id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8473 Show chain sequence: TypeError: __init__() got an unexpected keyword argument 'seq_viewer' weberm@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19044 ChimeraX Version: 1.6.dev202302100235 (2023-02-10 02:35:09 UTC) Description (Describe the actions that caused this problem to occur here) The sequence viewer tool does not work properly anymore in the ChimeraX daily build (2023/02/09) version. (By the way: I used the daily build, because ChimeraX 1.5 has a bug which is raised upon once using the ""repaired"" DockView tool with a SwissDock output: the ""models"" window now remains permanently / by default unchecked in the tools menu and the ""models"" tab permanently appears as separate window upon ChimeraX startup - which requires manuel window closing (or double-clicking in the side panel to place it there; it's really ""annoying"".) Back on topic: Did a matchmaker overlay with 3 models of the same protein (2 of these in complex with another protein: a homodimer model plus a heterodimer overlayed on the monomeric model) and wanted to get the same sequence regions highlighted in the viewing panel. Just an error message appears with and/or without same sequences grouped/not grouped: ui tool show ""Show Sequence Viewer"" sequence chain #1/A #2/A #2/B #3/A Alignment identifier is 1 Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\show_sequences\tool.py"", line 64, in show_seqs run(self.session, ""seq chain %s"" % "" "".join([chain.atomspec for chain in chains])) File ""C:\Program Files\ChimeraX\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\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seqalign\cmd.py"", line 232, in seqalign_chain alignment = session.alignments.new_alignment([seq], None, seq_viewer=""sv"", File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seqalign\manager.py"", line 242, in new_alignment alignment = Alignment(self.session, seqs, identify_as, attrs, markups, auto_destroy, TypeError: __init__() got an unexpected keyword argument 'seq_viewer' TypeError: __init__() got an unexpected keyword argument 'seq_viewer' File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seqalign\manager.py"", line 242, in new_alignment alignment = Alignment(self.session, seqs, identify_as, attrs, markups, auto_destroy, See log for complete Python traceback. ui tool show ""Show Sequence Viewer"" sequence chain #1/A Alignment identifier is 1/A Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\show_sequences\tool.py"", line 64, in show_seqs run(self.session, ""seq chain %s"" % "" "".join([chain.atomspec for chain in chains])) File ""C:\Program Files\ChimeraX\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\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seqalign\cmd.py"", line 212, in seqalign_chain alignment = session.alignments.new_alignment([chain], ident, seq_viewer=""sv"", File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seqalign\manager.py"", line 242, in new_alignment alignment = Alignment(self.session, seqs, identify_as, attrs, markups, auto_destroy, TypeError: __init__() got an unexpected keyword argument 'seq_viewer' TypeError: __init__() got an unexpected keyword argument 'seq_viewer' File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seqalign\manager.py"", line 242, in new_alignment alignment = Alignment(self.session, seqs, identify_as, attrs, markups, auto_destroy, See log for complete Python traceback. Log: UCSF ChimeraX version: 1.6.dev202302100235 (2023-02-10) © 2016-2023 Regents of the University of California. All rights reserved. > open C:\\\MW\\\MW_2022\\\Arnim\\\antibody_project\\\CAD_CAD2_CADiCAD_Fab- > full.cxs Log from Fri Feb 10 17:20:21 2023 Startup Messages --- warnings | QWindowsWindow::setDarkBorderToWindow: Unable to set dark window border. QWindowsWindow::setDarkBorderToWindow: Unable to set dark window border. note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.6.dev202302100235 (2023-02-10) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""C:/MW/MW_2022/Arnim/CAD Docking/proteins & > ligands/2022-12-16/AF-O76075-F1-model_v2.pdb"" AF-O76075-F1-model_v2.pdb title: Alphafold monomer V2.0 prediction for DNA fragmentation factor subunit β (O76075) [more info...] Chain information for AF-O76075-F1-model_v2.pdb #1 --- Chain | Description | UniProt A | DNA fragmentation factor subunit β | DFFB_HUMAN 1-338 > lighting full > open ""C:/MW/MW_2022/Arnim/CAD Docking/proteins & > ligands/CAD_dimer_Deepmind_selected_prediction.pdb"" Chain information for CAD_dimer_Deepmind_selected_prediction.pdb #2 --- Chain | Description A B | 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 AF-O76075-F1-model_v2.pdb, chain A (#1) with CAD_dimer_Deepmind_selected_prediction.pdb, chain A (#2), sequence alignment score = 1738.9 RMSD between 235 pruned atom pairs is 0.565 angstroms; (across all 338 pairs: 3.948) > open ""C:/MW/MW_2022/Arnim/CAD Docking/proteins & > ligands/CAD_iCAD_dimer_Deepmind_selected_prediction.pdb"" Chain information for CAD_iCAD_dimer_Deepmind_selected_prediction.pdb #3 --- Chain | Description A | No description available B | 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 AF-O76075-F1-model_v2.pdb, chain A (#1) with CAD_iCAD_dimer_Deepmind_selected_prediction.pdb, chain A (#3), sequence alignment score = 1713.1 RMSD between 79 pruned atom pairs is 0.270 angstroms; (across all 338 pairs: 34.008) > hide #1 models > show #1 models > hide #3 models > color #1-2 bychain > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > color #1 #55aaffff > show #2 models > hide #2 models > show #3 models > hide #1 models > show #2 models > hide #2 models > hide #3 models > show #3 models > color #3 bychain > show #2 models > show #1 models > hide #1 models > hide #2 models > hide #3 models > show #2 models > color #2 bypolymer > color #2 bychain > color #2 #00aa7fff > color #2 #aa55ffff > color #2 #aa0000ff > color #2 #aa007fff > color #2 #55aaffff > color #2 bychain > show #3 models > hide #2 models > matchmaker #3 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 CAD_dimer_Deepmind_selected_prediction.pdb, chain A (#2) with CAD_iCAD_dimer_Deepmind_selected_prediction.pdb, chain A (#3), sequence alignment score = 1719.1 RMSD between 86 pruned atom pairs is 0.543 angstroms; (across all 338 pairs: 30.269) > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > hide #3 models > show #2 models > show #1 models > hide #2 models > show #1 surfaces > show #2 models > hide #2 models > show #3 models > 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 AF-O76075-F1-model_v2.pdb, chain A (#1) with CAD_iCAD_dimer_Deepmind_selected_prediction.pdb, chain A (#3), sequence alignment score = 1713.1 RMSD between 79 pruned atom pairs is 0.270 angstroms; (across all 338 pairs: 34.008) > matchmaker #3 to #1:A No 'to' model specified > 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 AF-O76075-F1-model_v2.pdb, chain A (#1) with CAD_iCAD_dimer_Deepmind_selected_prediction.pdb, chain A (#3), sequence alignment score = 1713.1 RMSD between 79 pruned atom pairs is 0.270 angstroms; (across all 338 pairs: 34.008) > select add #1 2751 atoms, 2811 bonds, 338 residues, 1 model selected > hide sel surfaces > select add #2 13731 atoms, 13911 bonds, 1014 residues, 3 models selected > select subtract #1 10980 atoms, 11100 bonds, 676 residues, 2 models selected > select add #3 21577 atoms, 21787 bonds, 1345 residues, 2 models selected > select subtract #2 10597 atoms, 10687 bonds, 669 residues, 1 model selected > select subtract #3 Nothing selected > hide #3 models > show #2 models > select add #2 10980 atoms, 11100 bonds, 676 residues, 1 model selected > select subtract #2 Nothing selected > select add #1 2751 atoms, 2811 bonds, 338 residues, 1 model selected > open C:/MW/MW_2022/Arnim/antibody_project/1r70(1).pdb 1r70(1).pdb title: Model of human IGA2 determined by solution scattering, curve fitting and homology modelling [more info...] Chain information for 1r70(1).pdb #4 --- Chain | Description A C | human IGA2(M1) light chain B D | human IGA2(M1) heavy chain > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > matchmaker #4 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 AF-O76075-F1-model_v2.pdb, chain A (#1) with 1r70(1).pdb, chain B (#4), sequence alignment score = 30 RMSD between 7 pruned atom pairs is 1.028 angstroms; (across all 29 pairs: 32.437) > show sel surfaces > select subtract #1 1 model selected > show #3 models > show surfaces > hide #4.2 models > hide #4.3 models > hide #4.4 models > hide #4.5 models > color bychain > hide #!4 models > show #!4 models > hide #!3 models > show #!3 models > hide #!2 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!1 models > hide #1.1 models > color #1 #00aaffff > show #!1 models > show #1.1 models > hide #1.1 models > show #1.1 models > hide #1.1 models > show #!2 models > hide #2.1 models > hide #2.2 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > show #2.1 models > hide #2.1 models > show #2.2 models > hide #2.2 models > show #2.2 models > hide #2.2 models > save C:/MW/MW_2022/Arnim/antibody_project/CAD_CAD2_CADiCAD_Fab-full.cxs > lighting full > save C:/MW/MW_2022/Arnim/antibody_project/CAD_CAD2_CADiCAD_Fab-full.cxs ——— End of log from Fri Feb 10 17:20:21 2023 ——— opened ChimeraX session > show #!3 models > hide #3.1 models > hide #3.2 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > movie record > turn y 2 180 > wait 180 > movie encode C:\Users\weber\Desktop\movie1.mp4 Movie saved to \C:Users\\...\Desktop\movie1.mp4 > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > rename #4 1r70.pdb > lighting full > show surfaces > hide surfaces > select add #4.2 214 atoms, 214 residues, 1 model selected > select subtract #4.2 1 model selected > select add #4.2 214 atoms, 214 residues, 1 model selected > select subtract #4.2 1 model selected > select add #4.2 214 atoms, 214 residues, 1 model selected > hide #!2 models > show #!2 models > hide #!3 models > hide #!4 models > show #!4 models > show #!3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > select #3/B 5107 atoms, 5137 bonds, 331 residues, 1 model selected > hide #!4 models > hide #!2 models > show #!2 models > hide #2.1 models > show #2.1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > 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 AF-O76075-F1-model_v2.pdb, chain A (#1) with CAD_iCAD_dimer_Deepmind_selected_prediction.pdb, chain A (#3), sequence alignment score = 1713.1 RMSD between 79 pruned atom pairs is 0.270 angstroms; (across all 338 pairs: 34.008) > matchmaker #3 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 CAD_dimer_Deepmind_selected_prediction.pdb, chain A (#2) with CAD_iCAD_dimer_Deepmind_selected_prediction.pdb, chain A (#3), sequence alignment score = 1719.1 RMSD between 86 pruned atom pairs is 0.543 angstroms; (across all 338 pairs: 30.269) > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > ui tool show ""Show Sequence Viewer"" > sequence chain #3/B Alignment identifier is 3/B Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\show_sequences\tool.py"", line 64, in show_seqs run(self.session, ""seq chain %s"" % "" "".join([chain.atomspec for chain in chains])) File ""C:\Program Files\ChimeraX\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\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\seqalign\cmd.py"", line 212, in seqalign_chain alignment = session.alignments.new_alignment([chain], ident, seq_viewer=""sv"", File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\seqalign\manager.py"", line 242, in new_alignment alignment = Alignment(self.session, seqs, identify_as, attrs, markups, auto_destroy, TypeError: __init__() got an unexpected keyword argument 'seq_viewer' TypeError: __init__() got an unexpected keyword argument 'seq_viewer' File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\seqalign\manager.py"", line 242, in new_alignment alignment = Alignment(self.session, seqs, identify_as, attrs, markups, auto_destroy, See log for complete Python traceback. > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A #2/A #2/B #3/A Alignment identifier is 1 Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\show_sequences\tool.py"", line 64, in show_seqs run(self.session, ""seq chain %s"" % "" "".join([chain.atomspec for chain in chains])) File ""C:\Program Files\ChimeraX\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\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\seqalign\cmd.py"", line 232, in seqalign_chain alignment = session.alignments.new_alignment([seq], None, seq_viewer=""sv"", File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\seqalign\manager.py"", line 242, in new_alignment alignment = Alignment(self.session, seqs, identify_as, attrs, markups, auto_destroy, TypeError: __init__() got an unexpected keyword argument 'seq_viewer' TypeError: __init__() got an unexpected keyword argument 'seq_viewer' File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\seqalign\manager.py"", line 242, in new_alignment alignment = Alignment(self.session, seqs, identify_as, attrs, markups, auto_destroy, See log for complete Python traceback. > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Alignment identifier is 1/A Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\show_sequences\tool.py"", line 64, in show_seqs run(self.session, ""seq chain %s"" % "" "".join([chain.atomspec for chain in chains])) File ""C:\Program Files\ChimeraX\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\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\seqalign\cmd.py"", line 212, in seqalign_chain alignment = session.alignments.new_alignment([chain], ident, seq_viewer=""sv"", File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\seqalign\manager.py"", line 242, in new_alignment alignment = Alignment(self.session, seqs, identify_as, attrs, markups, auto_destroy, TypeError: __init__() got an unexpected keyword argument 'seq_viewer' TypeError: __init__() got an unexpected keyword argument 'seq_viewer' File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\seqalign\manager.py"", line 242, in new_alignment alignment = Alignment(self.session, seqs, identify_as, attrs, markups, auto_destroy, See log for complete Python traceback. > hide #1.1 models > hide #2.1 models > hide #2.2 models > hide #3.1 models > hide #3.2 models > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A #2/A #2/B #3/A Alignment identifier is 1 Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\show_sequences\tool.py"", line 64, in show_seqs run(self.session, ""seq chain %s"" % "" "".join([chain.atomspec for chain in chains])) File ""C:\Program Files\ChimeraX\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\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\seqalign\cmd.py"", line 232, in seqalign_chain alignment = session.alignments.new_alignment([seq], None, seq_viewer=""sv"", File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\seqalign\manager.py"", line 242, in new_alignment alignment = Alignment(self.session, seqs, identify_as, attrs, markups, auto_destroy, TypeError: __init__() got an unexpected keyword argument 'seq_viewer' TypeError: __init__() got an unexpected keyword argument 'seq_viewer' File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\seqalign\manager.py"", line 242, in new_alignment alignment = Alignment(self.session, seqs, identify_as, attrs, markups, auto_destroy, See log for complete Python traceback. > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Alignment identifier is 1/A Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\show_sequences\tool.py"", line 64, in show_seqs run(self.session, ""seq chain %s"" % "" "".join([chain.atomspec for chain in chains])) File ""C:\Program Files\ChimeraX\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\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\seqalign\cmd.py"", line 212, in seqalign_chain alignment = session.alignments.new_alignment([chain], ident, seq_viewer=""sv"", File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\seqalign\manager.py"", line 242, in new_alignment alignment = Alignment(self.session, seqs, identify_as, attrs, markups, auto_destroy, TypeError: __init__() got an unexpected keyword argument 'seq_viewer' TypeError: __init__() got an unexpected keyword argument 'seq_viewer' File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\seqalign\manager.py"", line 242, in new_alignment alignment = Alignment(self.session, seqs, identify_as, attrs, markups, auto_destroy, See log for complete Python traceback. OpenGL version: 3.3.14831 Core Profile Forward-Compatible Context 21.5.2 27.20.20903.8001 OpenGL renderer: AMD Radeon R9 200 Series OpenGL vendor: ATI Technologies Inc. Python: 3.9.11 Locale: de_DE.cp1252 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.2 Qt platform: windows Manufacturer: Gigabyte Technology Co., Ltd. Model: H67MA-UD2H OS: Microsoft Windows 10 Pro (Build 19044) Memory: 17,162,481,664 MaxProcessMemory: 137,438,953,344 CPU: 4 Intel(R) Core(TM) i5-2500K CPU @ 3.30GHz OSLanguage: de-DE Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 asttokens: 2.2.1 Babel: 2.11.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.2 charset-normalizer: 3.0.1 ChimeraX-AddCharge: 1.5.8 ChimeraX-AddH: 2.2.3 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.7 ChimeraX-AtomicLibrary: 10.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.1 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.dev202302100235 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3.3 ChimeraX-DockPrep: 1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.11 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.11 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.8 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.6.13 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.0 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.1 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.27 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.2 comtypes: 1.1.14 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.6 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.38.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.9.26 imagesize: 1.4.1 importlib-metadata: 6.0.0 ipykernel: 6.21.1 ipython: 8.9.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.4 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.2.0 jupyterlab-widgets: 3.0.5 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 23.0 pandas: 1.5.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.0.0 prompt-toolkit: 3.0.36 psutil: 5.9.4 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.2 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.2 python-dateutil: 2.8.2 pytz: 2022.7.1 pywin32: 305 pyzmq: 25.0.0 qtconsole: 5.4.0 QtPy: 2.3.0 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 65.1.1 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.3.2.post1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.0.2 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.9.0 urllib3: 1.26.14 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.5 WMI: 1.5.1 zipp: 3.13.0 }}} " defect closed major 1.6 Sequence fixed all ChimeraX