id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
763	undisplayed labels make everything really slow (and closing gives traceback?)	Elaine Meng	Tom Goddard	"I don't know if the traceback is from the undisplayed labels, but I'm reporting both in this ticket since they occur with the same simple test case:

open 2gbp
hide
~cartoon
show ligand
la #1

... response time becomes very very slow. Maybe only the labels for the displayed subset of #1 should be created instead of all atoms of #1?  Closing #1 at this point gives the traceback:


close
Traceback (most recent call last):
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/cmd_line/tool.py"", line 178, in execute
cmd.run(cmd_text)
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/cli.py"", line 2395, in run
result = ci.function(session, **kw_args)
File ""/Users/chimera/Applications/ChimeraX_Daily.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/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/models.py"", line 403, in close
m.delete()
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/pbgroup.py"", line 39, in delete
self.session.models.remove([self])
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/models.py"", line 379, in remove
mlist.sort(key=lambda m: len(m.id), reverse=True)
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/models.py"", line 379, in <lambda>
mlist.sort(key=lambda m: len(m.id), reverse=True)
TypeError: object of type 'NoneType' has no len()

TypeError: object of type 'NoneType' has no len()

File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/models.py"", line 379, in 
mlist.sort(key=lambda m: len(m.id), reverse=True)

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.

Error processing trigger ""graphics update""
Traceback (most recent call last):
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/triggerset.py"", line 126, in invoke
return self._func(self._name, data)
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/label/label3d.py"", line 231, in _update_graphics_if_needed
ld._update_graphics()
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/label/label3d.py"", line 357, in _update_graphics
self._position_label()
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/label/label3d.py"", line 387, in _position_label
xyz = self.location()
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/label/label3d.py"", line 416, in location
return self.atom.coord
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/molc.py"", line 67, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
AttributeError: 'Atom' object has no attribute '_c_pointer_ref'"	defect	closed	major		Graphics		fixed						all	ChimeraX