id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
388	surface doesn't notice when some of its atoms are deleted	Elaine Meng	Tom Goddard	"for example

open 2gbp
surf
color :lys yellow targ as
delete :lys

... yellow stuff still shown.  Actually I wasn't sure if the surface was supposed to adjust instantly but if you try to do other stuff, there is a traceback, e.g.

color pink

Traceback (most recent call last):
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/cmd_line/gui.py"", line 195, in execute
cmd.run(cmd_text)
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/cli.py"", line 2194, in run
results.append(ci.function(session, **kw_args))
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/color.py"", line 107, in color
ns = _set_surface_colors(session, satoms, color, opacity, bgcolor)
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/color.py"", line 232, in _set_surface_colors
ns = scolor(session, atoms, color, opacity=opacity)
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/scolor.py"", line 50, in scolor
v = ai[v2a]	# Vertices for the given atoms
IndexError: index 2082 is out of bounds for axis 0 with size 2069

"	defect	closed	major		Surface		fixed						all	ChimeraX