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Opened 3 years ago
Closed 3 years ago
#8062 closed defect (duplicate)
Status bar: wrapped C/C++ object of type QScreen has been deleted
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19041
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:\Users\hellmold\Downloads\4f5s.pdb format pdb
4f5s.pdb title:
Crystal structure of bovine serum albumin [more info...]
Chain information for 4f5s.pdb #1
---
Chain | Description
A B | BSA
Non-standard residues in 4f5s.pdb #1
---
PGE — triethylene glycol
Alignment identifier is 1
> select :11,19
44 atoms, 44 bonds, 4 residues, 1 model selected
> select :11,19,40
58 atoms, 56 bonds, 6 residues, 1 model selected
> select :12,20,41
54 atoms, 48 bonds, 6 residues, 1 model selected
> select :12,20,41,51,64,76
108 atoms, 96 bonds, 12 residues, 1 model selected
> select :41,173
36 atoms, 32 bonds, 4 residues, 1 model selected
> select :499,224
36 atoms, 32 bonds, 4 residues, 1 model selected
QWindowsContext::windowsProc: No Qt Window found for event 0x2e0 (Unknown),
hwnd=0x0x30956.
> close session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 932, in <lambda>
close_action.triggered.connect(lambda *, s=self, sess=session:
s.file_close_cb(sess))
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 652, in file_close_cb
run(session, 'close session')
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\std_commands\close.py", line 60, in close_session
session.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\manager.py", line 252, in reset_state
alignment._destroy()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 603, in _destroy
self._notify_observers(self.NOTE_DESTROYED, None)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 652, in _notify_observers
recipient.alignment_notification(note_name, note_data)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 474, in alignment_notification
self.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 512, in delete
ToolInstance.delete(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 154, in delete
self.session.ui.remove_tool(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 345, in remove_tool
self.main_window.remove_tool(tool_instance)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 725, in remove_tool
tw._destroy()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 2049, in _destroy
self.__toolkit.destroy()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 2189, in destroy
sbar.destroy()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\statusbar.py", line 51, in destroy
v.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 438, in delete
self.make_current()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 478, in make_current
return self._opengl_context.make_current()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 99, in make_current
qc = self._initialize_context()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 125, in _initialize_context
qc.setScreen(self._screen)
RuntimeError: wrapped C/C++ object of type QScreen has been deleted
RuntimeError: wrapped C/C++ object of type QScreen has been deleted
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 125, in _initialize_context
qc.setScreen(self._screen)
See log for complete Python traceback.
> open
> C:/Users/hellmold/Nextcloud/Experiments/Protein_structure_prediction/AlphaFold/mccarty_5c6ba_unrelaxed_rank_1_model_3.pdb
Chain information for mccarty_5c6ba_unrelaxed_rank_1_model_3.pdb #1
---
Chain | Description
B | No description available
C | No description available
> close session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 932, in <lambda>
close_action.triggered.connect(lambda *, s=self, sess=session:
s.file_close_cb(sess))
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 652, in file_close_cb
run(session, 'close session')
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\std_commands\close.py", line 60, in close_session
session.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
ValueError: list.remove(x): x not in list
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
See log for complete Python traceback.
> open
> C:/Users/hellmold/Nextcloud/Experiments/Protein_structure_prediction/AlphaFold/HupLS_e123e.result/HupLS_e123e_unrelaxed_rank_1_model_3.pdb
Chain information for HupLS_e123e_unrelaxed_rank_1_model_3.pdb #1
---
Chain | Description
B | No description available
C | No description available
> set bgColor white
> open
> "C:/Users/hellmold/Nextcloud/University/190718_Masterarbeit/ITASSER/complex/cluspro/HupL_HupS_masked
> TM/first hydrophobic favored.pdb"
Summary of feedback from opening
C:/Users/hellmold/Nextcloud/University/190718_Masterarbeit/ITASSER/complex/cluspro/HupL_HupS_masked
TM/first hydrophobic favored.pdb
---
warnings | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
2864 messages similar to the above omitted
Chain information for first hydrophobic favored.pdb #2
---
Chain | Description
A | No description available
> matchmaker !#2 to #1
Missing or invalid "matchAtoms" argument: invalid atoms specifier
> matchmaker #!2 to #1
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 HupLS_e123e_unrelaxed_rank_1_model_3.pdb, chain B (#1) with first
hydrophobic favored.pdb, chain A (#2), sequence alignment score = 2621.1
RMSD between 440 pruned atom pairs is 0.844 angstroms; (across all 526 pairs:
5.681)
> delete #2
> open
> "C:/Users/hellmold/Nextcloud/University/190718_Masterarbeit/ITASSER/complex/HupL/RESULTS/Model
> 1/HupL_NiFe.pdb"
Summary of feedback from opening
C:/Users/hellmold/Nextcloud/University/190718_Masterarbeit/ITASSER/complex/HupL/RESULTS/Model
1/HupL_NiFe.pdb
---
warnings | Duplicate atom serial number found: 6902
Duplicate atom serial number found: 6903
Duplicate atom serial number found: 6904
Duplicate atom serial number found: 6905
Duplicate atom serial number found: 6906
3 messages similar to the above omitted
Ignored bad PDB record found on line 8107
TER TM-SITE 3rgwL_BS01 NFU:60,63,66,67,436,437,438,441,459,460,461,505,508
Chain information for HupL_NiFe.pdb #2
---
Chain | Description
A | No description available
> matchmaker #!2 to #1
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 HupLS_e123e_unrelaxed_rank_1_model_3.pdb, chain B (#1) with
HupL_NiFe.pdb, chain A (#2), sequence alignment score = 2613.9
RMSD between 440 pruned atom pairs is 0.844 angstroms; (across all 526 pairs:
5.681)
> open
> "C:/Users/hellmold/Nextcloud/University/190718_Masterarbeit/ITASSER/complex/HupS/RESULTS/Model
> 1/HupS_SF4_F3S_FSX.pdb"
Chain information for HupS_SF4_F3S_FSX.pdb #3
---
Chain | Description
A B C D | No description available
> matchmaker #!3 to #1
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 HupLS_e123e_unrelaxed_rank_1_model_3.pdb, chain C (#1) with
HupS_SF4_F3S_FSX.pdb, chain A (#3), sequence alignment score = 1175.6
RMSD between 235 pruned atom pairs is 0.912 angstroms; (across all 326 pairs:
12.245)
> hide #1 models
> open
> "C:/Users/hellmold/Nextcloud/University/190718_Masterarbeit/ITASSER/complex/cluspro/HupL_HupS_masked
> TM/first hydrophobic favored.pdb"
Summary of feedback from opening
C:/Users/hellmold/Nextcloud/University/190718_Masterarbeit/ITASSER/complex/cluspro/HupL_HupS_masked
TM/first hydrophobic favored.pdb
---
warnings | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
2864 messages similar to the above omitted
Chain information for first hydrophobic favored.pdb #4
---
Chain | Description
A | No description available
> matchmaker #!4 to #2
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 HupL_NiFe.pdb, chain A (#2) with first hydrophobic favored.pdb,
chain A (#4), sequence alignment score = 2752.5
RMSD between 526 pruned atom pairs is 0.000 angstroms; (across all 526 pairs:
0.000)
> matchmaker #!4 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 HupS_SF4_F3S_FSX.pdb, chain A (#3) with first hydrophobic
favored.pdb, chain A (#4), sequence alignment score = 1140.8
RMSD between 300 pruned atom pairs is 1.047 angstroms; (across all 326 pairs:
1.255)
> hide #4 models
> show #4 models
> hide #!3 models
> hide #!2 models
> hide #4 models
> show #1 models
> show #!2 models
> show #!3 models
> hide #1 models
> hide #!2 models
> show #4 models
> show #!2 models
> hide #4 models
> select all
41672 atoms, 42278 bonds, 43 pseudobonds, 3538 residues, 6 models selected
> cartoon style width 1.5 thickness 0.3
> cartoon style width 1 thickness 0.3
> cartoon style width 0.8 thickness 0.3
> ui mousemode right distance
> distance #3/D:269@FE1 #2/L:1004@FE
Distance between HupS_SF4_F3S_FSX.pdb #3/D FSX 269 FE1 and HupL_NiFe.pdb #2/L
NFU 1004 FE: 12.810Å
> set bgColor black
> ~select
Nothing selected
> set bgColor white
> select #3
19269 atoms, 19470 bonds, 39 pseudobonds, 1307 residues, 2 models selected
> ui tool show "Color Actions"
> color (#!3 & sel) #1aaee3ff
> select #2
8104 atoms, 8199 bonds, 4 pseudobonds, 527 residues, 2 models selected
> color (#!2 & sel) #0f7ac7ff
> select all
41672 atoms, 42278 bonds, 44 pseudobonds, 3538 residues, 8 models selected
> select ::name="F3S"::name="FSX"::name="NFU"::name="SF4"
33 atoms, 9 bonds, 44 pseudobonds, 4 residues, 5 models selected
> color sel byelement
> ui mousemode right translate
> ~select
Nothing selected
> hide #!5 models
> hide #5.1 models
> matchmaker #!2 to #4
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 first hydrophobic favored.pdb, chain A (#4) with HupL_NiFe.pdb,
chain A (#2), sequence alignment score = 2752.5
RMSD between 526 pruned atom pairs is 0.000 angstroms; (across all 526 pairs:
0.000)
> matchmaker #!3 to #4
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 first hydrophobic favored.pdb, chain A (#4) with
HupS_SF4_F3S_FSX.pdb, chain A (#3), sequence alignment score = 1140.8
RMSD between 300 pruned atom pairs is 1.047 angstroms; (across all 326 pairs:
1.255)
> ui mousemode right distance
> distance #2/L:1004@FE #2/L:1004@NI
Distance between HupL_NiFe.pdb #2/L NFU 1004 FE and NI: 2.593Å
> distance #3/D:269@FE1 #2/L:1004@NI
Distance between HupS_SF4_F3S_FSX.pdb #3/D FSX 269 FE1 and HupL_NiFe.pdb #2/L
NFU 1004 NI: 13.976Å
> distance #2/L:1004@NI #3/D:269@FE1
Distance already exists; modify distance properties with 'distance style'
> show #!5 models
> show #5.1 models
> delete #5
> ~distance
> ui mousemode right distance
> distance #3/D:269@FE1 #2/L:1004@NI
Distance between HupS_SF4_F3S_FSX.pdb #3/D FSX 269 FE1 and HupL_NiFe.pdb #2/L
NFU 1004 NI: 13.976Å
> ui mousemode right translate
> save
> C:/Users/hellmold/Nextcloud/Experiments/Protein_structure_prediction/Chimera_Sessions/HupLS_AlphaFold.cxs
> close session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 932, in <lambda>
close_action.triggered.connect(lambda *, s=self, sess=session:
s.file_close_cb(sess))
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 652, in file_close_cb
run(session, 'close session')
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\std_commands\close.py", line 60, in close_session
session.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
ValueError: list.remove(x): x not in list
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
See log for complete Python traceback.
> open
> C:/Users/hellmold/Nextcloud/Experiments/Protein_structure_prediction/Chimera_Sessions/AlphaFold_OmeAB_HupX+RdhA.cxs
Unable to restore session, resetting.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 679, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 679, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 155, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 179, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 422, in collated_open
return func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 982, in open
session.restore(stream, path=path, resize_window=resize_window)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 721, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
ValueError: list.remove(x): x not in list
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
See log for complete Python traceback.
> open
> C:\Users\hellmold\Nextcloud\Experiments\Protein_structure_prediction\Rosetta_Dock\OmeAB_HupX+RdhA\r_0001.pdb
> format pdb
No such file/path:
C:\Users\hellmold\Nextcloud\Experiments\Protein_structure_prediction\Rosetta_Dock\OmeAB_HupX+RdhA\r_0001.pdb
> open
> C:\Users\hellmold\Nextcloud\Experiments\Protein_structure_prediction\PDB_Files\AlphFold_OmeAB_HupX+RdhA.pdb
> format pdb
Summary of feedback from opening
C:\Users\hellmold\Nextcloud\Experiments\Protein_structure_prediction\PDB_Files\AlphFold_OmeAB_HupX+RdhA.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 56
LEU B 62 1 7
Start residue of secondary structure not found: HELIX 2 2 TRP B 87 SER B 104 1
18
Start residue of secondary structure not found: HELIX 3 3 ASN B 132 ALA B 144
1 13
Start residue of secondary structure not found: HELIX 4 4 GLN B 153 LEU B 156
1 4
Start residue of secondary structure not found: HELIX 5 5 ALA B 159 PHE B 169
1 11
119 messages similar to the above omitted
Chain information for AlphFold_OmeAB_HupX+RdhA.pdb
---
Chain | Description
1.2/A | No description available
1.1/B | No description available
1.1/C | No description available
1.1/D | No description available
> close session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 932, in <lambda>
close_action.triggered.connect(lambda *, s=self, sess=session:
s.file_close_cb(sess))
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 652, in file_close_cb
run(session, 'close session')
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\std_commands\close.py", line 60, in close_session
session.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
ValueError: list.remove(x): x not in list
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
See log for complete Python traceback.
> open
> C:\Users\hellmold\Nextcloud\Experiments\Protein_structure_prediction\PDB_Files\AlphFold_OmeAB_HupX+RdhA.pdb
> format pdb
Summary of feedback from opening
C:\Users\hellmold\Nextcloud\Experiments\Protein_structure_prediction\PDB_Files\AlphFold_OmeAB_HupX+RdhA.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 56
LEU B 62 1 7
Start residue of secondary structure not found: HELIX 2 2 TRP B 87 SER B 104 1
18
Start residue of secondary structure not found: HELIX 3 3 ASN B 132 ALA B 144
1 13
Start residue of secondary structure not found: HELIX 4 4 GLN B 153 LEU B 156
1 4
Start residue of secondary structure not found: HELIX 5 5 ALA B 159 PHE B 169
1 11
119 messages similar to the above omitted
Chain information for AlphFold_OmeAB_HupX+RdhA.pdb
---
Chain | Description
1.2/A | No description available
1.1/B | No description available
1.1/C | No description available
1.1/D | No description available
> close session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 932, in <lambda>
close_action.triggered.connect(lambda *, s=self, sess=session:
s.file_close_cb(sess))
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 652, in file_close_cb
run(session, 'close session')
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\std_commands\close.py", line 60, in close_session
session.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
ValueError: list.remove(x): x not in list
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
See log for complete Python traceback.
> open
> C:\Users\hellmold\Nextcloud\Experiments\Protein_structure_prediction\Chimera_Sessions\RdhA_putative_proton_Channel.cxs
> format session
Unable to restore session, resetting.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 679, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 679, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 324, in interceptRequest
self._callback(info)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 85, in _intercept
return interceptor(request_info, *args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 357, in intercept
chimerax_intercept(*args, view=view, session=session)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 453, in chimerax_intercept
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 366, in thread_safe
func(*args, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 444, in defer
cxcmd(session, topic)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 462, in cxcmd
run(session, cmd)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 179, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 422, in collated_open
return func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 982, in open
session.restore(stream, path=path, resize_window=resize_window)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 721, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
ValueError: list.remove(x): x not in list
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
See log for complete Python traceback.
> open
> C:\Users\hellmold\Nextcloud\Experiments\Protein_structure_prediction\Chimera_Sessions\HupL-
> HupS-HupX-OmeA.cxs format session
Unable to restore session, resetting.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 679, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 679, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 324, in interceptRequest
self._callback(info)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 85, in _intercept
return interceptor(request_info, *args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 357, in intercept
chimerax_intercept(*args, view=view, session=session)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 453, in chimerax_intercept
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 366, in thread_safe
func(*args, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 444, in defer
cxcmd(session, topic)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 462, in cxcmd
run(session, cmd)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 179, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 422, in collated_open
return func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 982, in open
session.restore(stream, path=path, resize_window=resize_window)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 721, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
ValueError: list.remove(x): x not in list
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
See log for complete Python traceback.
> open C:\ProgramData\ChimeraX\AlphFold_OmeAB_HupX+RdhA.pdb format pdb
No such file/path: C:\ProgramData\ChimeraX\AlphFold_OmeAB_HupX+RdhA.pdb
> open
> C:/Users/hellmold/Nextcloud/Experiments/Protein_structure_prediction/Chimera_Sessions/AlphaFold_OmeAB_HupX+RdhA.cxs
Unable to restore session, resetting.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 679, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 679, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 155, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 179, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 422, in collated_open
return func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 982, in open
session.restore(stream, path=path, resize_window=resize_window)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 721, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
ValueError: list.remove(x): x not in list
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
See log for complete Python traceback.
> open
> C:/Users/hellmold/Nextcloud/Experiments/Protein_structure_prediction/Chimera_Sessions/RdhA_putative_proton_Channel.cxs
Unable to restore session, resetting.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 679, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 679, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 155, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 179, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 422, in collated_open
return func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 982, in open
session.restore(stream, path=path, resize_window=resize_window)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 721, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
ValueError: list.remove(x): x not in list
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
See log for complete Python traceback.
> open C:\ProgramData\ChimeraX\OmeAB_HupX+HupLS.pdb format pdb
No such file/path: C:\ProgramData\ChimeraX\OmeAB_HupX+HupLS.pdb
> open
> C:/Users/hellmold/Nextcloud/Experiments/Protein_structure_prediction/Chimera_Sessions/AlphaFold_OmeAB_HupX+RdhA.cxs
Unable to restore session, resetting.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 679, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 679, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 155, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 179, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 422, in collated_open
return func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 982, in open
session.restore(stream, path=path, resize_window=resize_window)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 721, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
ValueError: list.remove(x): x not in list
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
See log for complete Python traceback.
> open
> C:\Users\hellmold\Nextcloud\Experiments\Protein_structure_prediction\PDB_Files\AlphFold_OmeAB_HupX+RdhA.pdb
> format pdb
Summary of feedback from opening
C:\Users\hellmold\Nextcloud\Experiments\Protein_structure_prediction\PDB_Files\AlphFold_OmeAB_HupX+RdhA.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 56
LEU B 62 1 7
Start residue of secondary structure not found: HELIX 2 2 TRP B 87 SER B 104 1
18
Start residue of secondary structure not found: HELIX 3 3 ASN B 132 ALA B 144
1 13
Start residue of secondary structure not found: HELIX 4 4 GLN B 153 LEU B 156
1 4
Start residue of secondary structure not found: HELIX 5 5 ALA B 159 PHE B 169
1 11
119 messages similar to the above omitted
Chain information for AlphFold_OmeAB_HupX+RdhA.pdb
---
Chain | Description
1.2/A | No description available
1.1/B | No description available
1.1/C | No description available
1.1/D | No description available
> close session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 932, in <lambda>
close_action.triggered.connect(lambda *, s=self, sess=session:
s.file_close_cb(sess))
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 652, in file_close_cb
run(session, 'close session')
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\std_commands\close.py", line 60, in close_session
session.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
ValueError: list.remove(x): x not in list
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
See log for complete Python traceback.
> open
> C:\Users\hellmold\Nextcloud\Experiments\Protein_structure_prediction\Rosetta_Dock\OmeAB_HupX+RdhA\r_0001.pdb
> format pdb
No such file/path:
C:\Users\hellmold\Nextcloud\Experiments\Protein_structure_prediction\Rosetta_Dock\OmeAB_HupX+RdhA\r_0001.pdb
> open
> C:\Users\hellmold\Nextcloud\Experiments\Protein_structure_prediction\PDB_Files\OmeAB_HupX+HupLS.pdb
> format pdb
Summary of feedback from opening
C:\Users\hellmold\Nextcloud\Experiments\Protein_structure_prediction\PDB_Files\OmeAB_HupX+HupLS.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 56
LEU B 62 1 7
Start residue of secondary structure not found: HELIX 2 2 TRP B 87 SER B 104 1
18
Start residue of secondary structure not found: HELIX 3 3 ASN B 132 ALA B 144
1 13
Start residue of secondary structure not found: HELIX 4 4 GLN B 153 LEU B 156
1 4
Start residue of secondary structure not found: HELIX 5 5 ALA B 159 PHE B 169
1 11
119 messages similar to the above omitted
Chain information for OmeAB_HupX+HupLS.pdb
---
Chain | Description
1.2/A | No description available
1.1/B | No description available
1.1/C | No description available
1.1/D | No description available
> close session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 932, in <lambda>
close_action.triggered.connect(lambda *, s=self, sess=session:
s.file_close_cb(sess))
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 652, in file_close_cb
run(session, 'close session')
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\std_commands\close.py", line 60, in close_session
session.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
ValueError: list.remove(x): x not in list
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
See log for complete Python traceback.
> open
> C:\Users\hellmold\Nextcloud\Experiments\Protein_structure_prediction\Chimera_Sessions\RdhA_putative_proton_Channel.cxs
> format session
Unable to restore session, resetting.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 679, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 679, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 324, in interceptRequest
self._callback(info)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 85, in _intercept
return interceptor(request_info, *args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 357, in intercept
chimerax_intercept(*args, view=view, session=session)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 453, in chimerax_intercept
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 366, in thread_safe
func(*args, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 444, in defer
cxcmd(session, topic)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 462, in cxcmd
run(session, cmd)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 179, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 422, in collated_open
return func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 982, in open
session.restore(stream, path=path, resize_window=resize_window)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 721, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
ValueError: list.remove(x): x not in list
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
See log for complete Python traceback.
> open
> C:\Users\hellmold\Nextcloud\Experiments\Protein_structure_prediction\Chimera_Sessions\RdhA_putative_proton_Channel.cxs
> format session
Unable to restore session, resetting.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 679, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 679, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 324, in interceptRequest
self._callback(info)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 85, in _intercept
return interceptor(request_info, *args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 357, in intercept
chimerax_intercept(*args, view=view, session=session)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 453, in chimerax_intercept
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 366, in thread_safe
func(*args, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 444, in defer
cxcmd(session, topic)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 462, in cxcmd
run(session, cmd)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 179, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 422, in collated_open
return func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 982, in open
session.restore(stream, path=path, resize_window=resize_window)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 721, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
ValueError: list.remove(x): x not in list
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
See log for complete Python traceback.
> open
> C:\Users\hellmold\Nextcloud\Experiments\Protein_structure_prediction\Chimera_Sessions\RdhA_putative_proton_Channel.cxs
> format session
Unable to restore session, resetting.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 679, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 679, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 324, in interceptRequest
self._callback(info)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 85, in _intercept
return interceptor(request_info, *args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 357, in intercept
chimerax_intercept(*args, view=view, session=session)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 453, in chimerax_intercept
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 366, in thread_safe
func(*args, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 444, in defer
cxcmd(session, topic)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 462, in cxcmd
run(session, cmd)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 179, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 422, in collated_open
return func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 982, in open
session.restore(stream, path=path, resize_window=resize_window)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 721, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 507, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
ValueError: list.remove(x): x not in list
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 379, in detach_viewer
self.viewers.remove(viewer)
See log for complete Python traceback.
> open
> Y:\Gruppen\ubt\\_ResearchGroups\WG_Adrian\Nadine\AlphaFold2\OHR_a4a69.result\OHR_a4a69_unrelaxed_rank_1_model_5.pdb
> format pdb
Chain information for OHR_a4a69_unrelaxed_rank_1_model_5.pdb #1
---
Chain | Description
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
OpenGL version: 3.3.0 - Build 27.20.100.8935
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel
Manufacturer: LENOVO
Model: 20Q1S7KS00
OS: Microsoft Windows 10 Enterprise (Build 19044)
Memory: 8,359,190,528
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8265U CPU @ 1.60GHz
OSLanguage: de-DE
Locale: ('de_DE', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.5.0
chardet: 3.0.4
ChimeraX-AddCharge: 1.0.1
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.2
ChimeraX-AtomicLibrary: 3.1.3
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.5
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.3
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.6
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.9
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 2.0.1
matplotlib: 3.3.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pywin32: 228
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
Send2Trash: 1.8.0
SEQCROW: 1.5.8
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (2)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Graphics |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Status bar: wrapped C/C++ object of type QScreen has been deleted |
comment:2 by , 3 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
This bug was fixed about a year ago. It happens when running ChimeraX with two screens and disconnecting one of the screens.
Update to a current ChimeraX version to avoid this problem or avoid disconnecting a second screen after starting ChimeraX.
Note:
See TracTickets
for help on using tickets.
Reported by Nadine Hellmold