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pywin32: 310
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
WMI: 1.5.1
Change History (2)
comment:1 by , 2 months ago
| Component: | Unassigned → Structure Editing |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Deleting atoms: OSError: access violation |
comment:2 by , 2 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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