id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1395 Sequence session-restore failure: get_class() missing 1 required positional argument: 'logger' pascal.albanese@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.17134 ChimeraX Version: 0.8 (2018-10-20) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.8 (2018-10-20) How to cite UCSF ChimeraX open D:/UTRECHT_MS/Xlink_results/TL183/Docking.cxs open D:/UTRECHT_MS/Xlink_results/TL183/Docking.cxs Summary of feedback from opening D:/UTRECHT_MS/Xlink_results/TL183/Docking.cxs --- error | Unable to restore session, resetting. Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 590, in restore obj = sm.restore_snapshot(self, data) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq- view\tool.py"", line 574, in restore_snapshot inst.seq_canvas.restore_state(session, data['seq canvas']) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq- view\seq_canvas.py"", line 1085, in restore_state header_class = bundle.get_class(class_name) TypeError: get_class() missing 1 required positional argument: 'logger' Traceback (most recent call last):   File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py"", line 542, in _qt_safe     run(session, ""open "" \+ quote_if_necessary(paths[0]))   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 31, in run     results = command.run(text, log=log)   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2563, in run     result = ci.function(session, **kw_args)   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py"", line 41, in open     from_database=from_database, ignore_cache=ignore_cache, **kw))   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py"", line 110, in open     models = handle_unknown_kw(session.models.open, paths, format=format, name=name, **kw)   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py"", line 62, in handle_unknown_kw     return f(*args, **kw)   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py"", line 577, in open     session, filenames, format=format, name=name, **kw)   File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py"", line 444, in open_multiple_data     models, status = open_data(session, fspec, format=format, name=name, **kw)   File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py"", line 404, in open_data     models, status = open_func(*args, **kw)   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 815, in open     session.restore(stream, path=path, resize_window=resize_window)   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 596, in restore     self.reset()   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 410, in reset     sm.reset_state(container, self)   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\molobject.py"", line 576, in reset_state     for pbg in list(self.group_map.values()):   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 39, in __getattr__     return look_in_class._attr_registration.get_attr(attr_name)   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 64, in get_attr     raise AttributeError(""Execution of '%s' object's '%s' property raised AttributeError"" % (self.class_.__name__, attr_name)) from None AttributeError: Execution of 'PseudobondManager' object's 'group_map' property raised AttributeError AttributeError: Execution of 'PseudobondManager' object's 'group_map' property raised AttributeError File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 64, in get_attr raise AttributeError(""Execution of '%s' object's '%s' property raised AttributeError"" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. Traceback (most recent call last):   File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq- view\seq_canvas.py"", line 229, in _actually_resize     self._reformat()   File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq- view\seq_canvas.py"", line 995, in _reformat     self.label_width, self.font_pixels, self.numbering_widths, self.letter_gaps())   File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq- view\seq_canvas.py"", line 1566, 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 2208, 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 2158, in _layout_line     font=self._label_font(line))   File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq- view\seq_canvas.py"", line 2098, in _label_font     if self.has_associated_structures(line):   File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq- view\seq_canvas.py"", line 2036, in has_associated_structures     and [chain for chain in line.match_maps.keys() if not chain.structure.deleted]:   File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq- view\seq_canvas.py"", line 2036, in     and [chain for chain in line.match_maps.keys() if not chain.structure.deleted]:   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 39, in __getattr__     return look_in_class._attr_registration.get_attr(attr_name)   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 66, in get_attr     raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None AttributeError: 'Sequence' object has no attribute 'structure' AttributeError: 'Sequence' object has no attribute 'structure' File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 66, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. open D:\UTRECHT_MS\Xlink_results\TL183\Docking.cxs format session open D:\UTRECHT_MS\Xlink_results\TL183\Docking.cxs format session Summary of feedback from opening D:\UTRECHT_MS\Xlink_results\TL183\Docking.cxs --- error | Unable to restore session, resetting. Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 562, in restore self.reset() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 410, in reset sm.reset_state(container, self) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\molobject.py"", line 576, in reset_state for pbg in list(self.group_map.values()): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 39, in __getattr__ return look_in_class._attr_registration.get_attr(attr_name) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 64, in get_attr raise AttributeError(""Execution of '%s' object's '%s' property raised AttributeError"" % (self.class_.__name__, attr_name)) from None AttributeError: Execution of 'PseudobondManager' object's 'group_map' property raised AttributeError Traceback (most recent call last):   File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py"", line 529, in customEvent     func(*args, **kw)   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\ui\widgets\htmlview.py"", line 278, in defer     cxcmd(session, topic)   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\ui\widgets\htmlview.py"", line 374, in cxcmd     run(session, cmd)   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 31, in run     results = command.run(text, log=log)   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2563, in run     result = ci.function(session, **kw_args)   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py"", line 41, in open     from_database=from_database, ignore_cache=ignore_cache, **kw))   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py"", line 110, in open     models = handle_unknown_kw(session.models.open, paths, format=format, name=name, **kw)   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py"", line 62, in handle_unknown_kw     return f(*args, **kw)   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py"", line 577, in open     session, filenames, format=format, name=name, **kw)   File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py"", line 444, in open_multiple_data     models, status = open_data(session, fspec, format=format, name=name, **kw)   File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py"", line 404, in open_data     models, status = open_func(*args, **kw)   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 815, in open     session.restore(stream, path=path, resize_window=resize_window)   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 596, in restore     self.reset()   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 410, in reset     sm.reset_state(container, self)   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\molobject.py"", line 576, in reset_state     for pbg in list(self.group_map.values()):   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 39, in __getattr__     return look_in_class._attr_registration.get_attr(attr_name)   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 64, in get_attr     raise AttributeError(""Execution of '%s' object's '%s' property raised AttributeError"" % (self.class_.__name__, attr_name)) from None AttributeError: Execution of 'PseudobondManager' object's 'group_map' property raised AttributeError AttributeError: Execution of 'PseudobondManager' object's 'group_map' property raised AttributeError File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\attr_registration.py"", line 64, in get_attr raise AttributeError(""Execution of '%s' object's '%s' property raised AttributeError"" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 388.75 OpenGL renderer: GeForce 940M/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Sequence fixed all ChimeraX