traceback closing all models aftering coloring by ESP

[Elaine Meng]

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 <lambda>

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 <listcomp>

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@… 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.

[Tom Goddard]

Fixed.

Code to delete drawings forgot to delete auto recoloring method which then tried to recolor surface after it was partially deleted.