id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
1009	molecular surface not included in command-line specifiers of corresponding atoms (protein, nucleic, many others)	Elaine Meng	Conrad Huang	"For example, structure 1ncc is antibody H and L chains, and N chain mostly protein but also some glycosylations.  The first ~protein in the commands below specifies what I expect, only the glycosylations, but the second one also colors the antibody surfaces.

open 1ncc
select ~protein
surf
surf /n enclose /n include ligand
color ~protein steel blue

I'm thinking this affects all the command-line specifiers of sets of atoms (protein, nucleic, sidechain, ligand ...).  Yes, molecular surface models are not atoms, but I think this is wrong behavior.  The atomic patches of a molecular surface should be specified along with the corresponding atoms.

I don't know to whom this should be assigned."	defect	closed	major		Command Line		fixed		chimera-programmers				all	ChimeraX