id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1500 Errorpalooza chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.17134 ChimeraX Version: 0.8 (2018-11-26) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.8 (2018-11-26) How to cite UCSF ChimeraX > open C:\Users\Jacobson Lab\Desktop\Aligned\aligned_right.pyc File not found: C:\Users\Jacobson File not found: C:\Users\Jacobson > open ""C:/Users/Jacobson Lab/Desktop/Aligned/aligned_right.pyc"" Traceback (most recent call last): File ""C:\Program Files\ChimeraX-Nov-27-2018\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-Nov-27-2018\bin\lib\site- packages\chimerax\core\commands\run.py"", line 31, in run results = command.run(text, log=log) File ""C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2581, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX-Nov-27-2018\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-Nov-27-2018\bin\lib\site- packages\chimerax\core\commands\open.py"", line 117, in open models = handle_unknown_kw(session.models.open, paths, format=format, name=name, **kw) File ""C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site- packages\chimerax\core\commands\open.py"", line 62, in handle_unknown_kw return f(*args, **kw) File ""C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site- packages\chimerax\core\models.py"", line 586, in open session, filenames, format=format, name=name, **kw) File ""C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site- packages\chimerax\core\io.py"", line 461, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File ""C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site- packages\chimerax\core\io.py"", line 414, in open_data models, status = open_func(*args, **kw) File ""C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site- packages\chimerax\core\scripting.py"", line 57, in open_python_script code = compile(data, file_name, 'exec') ValueError: source code string cannot contain null bytes ValueError: source code string cannot contain null bytes File ""C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site- packages\chimerax\core\scripting.py"", line 57, in open_python_script code = compile(data, file_name, 'exec') See log for complete Python traceback. > open ""C:\Users\Jacobson Lab\Desktop\Aligned\MRP4_MRP1bound.pdb"" MRP4_MRP1bound.pdb title: SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more info...] Chain information for MRP4_MRP1bound.pdb #1 --- Chain | Description A | No description available Opened cryosparc_P5_J61__localfilter_052918titanbestreconstruction.mrc, grid size 150,150,150, pixel 1.63, shown at level 0.68, step 1, values float32 cryosparc_P5_J61__localfilter_052918titanbestreconstruction.mrc title: Cryo-em structure of bovine multidrug resistance protein 1 (MRP1) [more info...] cryosparc_P5_J61__localfilter_052918titanbestreconstruction.mrc title: Cryo-em structure of bovine multidrug resistance protein 1 (MRP1) bound to leukotriene C4 [more info...] cryosparc_P5_J61__localfilter_052918titanbestreconstruction.mrc title: SWISS-MODEL SERVER (https://swissmodel.expasy.org) MRP4-MRP1apo [more info...] Traceback (most recent call last): File ""C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site- packages\chimerax\atomic\molarray.py"", line 111, in __init__ pointers = numpy.array([i._c_pointer.value for i in items], cptr) File ""C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site- packages\chimerax\atomic\molarray.py"", line 111, in pointers = numpy.array([i._c_pointer.value for i in items], cptr) AttributeError: 'Volume' object has no attribute '_c_pointer' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site- packages\chimerax\ui\gui.py"", line 546, in _qt_safe session.models.open(paths) File ""C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site- packages\chimerax\core\models.py"", line 596, in open self.add_group(models, name=name) File ""C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site- packages\chimerax\core\models.py"", line 526, in add_group self.add([parent]) File ""C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site- packages\chimerax\core\models.py"", line 456, in add m.added_to_session(session) File ""C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site- packages\chimerax\atomic\structure.py"", line 2111, in added_to_session self._report_ensemble_chain_descriptions(session, sibs) File ""C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site- packages\chimerax\atomic\structure.py"", line 2343, in _report_ensemble_chain_descriptions structs = AtomicStructures(ensemble) File ""C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site- packages\chimerax\atomic\molarray.py"", line 393, in __init__ Collection.__init__(self, mol_pointers, AtomicStructure, AtomicStructures) File ""C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site- packages\chimerax\atomic\molarray.py"", line 116, in __init__ raise ValueError('Collection items of unrecognized type ""%s""' % t) ValueError: Collection items of unrecognized type """" ValueError: Collection items of unrecognized type """" File ""C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site- packages\chimerax\atomic\molarray.py"", line 116, in __init__ raise ValueError('Collection items of unrecognized type ""%s""' % t) See log for complete Python traceback. > open ""C:/Users/Jacobson Lab/Desktop/Aligned/5uja_bound.pdb"" 5uja_bound.pdb title: Cryo-em structure of bovine multidrug resistance protein 1 (MRP1) bound to leukotriene C4 [more info...] Chain information for 5uja_bound.pdb #3 --- Chain | Description A | bovine multidrug resistance protein 1 (MRP1),multidrug resistance- associated protein 1 > hide #!3 models > show #!2 models > hide #!2 models > hide #!1 models > show #!3 models > show #!1 models > hide #!1 models > show #!1 models > show #!2 models > open ""C:/Users/Jacobson Lab/Desktop/Aligned/MRP4_MRP1apo.pdb"" MRP4_MRP1apo.pdb title: SWISS-MODEL SERVER (https://swissmodel.expasy.org) MRP4-MRP1apo [more info...] Chain information for MRP4_MRP1apo.pdb #4 --- Chain | Description A | No description available > hide #!1 models Traceback (most recent call last): File ""C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site- packages\chimerax\map\volume_viewer.py"", line 1859, in sm.addAction(style, lambda s=style: self.representation_changed_cb(s)) File ""C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site- packages\chimerax\map\volume_viewer.py"", line 2363, in representation_changed_cb self.set_map_style(v, style) File ""C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site- packages\chimerax\map\volume_viewer.py"", line 2377, in set_map_style if style != 'box' and v.showing_box_faces(): AttributeError: 'NoneType' object has no attribute 'showing_box_faces' AttributeError: 'NoneType' object has no attribute 'showing_box_faces' File ""C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site- packages\chimerax\map\volume_viewer.py"", line 2377, in set_map_style if style != 'box' and v.showing_box_faces(): See log for complete Python traceback. Missing or invalid ""percent"" argument: Expected a number > transparency 70 > transparency 50 Expected an atoms specifier or a keyword Expected a keyword > transparency 30 > close > open ""C:/Users/Jacobson Lab/Desktop/Aligned/cryosparc_P5_J61__localfilter_052918titanbestreconstruction.mrc"" Opened cryosparc_P5_J61__localfilter_052918titanbestreconstruction.mrc, grid size 150,150,150, pixel 1.63, shown at level 0.68, step 1, values float32 5uj9_apo.pdb title: Cryo-em structure of bovine multidrug resistance protein 1 (MRP1) [more info...] Chain information for 5uj9_apo.pdb #2.1 --- Chain | Description A | bovine multidrug resistance protein 1 (MRP1),multidrug resistance- associated protein 1 5uja_bound.pdb title: Cryo-em structure of bovine multidrug resistance protein 1 (MRP1) bound to leukotriene C4 [more info...] Chain information for 5uja_bound.pdb #2.2 --- Chain | Description A | bovine multidrug resistance protein 1 (MRP1),multidrug resistance- associated protein 1 MRP4_MRP1apo.pdb title: SWISS-MODEL SERVER (https://swissmodel.expasy.org) MRP4-MRP1apo [more info...] Chain information for MRP4_MRP1apo.pdb #2.3 --- Chain | Description A | No description available MRP4_MRP1bound.pdb title: SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more info...] Chain information for MRP4_MRP1bound.pdb #2.4 --- Chain | Description A | No description available > color selAtoms byhetero > vr on started SteamVR rendering > vr off > vr on started SteamVR rendering > transparency #1 50 > show ligand :<10 > hide HC > select ligand 43 atoms, 42 bonds, 1 model selected > style selAtoms sphere Changed 43 atom styles > style selAtoms ball Changed 43 atom styles > hide #!2.1 models > show #!2.1 models > hide #!2.1 models > show #!2.1 models > hide #!2.1 models > show #!2.1 models > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > hide #!2.3 models > show #!2.3 models > hide #!2.3 models > show #!2.3 models > show #!2.3 models > hide #!2.4 models > show #!2.4 models > show ligand :<5 > hide #!2.3 models > hide #!2.1 models > show ligand :<10 > hide HC > meeting start Meeting at vive or 169.230.21.39 port 52194 Connection accepted from 169.230.21.70 port 54662 > vr on > show #!2.3 models > hide #!2.3 models > show #!2.1 models > show #!2.3 models > hide #!2.3 models > show #!2.3 models > hide #!2.3 models > hide #!2.3 models > show #!2.3 models > hide #!2.3 models > show #!2.3 models > color selAtoms byhetero > color selAtoms byhetero Traceback (most recent call last): File ""C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site- packages\chimerax\core\triggerset.py"", line 126, in invoke return self._func(self._name, data) File ""C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site- packages\chimerax\vive\vr.py"", line 447, in next_frame self.process_controller_events() File ""C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site- packages\chimerax\vive\vr.py"", line 476, in process_controller_events self.process_controller_motion() File ""C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site- packages\chimerax\vive\vr.py"", line 497, in process_controller_motion hc.process_motion(self) File ""C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site- packages\chimerax\vive\vr.py"", line 1126, in process_motion ui.drag(window_xy) File ""C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site- packages\chimerax\vive\vr.py"", line 763, in drag return self._click('move', window_xy) File ""C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site- packages\chimerax\vive\vr.py"", line 770, in _click if self._post_mouse_event(type, window_xy) and type != 'move': File ""C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site- packages\chimerax\vive\vr.py"", line 809, in _post_mouse_event w, pos = self._clicked_widget(window_xy) File ""C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site- packages\chimerax\vive\vr.py"", line 833, in _clicked_widget x,y = window_xy TypeError: 'NoneType' object is not iterable Error processing trigger ""new frame"": 'NoneType' object is not iterable: TypeError: 'NoneType' object is not iterable File ""C:\Program Files\ChimeraX-Nov-27-2018\bin\lib\site- packages\chimerax\vive\vr.py"", line 833, in _clicked_widget x,y = window_xy See log for complete Python traceback. > vr off > vr on started SteamVR rendering > hide #!2.2 models > hide #!2.4 models > hide #!2.1 models > show #!2.2 models > hide #!2.3 models > show #!2.4 models > transparency 50 > transparency 0 OpenGL version: 3.3.0 NVIDIA 391.58 OpenGL renderer: Quadro P6000/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal VR fixed all ChimeraX