Session save: Basic Actions: 'QEventLoop' object has no attribute 'exec_'

[david.barrass@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19043
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
I'm just trying to save the csx file of a really very standard protein. First tried to save onto one drive, but since tried to save to C: with same results

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "C:/Users/dbarrass/OneDrive - University of Edinburgh/BTO
> docs/Structures/EcoR1.cxs"

Log from Wed Apr 20 15:42:30 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "C:/Users/david/OneDrive - University of Edinburgh/BTO
> docs/Structures/EcoR1.cxs"

Log from Fri Apr 8 12:12:00 2022 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> help help:quickstart

> preset cartoons/nucleotides ribbons/slabs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> show # target m

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

> open C:/Users/dbarrass/Downloads/1ERI.cif

mmCIF parsing error: PDBx/mmCIF styling lost near line 1012  

> open C:/Users/dbarrass/Downloads/1ERI.cif

mmCIF parsing error: PDBx/mmCIF styling lost near line 1012  

> open C:/Users/dbarrass/Downloads/1ERI.bcif

Unrecognized file suffix '.bcif'  

> open "C:/Users/dbarrass/Downloads/1eri (1).cif"

1eri (1).cif title:  
X-ray structure of the DNA-eco ri endonuclease-DNA recognition complex: the
recognition network and the integration of recognition and cleavage [more
info...]  
  
Chain information for 1eri (1).cif #1  
---  
Chain | Description | UniProt  
A | protein (eco ri endonuclease (E.C.3.1.21.4)) | T2E1_ECOLI  
B | DNA (5'-D(*TP*CP*GP*CP*GP*ap*ap*TP*TP*CP*GP*CP*G)-3') |  
  
1eri (1).cif mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> nucleotides atoms

> style nucleic stick

Changed 263 atom styles  

> color bynucleotide

> preset cartoons/nucleotides ribbons/slabs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> open "C:/Users/dbarrass/Downloads/1ERI (2).cif"

mmCIF parsing error: PDBx/mmCIF styling lost near line 1012  

> help help:user

> open C:/Users/dbarrass/Downloads/1eri.pdb1.gz

1eri.pdb1.gz title:  
X-ray structure of the DNA-eco ri endonuclease-DNA recognition complex: the
recognition network and the integration of recognition and cleavage [more
info...]  
  
Chain information for 1eri.pdb1.gz  
---  
Chain | Description  
2.1/A 2.2/A | No description available  
2.1/B 2.2/B | No description available  
  

> nucleotides atoms

> style nucleic stick

Changed 789 atom styles  

> nucleotides fill

> style nucleic stick

Changed 789 atom styles  

> nucleotides fill

> style nucleic stick

Changed 789 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 789 atom styles  

> style sphere

Changed 7125 atom styles  

> color bychain

[Repeated 1 time(s)]

> color byhetero

> color bychain

> color bypolymer

> nucleotides atoms

> style nucleic stick

Changed 789 atom styles  

> show atoms

> hide atoms

> show cartoons

> hide cartoons

[Repeated 1 time(s)]

> show cartoons

> show surfaces

> style sphere

Changed 7125 atom styles  

> style sphere

Changed 7125 atom styles  

> hide cartoons

> show cartoons

> hide cartoons

> show atoms

> hide surfaces

> select protein

6153 atoms, 6252 bonds, 783 residues, 3 models selected  

> show sel cartoons

> hide sel atoms

> select ::name="HOH"

183 atoms, 183 residues, 3 models selected  

> hide sel atoms

> hide sel cartoons

> hide sel surfaces

> ui tool show "Basic Actions"

> ui tool show Contacts

> contacts

30943 contacts  

> ui tool show Contacts

> ui mousemode right "delete markers"

> ui tool show AlphaFold

> preset cartoons/nucleotides ribbons/slabs

Changed 7125 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> undo

[Repeated 3 time(s)]

> redo

> ui tool show "Scale Bar"

> help help:user/preferences.html#startup

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> cartoon style sel modeHelix tube sides 20

> undo

> toolshed show

Hide dust shortcut requires a displayed map surface  

> scalebar

> scalebar off

> ui tool show "Basic Actions"

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!2.1 models

> show #!2.1 models

> cartoon style

1eri (1).cif #1  
\- helix mode=default xsection=round width=2 height=0.4 arrow=False arrow
scale=2  
\- strand mode=default xsection=round width=2 height=0.4 arrow=True arrow
scale=2  
\- coil xsection=round width=0.4 height=0.4  
\- nucleic xsection=square width=0.4 height=2  
\- divisions=20  
\- oval parameters: sides=12  
\- barbell parameters: sides=18 scale=0.5  
1eri.pdb1.gz #2.1  
\- helix mode=default xsection=round width=2 height=0.4 arrow=False arrow
scale=2  
\- strand mode=default xsection=round width=2 height=0.4 arrow=True arrow
scale=2  
\- coil xsection=round width=0.4 height=0.4  
\- nucleic xsection=square width=0.4 height=2  
\- divisions=20  
\- oval parameters: sides=12  
\- barbell parameters: sides=18 scale=0.5  
1eri.pdb1.gz #2.2  
\- helix mode=default xsection=round width=2 height=0.4 arrow=False arrow
scale=2  
\- strand mode=default xsection=round width=2 height=0.4 arrow=True arrow
scale=2  
\- coil xsection=round width=0.4 height=0.4  
\- nucleic xsection=square width=0.4 height=2  
\- divisions=20  
\- oval parameters: sides=12  
\- barbell parameters: sides=18 scale=0.5  

> select #1

2375 atoms, 2378 bonds, 1746 pseudobonds, 335 residues, 2 models selected  

> close #1

> cartoon style

1eri.pdb1.gz #2.1  
\- helix mode=default xsection=round width=2 height=0.4 arrow=False arrow
scale=2  
\- strand mode=default xsection=round width=2 height=0.4 arrow=True arrow
scale=2  
\- coil xsection=round width=0.4 height=0.4  
\- nucleic xsection=square width=0.4 height=2  
\- divisions=20  
\- oval parameters: sides=12  
\- barbell parameters: sides=18 scale=0.5  
1eri.pdb1.gz #2.2  
\- helix mode=default xsection=round width=2 height=0.4 arrow=False arrow
scale=2  
\- strand mode=default xsection=round width=2 height=0.4 arrow=True arrow
scale=2  
\- coil xsection=round width=0.4 height=0.4  
\- nucleic xsection=square width=0.4 height=2  
\- divisions=20  
\- oval parameters: sides=12  
\- barbell parameters: sides=18 scale=0.5  

> hide #3 models

> cartoon style \- helix xsection=round width=2 height=2 arrow=False arrow
> scale=2

Expected an atoms specifier or a keyword  

> 1eri.pdb1.gz #2.1 cartoon style - helix xsection=round width=2 height=2
> arrow=False arrow scale=2

Unknown command: 1eri.pdb1.gz #2.1 cartoon style - helix xsection=round
width=2 height=2 arrow=False arrow scale=2  

> cartoon style 1eri.pdb1.gz #2.1 - helix xsection=round width=2 height=2
> arrow=False arrow scale=2

Expected an atoms specifier or a keyword  

> cartoon style helix width 1.5

> cartoon style helix width 2.5

> cartoon style helix hight 2.5

Expected a keyword  

> cartoon style helix height 2.5

Expected a keyword  

> cartoon style helix height=2.5

Expected a keyword  

> cartoon style helix xsection=round

Expected a keyword  

> cartoon style helix height 2.5

Expected a keyword  

> cartoon style helix section=round

Expected a keyword  

> cartoon style helix xsection=oval

Expected a keyword  

> cartoon style helix xsection oval

> cartoon style helix thickness 2.5

> cartoon style helix arrows true

> cartoon style helix arrows scale 3

Invalid "arrows" argument: Expected true or false (or 1 or 0)  

> cartoon style helix arrowScale 3

> cartoon style coil width 2 thickness 2

> cartoon style helix width 3 thickness 3

> cartoon style strand width 3 thickness 1

> cartoon style strand width 4 thickness 1

> cartoon style strand width 5 thickness 1

> cartoon style strand width 5.5 thickness 1.5

> cartoon style strand arrowScale 1

> cartoon style strand arrowScale 1.2

> cartoon style strand width 5 thickness 1.5 arrowScale 1.2

QFileSystemWatcher::addPaths: list is empty  

> save "C:/Users/dbarrass/OneDrive - University of Edinburgh/BTO docs/New
> Folder/Eco R1.cxs"

No model chosen to save relative to  

> save "C:/Users/dbarrass/OneDrive - University of Edinburgh/BTO docs/New
> Folder/EcoR1.stl"

> save "C:/Users/dbarrass/OneDrive - University of Edinburgh/BTO
> docs/Structures/EcoR1.stl"

> save "C:/Users/dbarrass/OneDrive - University of Edinburgh/BTO
> docs/Structures/EcoR1.cxs"

——— End of log from Fri Apr 8 12:12:00 2022 ———

opened ChimeraX session  

> cartoon style helix width 3 thickness 3

> cartoon style coil width 2.5 thickness 2.5

> cartoon style coil width 3 thickness 3

> cartoon style helix width 2.5 thickness 2.5

> cartoon style coil width 3.5 thickness 3.5

> cartoon style strand width 6 thickness 2 arrowScale 1.2

> save "C:/Users/david/OneDrive - University of Edinburgh/BTO
> docs/Structures/EcoR1.cxs"

——— End of log from Wed Apr 20 15:42:30 2022 ———

opened ChimeraX session  

> select /A:48

16 atoms, 14 bonds, 2 residues, 2 models selected  

> show sel atoms

> select /A:20

14 atoms, 12 bonds, 2 residues, 2 models selected  

> show sel atoms

> select /A:45

10 atoms, 8 bonds, 2 residues, 2 models selected  

> show sel atoms

> select /A:41

16 atoms, 14 bonds, 2 residues, 2 models selected  

> show sel atoms

> select /A:37

18 atoms, 16 bonds, 2 residues, 2 models selected  

> select /A:38

14 atoms, 12 bonds, 2 residues, 2 models selected  

> show sel atoms

> select

4750 atoms, 4756 bonds, 3493 pseudobonds, 670 residues, 4 models selected  

> hide sel atoms

> undo

> hide sel atoms

> select #2.1/B

274 atoms, 294 bonds, 94 pseudobonds, 24 residues, 2 models selected  

> select #2.2/A

2101 atoms, 2084 bonds, 1565 pseudobonds, 311 residues, 2 models selected  

> select #2.1/A

2101 atoms, 2084 bonds, 1565 pseudobonds, 311 residues, 2 models selected  

> select #2.1/B

274 atoms, 294 bonds, 94 pseudobonds, 24 residues, 2 models selected  

> show sel atoms

> select #2.2/B

274 atoms, 294 bonds, 95 pseudobonds, 24 residues, 2 models selected  

> show sel atoms

> select solvent

122 atoms, 12 pseudobonds, 122 residues, 3 models selected  

> delete atoms (#!2.1-2 & sel)

> delete bonds (#!2.1-2 & sel)

> select sequence GTTAAC

Nothing selected  

> select sequence GAATTC

246 atoms, 274 bonds, 76 pseudobonds, 12 residues, 3 models selected  

> select sequence GCGAATTCGC

410 atoms, 458 bonds, 121 pseudobonds, 20 residues, 3 models selected  

> select sequence GCGAATTCGC

410 atoms, 458 bonds, 121 pseudobonds, 20 residues, 3 models selected  

> select ~sel

4218 atoms, 4294 bonds, 2898 pseudobonds, 528 residues, 4 models selected  

> hide sel atoms

> save "C:/Users/dbarrass/OneDrive - University of Edinburgh/BTO
> docs/Structures/Protein structures/EcoR1 for printing.cxs"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\basic_actions\tool.py", line 225, in take_snapshot  
self.add_webview_state(data)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\basic_actions\tool.py", line 260, in add_webview_state  
event_loop.exec_()  
AttributeError: 'QEventLoop' object has no attribute 'exec_'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000001B71A533E80> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x000001B73EC47160>
'Basic Actions'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000001B71A533E80> -> <chimerax.basic_actions.tool.BasicActionsTool object at
0x000001B73EC47160> 'Basic Actions': Error while saving session data for
'tools' -> <chimerax.core.tools.Tools object at 0x000001B71A533E80> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x000001B73EC47160>
'Basic Actions'  
  
ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while
saving session data for 'tools' -> -> 'Basic Actions'  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\basic_actions\tool.py", line 225, in take_snapshot  
self.add_webview_state(data)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\basic_actions\tool.py", line 260, in add_webview_state  
event_loop.exec_()  
AttributeError: 'QEventLoop' object has no attribute 'exec_'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000001B71A533E80> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x000001B73EC47160>
'Basic Actions'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000001B71A533E80> -> <chimerax.basic_actions.tool.BasicActionsTool object at
0x000001B73EC47160> 'Basic Actions': Error while saving session data for
'tools' -> <chimerax.core.tools.Tools object at 0x000001B71A533E80> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x000001B73EC47160>
'Basic Actions'  
  
ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while
saving session data for 'tools' -> -> 'Basic Actions'  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save "C:/Users/dbarrass/OneDrive - University of Edinburgh/BTO
> docs/Structures/Protein structures/EcoR1 for priniting.cxs"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\basic_actions\tool.py", line 225, in take_snapshot  
self.add_webview_state(data)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\basic_actions\tool.py", line 260, in add_webview_state  
event_loop.exec_()  
AttributeError: 'QEventLoop' object has no attribute 'exec_'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000001B71A533E80> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x000001B73EC47160>
'Basic Actions'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000001B71A533E80> -> <chimerax.basic_actions.tool.BasicActionsTool object at
0x000001B73EC47160> 'Basic Actions': Error while saving session data for
'tools' -> <chimerax.core.tools.Tools object at 0x000001B71A533E80> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x000001B73EC47160>
'Basic Actions'  
  
ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while
saving session data for 'tools' -> -> 'Basic Actions'  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\basic_actions\tool.py", line 225, in take_snapshot  
self.add_webview_state(data)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\basic_actions\tool.py", line 260, in add_webview_state  
event_loop.exec_()  
AttributeError: 'QEventLoop' object has no attribute 'exec_'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000001B71A533E80> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x000001B73EC47160>
'Basic Actions'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000001B71A533E80> -> <chimerax.basic_actions.tool.BasicActionsTool object at
0x000001B73EC47160> 'Basic Actions': Error while saving session data for
'tools' -> <chimerax.core.tools.Tools object at 0x000001B71A533E80> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x000001B73EC47160>
'Basic Actions'  
  
ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while
saving session data for 'tools' -> -> 'Basic Actions'  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save "C:/Users/dbarrass/Documents/EcoR1 for printing.cxs"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\basic_actions\tool.py", line 225, in take_snapshot  
self.add_webview_state(data)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\basic_actions\tool.py", line 260, in add_webview_state  
event_loop.exec_()  
AttributeError: 'QEventLoop' object has no attribute 'exec_'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000001B71A533E80> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x000001B73EC47160>
'Basic Actions'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000001B71A533E80> -> <chimerax.basic_actions.tool.BasicActionsTool object at
0x000001B73EC47160> 'Basic Actions': Error while saving session data for
'tools' -> <chimerax.core.tools.Tools object at 0x000001B71A533E80> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x000001B73EC47160>
'Basic Actions'  
  
ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while
saving session data for 'tools' -> -> 'Basic Actions'  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\basic_actions\tool.py", line 225, in take_snapshot  
self.add_webview_state(data)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\basic_actions\tool.py", line 260, in add_webview_state  
event_loop.exec_()  
AttributeError: 'QEventLoop' object has no attribute 'exec_'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000001B71A533E80> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x000001B73EC47160>
'Basic Actions'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000001B71A533E80> -> <chimerax.basic_actions.tool.BasicActionsTool object at
0x000001B73EC47160> 'Basic Actions': Error while saving session data for
'tools' -> <chimerax.core.tools.Tools object at 0x000001B71A533E80> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x000001B73EC47160>
'Basic Actions'  
  
ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while
saving session data for 'tools' -> -> 'Basic Actions'  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 30.0.101.1340
OpenGL renderer: Intel(R) HD Graphics 520
OpenGL vendor: Intel

Python: 3.9.11
Locale: en_GB.cp1252
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows

Manufacturer: HP
Model: HP EliteBook 840 G3
OS: Microsoft Windows 10 Education (Build 19043)
Memory: 16,550,371,328
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-6300U CPU @ 2.40GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pywin32: 303
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
    WMI: 1.5.1

[Eric Pettersen]

Hi David,

Thanks for reporting this problem. It is fixed in the daily build, so if you get that then things will work. Another alternative is to close the Basic Actions tool before you save a session, because it is that tool that has the bug that is fixed in the daily build. Sorry for the inconvenience.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab