id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
403	nonstandard RNA residues missing rungs	Elaine Meng	Tom Goddard	"Modified RNA residues in structures such as 1ehz are missing ""rung"" pseudobonds.  However, at least all the nonstandard bases I looked at were clearly identifiable as either purine- or pyrimidine-derived.  I don't know if mmCIF has something like the PDB-format MODRES that reveals this, but the ""easy"" way to tell if they are already known to be in a nucleic acid chain is by the last letter of the residue name.  For example, 2MG is derived from G.  In 1ehz:

purine-derived (use N1): 2MG OMG M2G YYG 7MG 1MA
pyrimidine-derived (use N3): H2U OMC PSU 5MC 5MU

I realize ""rungs"" is somewhat experimental so you may not want to spend time improving it in this way.  Just thought it would be good to record this information somewhere. The related problem with ribbons in general #402 is certainly worse."	defect	closed	major		Depiction		fixed						all	ChimeraX