id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7721 Session save: Basic Actions: 'QEventLoop' object has no attribute 'exec_' david.barrass@… Zach Pearson "{{{ 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' -> -> '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' -> -> 'Basic Actions': Error while saving session data for 'tools' -> -> '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' -> -> '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 *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' -> -> 'Basic Actions': Error while saving session data for 'tools' -> -> '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' -> -> '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' -> -> 'Basic Actions': Error while saving session data for 'tools' -> -> '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' -> -> '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 *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' -> -> 'Basic Actions': Error while saving session data for 'tools' -> -> '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' -> -> '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' -> -> 'Basic Actions': Error while saving session data for 'tools' -> -> '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' -> -> '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 *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' -> -> 'Basic Actions': Error while saving session data for 'tools' -> -> '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 }}} " defect closed normal Sessions duplicate Eric Pettersen all ChimeraX