amino-acid capping residues in polymer not classified as protein

[Elaine Meng]

If possible, would be nicer if these residues when appearing as part of the polymer chain were classified as protein, and as backbone:
NH2 (e.g. 1g1p, 6nnv chain k)
NME (e.g. 1apv)
ACE (e.g. 3pob, in middle of cyclic peptide 6nnv chain k)

These can also appear as free ligands, for example PDB IDs see
​http://www.rcsb.org/ligand/NH2
​http://www.rcsb.org/ligand/NME
​http://www.rcsb.org/ligand/ACE

[Eric Pettersen]

'protein' selector was easy to fix. 'backbone' selector already worked.

[Elaine Meng]

Oh, I see "backbone" includes NME atom C but not ACE atom CH3... they're both sort of honorary alpha-carbons, but the behavior is OK with me if there are technical reasons for omitting the latter, like the atom-name check is not residue-name-dependent.

[Eric Pettersen]

Yes, there is no graph analysis for what is or isn't the backbone -- it's just if the atom name matches the known backbone atom names or not.