id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9153 PyQt no longer accepting previously acceptable arguments chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.22621 ChimeraX Version: 1.7.dev202306080039 (2023-06-08 00:39:06 UTC) Description just open a molecule and try to make sequence display Log: UCSF ChimeraX version: 1.7.dev202306080039 (2023-06-08) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open C:/Users/sblat/Downloads/structures_2023-6-9-12-28-43/.cif 'C:/Users/sblat/Downloads/structures_2023-6-9-12-28-43/.cif' has no suffix > open ""C:/1_LAVORO/PROGETTI_TS_EUROSPITAL/ELASTASE/modelli > 3D/CELA3B_model_AF-P08861-F1-model_v4.pdb"" CELA3B_model_AF-P08861-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for chymotrypsin-like elastase family member 3B (P08861) [more info...] Chain information for CELA3B_model_AF-P08861-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | chymotrypsin-like elastase family member 3B | CEL3B_HUMAN 1-270 > open ""C:/1_LAVORO/PROGETTI_TS_EUROSPITAL/ELASTASE/modelli > 3D/CELA3A_modell_AF-P09093-F1-model_v4.pdb"" CELA3A_modell_AF-P09093-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for chymotrypsin-like elastase family member 3A (P09093) [more info...] Chain information for CELA3A_modell_AF-P09093-F1-model_v4.pdb #2 --- Chain | Description | UniProt A | chymotrypsin-like elastase family member 3A | CEL3A_HUMAN 1-270 > ui tool show Matchmaker > 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 CELA3B_model_AF-P08861-F1-model_v4.pdb, chain A (#1) with CELA3A_modell_AF-P09093-F1-model_v4.pdb, chain A (#2), sequence alignment score = 1331.1 RMSD between 243 pruned atom pairs is 0.290 angstroms; (across all 270 pairs: 4.246) > ui windowfill toggle [Repeated 1 time(s)] > open C:/Users/sblat/Downloads/5ire.cif Summary of feedback from opening C:/Users/sblat/Downloads/5ire.cif --- note | Fetching CCD NAG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NAG/NAG.cif 5ire.cif title: The cryo-EM structure of Zika Virus [more info...] Chain information for 5ire.cif #3 --- Chain | Description | UniProt A C E | E protein | A0A060H177_9FLAV 1-504 B D F | M protein | A0A096XFQ2_9FLAV 1-75 Non-standard residues in 5ire.cif #3 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose 5ire.cif mmCIF Assemblies --- 1| complete icosahedral assembly 2| icosahedral asymmetric unit 3| icosahedral pentamer 4| icosahedral 23 hexamer 5| icosahedral asymmetric unit, std point frame > hide #1 models > hide #2 models > show #!3 cartoons > style #!3 sphere Changed 11024 atom styles > style #!3 sphere Changed 11024 atom styles > style #!3 ball Changed 11024 atom styles > toolshed show > close #3 > show #1 models > show #2 models > close #2 > close > open C:\Users\sblat\Downloads\5ire.cif format mmcif 5ire.cif title: The cryo-EM structure of Zika Virus [more info...] Chain information for 5ire.cif #1 --- Chain | Description | UniProt A C E | E protein | A0A060H177_9FLAV 1-504 B D F | M protein | A0A096XFQ2_9FLAV 1-75 Non-standard residues in 5ire.cif #1 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose 5ire.cif mmCIF Assemblies --- 1| complete icosahedral assembly 2| icosahedral asymmetric unit 3| icosahedral pentamer 4| icosahedral 23 hexamer 5| icosahedral asymmetric unit, std point frame > close > open ""C:\1_LAVORO\PROGETTI_TS_EUROSPITAL\ELASTASE\modelli > 3D\CELA3A_modell_AF-P09093-F1-model_v4.pdb"" format pdb CELA3A_modell_AF-P09093-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for chymotrypsin-like elastase family member 3A (P09093) [more info...] Chain information for CELA3A_modell_AF-P09093-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | chymotrypsin-like elastase family member 3A | CEL3A_HUMAN 1-270 > open ""C:\1_LAVORO\PROGETTI_TS_EUROSPITAL\ELASTASE\modelli > 3D\CELA3B_model_AF-P08861-F1-model_v4.pdb"" format pdb CELA3B_model_AF-P08861-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for chymotrypsin-like elastase family member 3B (P08861) [more info...] Chain information for CELA3B_model_AF-P08861-F1-model_v4.pdb #2 --- Chain | Description | UniProt A | chymotrypsin-like elastase family member 3B | CEL3B_HUMAN 1-270 > matchmaker #1 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 CELA3B_model_AF-P08861-F1-model_v4.pdb, chain A (#2) with CELA3A_modell_AF-P09093-F1-model_v4.pdb, chain A (#1), sequence alignment score = 1331.1 RMSD between 243 pruned atom pairs is 0.290 angstroms; (across all 270 pairs: 4.246) Alignment identifier is 1/A Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\toolbar\tool.py"", line 205, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 386, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1291, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\\__init__.py"", line 52, in run_provider shortcuts.run_provider(session, name) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 1335, in run_provider keyboard_shortcuts(session).try_shortcut(name) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 390, in try_shortcut self.run_shortcut(keys) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 408, in run_shortcut sc.run(self.session, status = self._enabled) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 310, in run f(shortcut_atoms(s)) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 1047, in show_sequence run(session, 'sequence chain %s' % seq_chain_spec, log = False) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 513, in run run_command(session, command, **kw) 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, auto_associate=None, intrinsic=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seqalign\manager.py"", line 247, in new_alignment self._viewers[viewer_name].run_provider(self.session, viewer_name, self, alignment=alignment) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 386, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1291, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seq_view\\__init__.py"", line 37, in run_provider return _start_seq_viewer(session, ""Sequence Viewer"", alignment) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seq_view\tool.py"", line 858, in _start_seq_viewer return SequenceViewer(session, tool_name, alignment) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seq_view\tool.py"", line 55, in __init__ self._finalize_init(alignment, from_session=False) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seq_view\tool.py"", line 168, in _finalize_init self.seq_canvas = SeqCanvas(parent, self, self.alignment) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py"", line 194, in __init__ self.layout_alignment() File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py"", line 772, in layout_alignment self.lead_block = SeqBlock(label_scene, self.main_scene, None, self.font, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py"", line 1627, in __init__ self.layout_lines(alignment.seqs, self.normal_label_color) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py"", line 2323, in layout_lines self._layout_line(line, label_color, bli, end) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py"", line 2283, in _layout_line self._colorize_label(line) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py"", line 1935, in _colorize_label brush = QBrush(QColor(*color), Qt.SolidPattern) ^^^^^^^^^^^^^^ TypeError: arguments did not match any overloaded call: QColor(color: Qt.GlobalColor): argument 1 has unexpected type 'numpy.float64' QColor(rgb: int): argument 1 has unexpected type 'numpy.float64' QColor(rgba64: QRgba64): argument 1 has unexpected type 'numpy.float64' QColor(variant: Any): too many arguments QColor(): too many arguments QColor(r: int, g: int, b: int, alpha: int = 255): argument 1 has unexpected type 'numpy.float64' QColor(name: str): argument 1 has unexpected type 'numpy.float64' QColor(a0: QColor): argument 1 has unexpected type 'numpy.float64' TypeError: arguments did not match any overloaded call: QColor(color: Qt.GlobalColor): argument 1 has unexpected type 'numpy.float64' QColor(rgb: int): argument 1 has unexpected type 'numpy.float64' QColor(rgba64: QRgba64): argument 1 has unexpected type 'numpy.float64' QColor(variant: Any): too many arguments QColor(): too many arguments QColor(r: int, g: int, b: int, alpha: int = 255): argument 1 has unexpected type 'numpy.float64' QColor(name: str): argument 1 has unexpected type 'numpy.float64' QColor(a0: QColor): argument 1 has unexpected type 'numpy.float64' File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py"", line 1935, in _colorize_label brush = QBrush(QColor(*color), Qt.SolidPattern) ^^^^^^^^^^^^^^ See log for complete Python traceback. Destroying pre-existing alignment with identifier 1/A Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\toolbar\tool.py"", line 205, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 386, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1291, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\\__init__.py"", line 52, in run_provider shortcuts.run_provider(session, name) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 1335, in run_provider keyboard_shortcuts(session).try_shortcut(name) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 390, in try_shortcut self.run_shortcut(keys) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 408, in run_shortcut sc.run(self.session, status = self._enabled) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 310, in run f(shortcut_atoms(s)) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 1047, in show_sequence run(session, 'sequence chain %s' % seq_chain_spec, log = False) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 513, in run run_command(session, command, **kw) 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, auto_associate=None, intrinsic=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seqalign\manager.py"", line 224, in new_alignment self.destroy_alignment(self._alignments[identify_as]) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seqalign\manager.py"", line 119, in destroy_alignment alignment._destroy() File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seqalign\alignment.py"", line 659, in _destroy self._notify_observers(self.NOTE_DESTROYED, None) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seqalign\alignment.py"", line 711, in _notify_observers recipient.alignment_notification(note_name, note_data) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seq_view\tool.py"", line 472, in alignment_notification self.delete() File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seq_view\tool.py"", line 504, in delete self.region_browser.destroy() ^^^^^^^^^^^^^^^^^^^ AttributeError: 'SequenceViewer' object has no attribute 'region_browser' AttributeError: 'SequenceViewer' object has no attribute 'region_browser' File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seq_view\tool.py"", line 504, in delete self.region_browser.destroy() ^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. > close > open ""C:\1_LAVORO\PROGETTI_TS_EUROSPITAL\ELASTASE\modelli > 3D\CELA3A_modell_AF-P09093-F1-model_v4.pdb"" format pdb CELA3A_modell_AF-P09093-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for chymotrypsin-like elastase family member 3A (P09093) [more info...] Chain information for CELA3A_modell_AF-P09093-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | chymotrypsin-like elastase family member 3A | CEL3A_HUMAN 1-270 Alignment identifier is 1/A Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\toolbar\tool.py"", line 205, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 386, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1291, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\\__init__.py"", line 52, in run_provider shortcuts.run_provider(session, name) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 1335, in run_provider keyboard_shortcuts(session).try_shortcut(name) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 390, in try_shortcut self.run_shortcut(keys) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 408, in run_shortcut sc.run(self.session, status = self._enabled) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 310, in run f(shortcut_atoms(s)) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 1047, in show_sequence run(session, 'sequence chain %s' % seq_chain_spec, log = False) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 513, in run run_command(session, command, **kw) 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, auto_associate=None, intrinsic=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seqalign\manager.py"", line 247, in new_alignment self._viewers[viewer_name].run_provider(self.session, viewer_name, self, alignment=alignment) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 386, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1291, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seq_view\\__init__.py"", line 37, in run_provider return _start_seq_viewer(session, ""Sequence Viewer"", alignment) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seq_view\tool.py"", line 858, in _start_seq_viewer return SequenceViewer(session, tool_name, alignment) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seq_view\tool.py"", line 55, in __init__ self._finalize_init(alignment, from_session=False) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seq_view\tool.py"", line 168, in _finalize_init self.seq_canvas = SeqCanvas(parent, self, self.alignment) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py"", line 194, in __init__ self.layout_alignment() File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py"", line 772, in layout_alignment self.lead_block = SeqBlock(label_scene, self.main_scene, None, self.font, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py"", line 1627, in __init__ self.layout_lines(alignment.seqs, self.normal_label_color) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py"", line 2323, in layout_lines self._layout_line(line, label_color, bli, end) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py"", line 2283, in _layout_line self._colorize_label(line) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py"", line 1935, in _colorize_label brush = QBrush(QColor(*color), Qt.SolidPattern) ^^^^^^^^^^^^^^ TypeError: arguments did not match any overloaded call: QColor(color: Qt.GlobalColor): argument 1 has unexpected type 'numpy.float64' QColor(rgb: int): argument 1 has unexpected type 'numpy.float64' QColor(rgba64: QRgba64): argument 1 has unexpected type 'numpy.float64' QColor(variant: Any): too many arguments QColor(): too many arguments QColor(r: int, g: int, b: int, alpha: int = 255): argument 1 has unexpected type 'numpy.float64' QColor(name: str): argument 1 has unexpected type 'numpy.float64' QColor(a0: QColor): argument 1 has unexpected type 'numpy.float64' TypeError: arguments did not match any overloaded call: QColor(color: Qt.GlobalColor): argument 1 has unexpected type 'numpy.float64' QColor(rgb: int): argument 1 has unexpected type 'numpy.float64' QColor(rgba64: QRgba64): argument 1 has unexpected type 'numpy.float64' QColor(variant: Any): too many arguments QColor(): too many arguments QColor(r: int, g: int, b: int, alpha: int = 255): argument 1 has unexpected type 'numpy.float64' QColor(name: str): argument 1 has unexpected type 'numpy.float64' QColor(a0: QColor): argument 1 has unexpected type 'numpy.float64' File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py"", line 1935, in _colorize_label brush = QBrush(QColor(*color), Qt.SolidPattern) ^^^^^^^^^^^^^^ See log for complete Python traceback. Destroying pre-existing alignment with identifier 1/A Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\toolbar\tool.py"", line 205, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 386, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1291, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\\__init__.py"", line 52, in run_provider shortcuts.run_provider(session, name) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 1335, in run_provider keyboard_shortcuts(session).try_shortcut(name) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 390, in try_shortcut self.run_shortcut(keys) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 408, in run_shortcut sc.run(self.session, status = self._enabled) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 310, in run f(shortcut_atoms(s)) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 1047, in show_sequence run(session, 'sequence chain %s' % seq_chain_spec, log = False) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 513, in run run_command(session, command, **kw) 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, auto_associate=None, intrinsic=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seqalign\manager.py"", line 224, in new_alignment self.destroy_alignment(self._alignments[identify_as]) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seqalign\manager.py"", line 119, in destroy_alignment alignment._destroy() File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seqalign\alignment.py"", line 659, in _destroy self._notify_observers(self.NOTE_DESTROYED, None) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seqalign\alignment.py"", line 711, in _notify_observers recipient.alignment_notification(note_name, note_data) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seq_view\tool.py"", line 472, in alignment_notification self.delete() File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seq_view\tool.py"", line 504, in delete self.region_browser.destroy() ^^^^^^^^^^^^^^^^^^^ AttributeError: 'SequenceViewer' object has no attribute 'region_browser' AttributeError: 'SequenceViewer' object has no attribute 'region_browser' File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\seq_view\tool.py"", line 504, in delete self.region_browser.destroy() ^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 528.66 OpenGL renderer: NVIDIA GeForce MX150/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.2 Locale: it_IT.cp1252 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: windows Manufacturer: ASUSTeK COMPUTER INC. Model: UX430UNR OS: Microsoft Windows 11 Home (Build 22621) Memory: 17,033,650,176 MaxProcessMemory: 137,438,953,344 CPU: 8 Intel(R) Core(TM) i7-8550U CPU @ 1.80GHz OSLanguage: it-IT Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2023.5.7 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.11 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.45.7 ChimeraX-AtomicLibrary: 10.0.7 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: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.3 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 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: 1.7.dev202306080039 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: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.2 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 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: 1.2 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: 2.1 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 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-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.2 ChimeraX-PDB: 2.7.2 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: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 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: 2.8.3 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: 1.12 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 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: 1.2.2 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.6 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2.1 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: 0.1.3 comtypes: 1.1.14 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.4 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2023.3.16 imagesize: 1.4.1 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 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 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 23.1 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: 3.5.1 prompt-toolkit: 3.0.38 psutil: 5.9.4 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.6 PyOpenGL-accelerate: 3.1.6 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pywin32: 305 pyzmq: 25.1.0 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.9.3 setuptools: 67.4.0 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 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: 3.8.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.2 traitlets: 5.9.0 typing-extensions: 4.6.3 tzdata: 2023.3 urllib3: 2.0.3 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 WMI: 1.5.1 }}} " defect closed normal Window Toolkit fixed chimerax-programmers all ChimeraX