id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1094 traceback closing all models aftering coloring by ESP Elaine Meng Tom Goddard "version UCSF ChimeraX version: 0.7 (2018-04-21) I tried subsets of the commands but it seems like coloring by ESP first is required to give the error. I will attach the phi file. open 3eeb del /a open /Users/meng/Desktop/stash/3eebB.phi surf color electrostatic #1 map #2 palette redblue range -10,10 close Traceback (most recent call last): File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/cmd_line/tool.py"", line 205, in execute cmd.run(cmd_text) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/cli.py"", line 2622, in run result = ci.function(session, **kw_args) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/open.py"", line 42, in open from_database=from_database, ignore_cache=ignore_cache, **kw)) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/open.py"", line 112, in open models = handle_unknown_kw(session.models.open, paths, format=format, name=name, **kw) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/open.py"", line 63, in handle_unknown_kw return f(*args, **kw) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/models.py"", line 464, in open session, filenames, format=format, name=name, **kw) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/io.py"", line 444, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/io.py"", line 402, in open_data models, status = open_func(*args, **kw) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/scripting.py"", line 115, in open_command_script run(session, text) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/cli.py"", line 2622, in run result = ci.function(session, **kw_args) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/close.py"", line 32, in close m.close(cmodels) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/models.py"", line 439, in close m.delete() File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/models.py"", line 69, in delete Drawing.delete(self) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/graphics/drawing.py"", line 1025, in delete self._delete_geometry() File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/graphics/drawing.py"", line 1034, in _delete_geometry self.vertices = None File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/graphics/drawing.py"", line 212, in __setattr__ super(Drawing, self).__setattr__(key, value) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/graphics/drawing.py"", line 185, in _set_vertices self.auto_recolor_vertices() File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/scolor.py"", line 223, in arv = lambda self=self: self.set_vertex_colors(report_stats = False) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/scolor.py"", line 292, in set_vertex_colors s.vertex_colors = self.vertex_colors(report_stats) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/scolor.py"", line 264, in vertex_colors values, outside = self.volume_values() File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/scolor.py"", line 313, in volume_values tf = self.volume.scene_position.inverse() * s.scene_position File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/graphics/drawing.py"", line 418, in _get_scene_position return product([d.position for d in self.drawing_lineage]) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/graphics/drawing.py"", line 418, in return product([d.position for d in self.drawing_lineage]) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/graphics/drawing.py"", line 403, in get_position return self._positions[0] TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/graphics/drawing.py"", line 403, in get_position return self._positions[0] See log for complete Python traceback. If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and describe what you were doing and include a copy of the contents of the log. Don't include any data you wish to remain private since a publicly viewable bug report will be created." defect closed major Graphics fixed all ChimeraX