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Opened 19 months ago
Closed 19 months ago
#14832 closed defect (duplicate)
Access violation in python_instances_of_class
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.22621
ChimeraX Version: 1.8.dev202403200605 (2024-03-20 06:05:36 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.8.dev202403200605 (2024-03-20)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> C:/Users/piyus/Downloads/ChimeraX/AlphaFold/MNEI_4aaac_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
Chain information for
MNEI_4aaac_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #1
---
Chain | Description
A | No description available
> ui tool show AlphaFold
> alphafold predict
> LIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQKWENDECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLVCQCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLEEQCHIAEAAAKEAAAKEAAAKAAEAAAKEAAAKEAAAKAGEWEIIDIGPFTQNLGKFAVDEENKIGQYGRLTFNKVIRPCMKKTIYENEGFREIKGYEYQLYVYASDKLFRADISEDYKTRGRKLLRFNGPVPPP
Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.
Running AlphaFold prediction
> open
> C:/Users/piyus/Downloads/ChimeraX/AlphaFold/Mut9_e8977_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
Chain information for
Mut9_e8977_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #2
---
Chain | Description
A | No description available
> hide #1 models
> open
> C:/Users/piyus/Downloads/ChimeraX/AlphaFold/June_L2L2_Luna(Mut9)/af292_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb
Chain information for
af292_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb #3
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #2 to #3
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 af292_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain
A (#3) with Mut9_e8977_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#2), sequence alignment score = 398.7
RMSD between 31 pruned atom pairs is 0.992 angstroms; (across all 96 pairs:
7.627)
> alphafold predict
> LIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQKWENDECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLVCQCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLEEQCHIAEAAAKEAAAKEAAAKAAEAAAKEAAAKEAAAKAGEWEIIDIGPFTQNLGKFAVDEENKIGQYGRLTFNKVIRPCMKKTIYENEGFREIKGYEYQLYVYASDKLFRADISEDYKTRGRKLLRFNGPVPPP
Running AlphaFold prediction
> hide #3 models
> open
> C:/Users/piyus/Downloads/ChimeraX/AlphaFold/Luna(Mut9)_L2L2_June/af292_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb
Chain information for
af292_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb #4
---
Chain | Description
A | No description available
AlphaFold prediction finished
Results in C:\Users\piyus/Downloads/ChimeraX/AlphaFold/prediction_7
> open C:\Users\piyus/Downloads/ChimeraX/AlphaFold/prediction_7\best_model.pdb
Chain information for best_model.pdb #5
---
Chain | Description
A | No description available
AlphaFold prediction finished
Results in C:\Users\piyus/Downloads/ChimeraX/AlphaFold/prediction_7
> open C:\Users\piyus/Downloads/ChimeraX/AlphaFold/prediction_7\best_model.pdb
Chain information for best_model.pdb #6
---
Chain | Description
A | No description available
> hide #4 models
> hide #2 models
> hide #6 models
> hide #5 models
> show #6 models
> show #5 models
> hide #5 models
> alphafold predict
> GEWEIIDIGPFTQNLGKFAVDEENKIGQYGRLTFNKVIRPCMKKTIYENEGFREIKGYEYQLYVYASDKLFRADISEDYKTRGRKLLRFNGPVPPPAEAAAKEAAAKEAAAKAAEAAAKEAAAKEAAAKALIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQKWENDECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLVCQCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLEEQCHI
Running AlphaFold prediction
> close #5
AlphaFold prediction finished
Results in C:\Users\piyus/Downloads/ChimeraX/AlphaFold/prediction_7
> open C:\Users\piyus/Downloads/ChimeraX/AlphaFold/prediction_7\best_model.pdb
Chain information for best_model.pdb #5
---
Chain | Description
A | No description available
> hide #5 models
> hide #6 models
> show #5 models
AlphaFold prediction finished
Results in C:\Users\piyus/Downloads/ChimeraX/AlphaFold/prediction_7
> open C:\Users\piyus/Downloads/ChimeraX/AlphaFold/prediction_7\best_model.pdb
Chain information for best_model.pdb #7
---
Chain | Description
A | No description available
> hide #5 models
> hide #7 models
> open
> C:/Users/piyus/Downloads/Haddock/334804-June_L2L2_Titan_D21N_T1R2_T1R3_summary/cluster1_1.pdb
Summary of feedback from opening
C:/Users/piyus/Downloads/Haddock/334804-June_L2L2_Titan_D21N_T1R2_T1R3_summary/cluster1_1.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_16w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
Ignored bad PDB record found on line 3
REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_16.pdb
Ignored bad PDB record found on line 5
REMARK ===============================================================
29 messages similar to the above omitted
Chain information for cluster1_1.pdb #8
---
Chain | Description
A | No description available
B | No description available
> color #8 bychain
> coulombic #8
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for cluster1_1.pdb_A SES surface #8.1: minimum, -12.25, mean
-1.06, maximum 10.98
Coulombic values for cluster1_1.pdb_B SES surface #8.2: minimum, -17.39, mean
-1.14, maximum 16.54
To also show corresponding color key, enter the above coulombic command and
add key true
> alphafold predict
> GEWEIIDIGPFTQNLGKFAVDEENKIGQYGRLTFNKVIRPCMKKTIYENEGFREIKGYEYQLYVYASDKLFRADISEDYKTRGRKLLRFNGPVPPPAEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKALIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQKWENDECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLVCQCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLEEQCHI
Running AlphaFold prediction
> alphafold predict
> GEWEIIDIGPFTQNLGKFAVDEENKIGQYGRLTFNKVIRPCMKKTIYENEGFREIKGYEYQLYVYASDKLFRADISEDYKTRGRKLLRFNGPVPPPAEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKALIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQKWENDECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLVCQCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLEEQCHI
Running AlphaFold prediction
> alphafold predict
> GEWEIIDIGPFTQNLGKFAVDEENKIGQYGRLTFNKVIRPCMKKTIYENEGFREIKGYEYQLYVYASDKLFRADISEDYKTRGRKLLRFNGPVPPPAEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKALIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQKWENDECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLVCQCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLEEQCHI
Running AlphaFold prediction
> close #5
> close #6
> alphafold predict
> GEWEIIDIGPFTQNLGKFAVDEANKIGQYGRLTFNKVIRPAMKKTIYENEGFREIKGYEYQLYVRASDKLFRADIYEDYKTRGRKLLRFNGPVPPPAEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKALIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQKWENDECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLVCQCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLEEQCHI
Running AlphaFold prediction
> alphafold predict
> GEWEIIDIGPFTQNLGKFAVDEANKIGQYGRLTFNKVIRPAMKKTIYENEGFREIKGYEYQLYVRASDKLFRADIYEDYKTRGRKLLRFNGPVPPPAEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKALIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQKWENDECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLVCQCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLEEQCHI
Running AlphaFold prediction
> alphafold predict
> GEWEIIDIGPFTQNLGKFAVDEANKIGQYGRLTFNKVIRPAMKKTIYENEGFREIKGYEYQLYVRASDKLFRADIYEDYKTRGRKLLRFNGPVPPPAEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKALIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQKWENDECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLVCQCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLEEQCHI
Running AlphaFold prediction
> alphafold predict
> GEWEIIDIGPFTQNLGKFAVDEANKIGQYGRLTFNKVIRPAMKKTIYENEGFREIKGYEYQLYVRASDKLFRADIYEDYKTRGRKLLRFNGPVPPPAEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKALIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQKWENDECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLVCQCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLEEQCHI
Running AlphaFold prediction
> alphafold predict
> GEWEIIDIGPFTQNLGKFAVDEANKIGQYGRLTFNKVIRPAMKKTIYENEGFREIKGYEYQLYVRASDKLFRADIYEDYKTRGRKLLRFNGPVPPPAEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKALIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQKWENDECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLVCQCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLEEQCHI
Running AlphaFold prediction
> alphafold predict
> GEWEIIDIGPFTQNLGKFAVDEANKIGQYGRLTFNKVIRPAMKKTIYENEGFREIKGYEYQLYVRASDKLFRADIYEDYKTRGRKLLRFNGPVPPPAEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKALIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQKWENDECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLVCQCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLEEQCHI
Running AlphaFold prediction
Compositor returned null texture
> alphafold predict
> GEWEIIDIGPFTQNLGKFAVDEANKIGQYGRLTFNKVIRPAMKKTIYENEGFREIKGYEYQLYVRASDKLFRADIYEDYKTRGRKLLRFNGPVPPPAEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKALIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQKWENDECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLVCQCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLEEQCHI
Running AlphaFold prediction
AlphaFold prediction finished
Results in C:\Users\piyus/Downloads/ChimeraX/AlphaFold/prediction_7
> open C:\Users\piyus/Downloads/ChimeraX/AlphaFold/prediction_7\best_model.pdb
Chain information for best_model.pdb #5
---
Chain | Description
A | No description available
> color #5#!8 bypolymer
> hide #!8 models
> hide #5 models
> show #2 models
> alphafold predict
> GEWEIIDIGPFTQNLGKFAVDEANKIGQYGRLTFNKVIRPAMKKTIYENEGFREIKGYEYQLYVRASDKLFRADIYEDYKTRGRKLLRFNGPVPPPLIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQKWENDECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLVCQCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLEEQCHI
Running AlphaFold prediction
AlphaFold prediction finished
Results in C:\Users\piyus/Downloads/ChimeraX/AlphaFold/prediction_7
> open C:\Users\piyus/Downloads/ChimeraX/AlphaFold/prediction_7\best_model.pdb
Chain information for best_model.pdb #6
---
Chain | Description
A | No description available
> hide #6 models
> show #3 models
> hide #3 models
> show #4 models
> hide #4 models
> show #1 models
> open
> C:/Users/piyus/Downloads/Haddock/334804-June_L2L2_Titan_D21N_T1R2_T1R3_summary/cluster6_1.pdb
Summary of feedback from opening
C:/Users/piyus/Downloads/Haddock/334804-June_L2L2_Titan_D21N_T1R2_T1R3_summary/cluster6_1.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_21w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
Ignored bad PDB record found on line 3
REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_21.pdb
Ignored bad PDB record found on line 5
REMARK ===============================================================
29 messages similar to the above omitted
Chain information for cluster6_1.pdb #9
---
Chain | Description
A | No description available
B | No description available
> hide #2 models
> hide #1 models
> color #9 bypolymer
> coulombic #9
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for cluster6_1.pdb_A SES surface #9.1: minimum, -12.16, mean
-1.06, maximum 13.29
Coulombic values for cluster6_1.pdb_B SES surface #9.2: minimum, -21.41, mean
-1.14, maximum 15.49
To also show corresponding color key, enter the above coulombic command and
add key true
> color #!9 bypolymer
> show #!8 models
> ui tool show Matchmaker
> matchmaker #!9 to #8
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 cluster1_1.pdb, chain B (#8) with cluster6_1.pdb, chain B (#9),
sequence alignment score = 8843.1
RMSD between 1690 pruned atom pairs is 0.170 angstroms; (across all 1691
pairs: 0.177)
> matchmaker #!9 to #8
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 cluster1_1.pdb, chain B (#8) with cluster6_1.pdb, chain B (#9),
sequence alignment score = 8843.1
RMSD between 1690 pruned atom pairs is 0.170 angstroms; (across all 1691
pairs: 0.177)
> hide #!8 models
> hide #!9 surfaces
> hide #!9 models
> close #9
> close #5
> alphafold predict
> GEWEIIDIGPFTQNLGKFAVDEANKIGQYGRLTFNKVIRPAMKKTIYENEGFREIKGYEYQLYVRASDKLFRADIYEDYKTRGRKLLRFNGPVPPPPAPAPAPAPAPAPAPAPAPAPLIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQKWENDECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLVCQCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLEEQCHI
Running AlphaFold prediction
AlphaFold prediction finished
Results in C:\Users\piyus/Downloads/ChimeraX/AlphaFold/prediction_7
> open C:\Users\piyus/Downloads/ChimeraX/AlphaFold/prediction_7\best_model.pdb
Chain information for best_model.pdb #5
---
Chain | Description
A | No description available
> alphafold predict
> GEWEIIDIGPFTQNLGKFAVDEANKIGQYGRLTFNKVIRPAMKKTIYENEGFREIKGYEYQLYVRASDKLFRADIYEDYKTRGRKLLRFNGPVPPPPAPAPAPAPLIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQKWENDECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLVCQCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLEEQCHI
Running AlphaFold prediction
> hide #5 models
> show #7 models
> hide #7 models
> close #7
> close #6
> open
> C:/Users/piyus/Downloads/Haddock/336112-TitanD21N_L2L2_June_T1R2_T1R3_summary/cluster5_1.pdb
Summary of feedback from opening
C:/Users/piyus/Downloads/Haddock/336112-TitanD21N_L2L2_June_T1R2_T1R3_summary/cluster5_1.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_147w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
Ignored bad PDB record found on line 3
REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_147.pdb
Ignored bad PDB record found on line 5
REMARK ===============================================================
29 messages similar to the above omitted
Chain information for cluster5_1.pdb #6
---
Chain | Description
A | No description available
B | No description available
> coulombic #6
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for cluster5_1.pdb_A SES surface #6.1: minimum, -18.06, mean
-0.80, maximum 9.44
Coulombic values for cluster5_1.pdb_B SES surface #6.2: minimum, -19.34, mean
-1.13, maximum 15.79
To also show corresponding color key, enter the above coulombic command and
add key true
> color #!6 bychain
> hide #!6 models
> show #!8 models
> hide #!8 models
> show #4 models
> hide #4 models
> open
> C:/Users/piyus/Downloads/Haddock/336624-June_L7n2_Titan_D21N_T1R2_T1R3_summary/cluster4_1.pdb
Summary of feedback from opening
C:/Users/piyus/Downloads/Haddock/336624-June_L7n2_Titan_D21N_T1R2_T1R3_summary/cluster4_1.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_1w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
Ignored bad PDB record found on line 3
REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_1.pdb
Ignored bad PDB record found on line 5
REMARK ===============================================================
29 messages similar to the above omitted
Chain information for cluster4_1.pdb #7
---
Chain | Description
A | No description available
B | No description available
> color #7 bychain
> coulombic #7
Traceback (most recent call last):
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\toolbar\tool.py",
line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1302, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\\__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1387, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 402, in try_shortcut
self.run_shortcut(keys)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 420, in run_shortcut
sc.run(self.session, status = self._enabled)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 339, in run
f(s)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 72, in func_plus_tip
func(cmd + " %s")(session)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 593, in run_expanded_command
run(session, cmd)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 536, in run
run_command(session, command, **kw)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2904, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\coulombic\cmd.py",
line 102, in cmd_coulombic
assign_charges(session, needs_assignment, his_scheme, charge_method,
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\coulombic\coulombic.py", line 73, in assign_charges
charged_struct = struct.copy(name="copy of " + struct.name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\atomic\structure.py",
line 162, in copy
m._copy_custom_attrs(self)
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\atomic\structure.py",
line 176, in _copy_custom_attrs
py_objs = [py_obj for py_obj in python_instances_of_class(class_obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\atomic\molobject.py",
line 44, in python_instances_of_class
instances = f(inst_class)
^^^^^^^^^^^^^
OSError: exception: access violation reading 0x00000000016FAE56
OSError: exception: access violation reading 0x00000000016FAE56
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\atomic\molobject.py",
line 44, in python_instances_of_class
instances = f(inst_class)
^^^^^^^^^^^^^
See log for complete Python traceback.
> coulombic #7
Traceback (most recent call last):
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\toolbar\tool.py",
line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1302, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\\__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1387, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 402, in try_shortcut
self.run_shortcut(keys)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 420, in run_shortcut
sc.run(self.session, status = self._enabled)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 339, in run
f(s)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 72, in func_plus_tip
func(cmd + " %s")(session)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 593, in run_expanded_command
run(session, cmd)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 536, in run
run_command(session, command, **kw)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2904, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\coulombic\cmd.py",
line 102, in cmd_coulombic
assign_charges(session, needs_assignment, his_scheme, charge_method,
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\coulombic\coulombic.py", line 73, in assign_charges
charged_struct = struct.copy(name="copy of " + struct.name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\atomic\structure.py",
line 162, in copy
m._copy_custom_attrs(self)
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\atomic\structure.py",
line 176, in _copy_custom_attrs
py_objs = [py_obj for py_obj in python_instances_of_class(class_obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\atomic\molobject.py",
line 44, in python_instances_of_class
instances = f(inst_class)
^^^^^^^^^^^^^
OSError: exception: access violation reading 0x00000000016FAE56
OSError: exception: access violation reading 0x00000000016FAE56
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\atomic\molobject.py",
line 44, in python_instances_of_class
instances = f(inst_class)
^^^^^^^^^^^^^
See log for complete Python traceback.
> coulombic #7
Traceback (most recent call last):
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\toolbar\tool.py",
line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1302, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\\__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1387, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 402, in try_shortcut
self.run_shortcut(keys)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 420, in run_shortcut
sc.run(self.session, status = self._enabled)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 339, in run
f(s)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 72, in func_plus_tip
func(cmd + " %s")(session)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 593, in run_expanded_command
run(session, cmd)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 536, in run
run_command(session, command, **kw)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2904, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\coulombic\cmd.py",
line 102, in cmd_coulombic
assign_charges(session, needs_assignment, his_scheme, charge_method,
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\coulombic\coulombic.py", line 73, in assign_charges
charged_struct = struct.copy(name="copy of " + struct.name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\atomic\structure.py",
line 162, in copy
m._copy_custom_attrs(self)
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\atomic\structure.py",
line 176, in _copy_custom_attrs
py_objs = [py_obj for py_obj in python_instances_of_class(class_obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\atomic\molobject.py",
line 44, in python_instances_of_class
instances = f(inst_class)
^^^^^^^^^^^^^
OSError: exception: access violation reading 0x00000000016FAE56
OSError: exception: access violation reading 0x00000000016FAE56
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\atomic\molobject.py",
line 44, in python_instances_of_class
instances = f(inst_class)
^^^^^^^^^^^^^
See log for complete Python traceback.
> coulombic #7
Traceback (most recent call last):
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\toolbar\tool.py",
line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1302, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\\__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1387, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 402, in try_shortcut
self.run_shortcut(keys)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 420, in run_shortcut
sc.run(self.session, status = self._enabled)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 339, in run
f(s)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 72, in func_plus_tip
func(cmd + " %s")(session)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 593, in run_expanded_command
run(session, cmd)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 536, in run
run_command(session, command, **kw)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2904, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\coulombic\cmd.py",
line 102, in cmd_coulombic
assign_charges(session, needs_assignment, his_scheme, charge_method,
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\coulombic\coulombic.py", line 73, in assign_charges
charged_struct = struct.copy(name="copy of " + struct.name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\atomic\structure.py",
line 162, in copy
m._copy_custom_attrs(self)
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\atomic\structure.py",
line 176, in _copy_custom_attrs
py_objs = [py_obj for py_obj in python_instances_of_class(class_obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\atomic\molobject.py",
line 44, in python_instances_of_class
instances = f(inst_class)
^^^^^^^^^^^^^
OSError: exception: access violation reading 0x00000000016FAE56
OSError: exception: access violation reading 0x00000000016FAE56
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\atomic\molobject.py",
line 44, in python_instances_of_class
instances = f(inst_class)
^^^^^^^^^^^^^
See log for complete Python traceback.
> color #7 bychain
> color #7 bypolymer
> color #7 bychain
> coulombic #7
Traceback (most recent call last):
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\toolbar\tool.py",
line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1302, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\\__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1387, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 402, in try_shortcut
self.run_shortcut(keys)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 420, in run_shortcut
sc.run(self.session, status = self._enabled)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 339, in run
f(s)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 72, in func_plus_tip
func(cmd + " %s")(session)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 593, in run_expanded_command
run(session, cmd)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 536, in run
run_command(session, command, **kw)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2904, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\coulombic\cmd.py",
line 102, in cmd_coulombic
assign_charges(session, needs_assignment, his_scheme, charge_method,
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\coulombic\coulombic.py", line 73, in assign_charges
charged_struct = struct.copy(name="copy of " + struct.name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\atomic\structure.py",
line 162, in copy
m._copy_custom_attrs(self)
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\atomic\structure.py",
line 176, in _copy_custom_attrs
py_objs = [py_obj for py_obj in python_instances_of_class(class_obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\atomic\molobject.py",
line 44, in python_instances_of_class
instances = f(inst_class)
^^^^^^^^^^^^^
OSError: exception: access violation reading 0x00000000016FAE56
OSError: exception: access violation reading 0x00000000016FAE56
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\atomic\molobject.py",
line 44, in python_instances_of_class
instances = f(inst_class)
^^^^^^^^^^^^^
See log for complete Python traceback.
> coulombic #7
Traceback (most recent call last):
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\toolbar\tool.py",
line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1302, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\\__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1387, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 402, in try_shortcut
self.run_shortcut(keys)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 420, in run_shortcut
sc.run(self.session, status = self._enabled)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 339, in run
f(s)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 72, in func_plus_tip
func(cmd + " %s")(session)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 593, in run_expanded_command
run(session, cmd)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 536, in run
run_command(session, command, **kw)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2904, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\coulombic\cmd.py",
line 102, in cmd_coulombic
assign_charges(session, needs_assignment, his_scheme, charge_method,
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\coulombic\coulombic.py", line 73, in assign_charges
charged_struct = struct.copy(name="copy of " + struct.name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\atomic\structure.py",
line 162, in copy
m._copy_custom_attrs(self)
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\atomic\structure.py",
line 176, in _copy_custom_attrs
py_objs = [py_obj for py_obj in python_instances_of_class(class_obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\atomic\molobject.py",
line 44, in python_instances_of_class
instances = f(inst_class)
^^^^^^^^^^^^^
OSError: exception: access violation reading 0x00000000016FAE56
OSError: exception: access violation reading 0x00000000016FAE56
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\atomic\molobject.py",
line 44, in python_instances_of_class
instances = f(inst_class)
^^^^^^^^^^^^^
See log for complete Python traceback.
> mlp #7
Map values for surface "cluster4_1.pdb_A SES surface": minimum -27.75, mean
-5.172, maximum 24.07
Map values for surface "cluster4_1.pdb_B SES surface": minimum -27.66, mean
-3.081, maximum 25.04
To also show corresponding color key, enter the above mlp command and add key
true
> color #!7 bychain
> coulombic #!7
Traceback (most recent call last):
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\toolbar\tool.py",
line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1302, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\\__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1387, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 402, in try_shortcut
self.run_shortcut(keys)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 420, in run_shortcut
sc.run(self.session, status = self._enabled)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 339, in run
f(s)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 72, in func_plus_tip
func(cmd + " %s")(session)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 593, in run_expanded_command
run(session, cmd)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 536, in run
run_command(session, command, **kw)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2904, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\coulombic\cmd.py",
line 102, in cmd_coulombic
assign_charges(session, needs_assignment, his_scheme, charge_method,
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\coulombic\coulombic.py", line 73, in assign_charges
charged_struct = struct.copy(name="copy of " + struct.name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\atomic\structure.py",
line 162, in copy
m._copy_custom_attrs(self)
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\atomic\structure.py",
line 176, in _copy_custom_attrs
py_objs = [py_obj for py_obj in python_instances_of_class(class_obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\atomic\molobject.py",
line 44, in python_instances_of_class
instances = f(inst_class)
^^^^^^^^^^^^^
OSError: exception: access violation writing 0x000001678AB9A210
OSError: exception: access violation writing 0x000001678AB9A210
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\atomic\molobject.py",
line 44, in python_instances_of_class
instances = f(inst_class)
^^^^^^^^^^^^^
See log for complete Python traceback.
> coulombic #!7
Traceback (most recent call last):
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\toolbar\tool.py",
line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1302, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\\__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1387, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 402, in try_shortcut
self.run_shortcut(keys)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 420, in run_shortcut
sc.run(self.session, status = self._enabled)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 339, in run
f(s)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 72, in func_plus_tip
func(cmd + " %s")(session)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 593, in run_expanded_command
run(session, cmd)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 536, in run
run_command(session, command, **kw)
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2904, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\coulombic\cmd.py",
line 102, in cmd_coulombic
assign_charges(session, needs_assignment, his_scheme, charge_method,
File "C:\Windows\ChimeraX\bin\Lib\site-
packages\chimerax\coulombic\coulombic.py", line 73, in assign_charges
charged_struct = struct.copy(name="copy of " + struct.name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\atomic\structure.py",
line 162, in copy
m._copy_custom_attrs(self)
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\atomic\structure.py",
line 176, in _copy_custom_attrs
py_objs = [py_obj for py_obj in python_instances_of_class(class_obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\atomic\molobject.py",
line 44, in python_instances_of_class
instances = f(inst_class)
^^^^^^^^^^^^^
OSError: exception: access violation writing 0x000001678AB9A210
OSError: exception: access violation writing 0x000001678AB9A210
File "C:\Windows\ChimeraX\bin\Lib\site-packages\chimerax\atomic\molobject.py",
line 44, in python_instances_of_class
instances = f(inst_class)
^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 30.0.101.1692
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel
Python: 3.11.4
Locale: en_IN.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: windows
Manufacturer: LENOVO
Model: 81X7
OS: Microsoft Windows 11 Home Single Language (Build 22621)
Memory: 8,379,490,304
MaxProcessMemory: 137,438,953,344
CPU: 4 11th Gen Intel(R) Core(TM) i3-1115G4 @ 3.00GHz
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.14.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.5.1
build: 1.1.1
certifi: 2024.2.2
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.16
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.3
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.5
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.56
ChimeraX-AtomicLibrary: 14.0.2
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8.dev202403200605
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.9
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.13
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.15
ChimeraX-ModelPanel: 1.5
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-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.3
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.37.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.3.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.9
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.1
fonttools: 4.50.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.10.0
html2text: 2024.2.26
idna: 3.6
ihm: 0.43
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
Jinja2: 3.1.3
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.1.0
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.3
matplotlib-inline: 0.1.6
msgpack: 1.0.8
ndindex: 1.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.2.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.9.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 24.0
ParmEd: 4.2.2
parso: 0.8.3
pep517: 0.13.1
pillow: 10.2.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.0
prompt-toolkit: 3.0.43
psutil: 5.9.8
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.3.0
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3302
pyparsing: 3.1.2
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.2
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.2
python-dateutil: 2.9.0.post0
pytz: 2024.1
pywin32: 306
pyzmq: 25.1.2
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.12.0
setuptools: 69.2.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.0
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.1
tables: 3.9.2
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.1
typing-extensions: 4.10.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
WMI: 1.5.1
Change History (2)
comment:1 by , 19 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Access violation in python_instances_of_class |
comment:2 by , 19 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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