id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
1178	Handling of poor geometry in AddH	Tristan Croll	Eric Pettersen	"Background: ISOLDE's chirality restraints aren't yet perfect - they will *restrain* a chiral centre to the correct chirality, but they're unable to *flip* the chirality of an incorrect centre. They try hard, but the atoms are unable to find their way past each other. In the case of a threonine side chain for example, the CB-CG2 and CB-OG1 bonds end up almost co-planar with the HB preventing them from flipping further.

Something I'm planning to take care of (with a tool to flag incorrect chiral centres to the user and aid them in interactively correcting them), but it does flag up what I see as an issue with how AddH decides on adding hydrogens. If I remove and re-add hydrogens, then a threonine like the above is treated as a ketone (only two hydrogens added to CG2, none to OG1). I've also seen it treat one of the C-C bonds in a lysine sidechain as double-bonded, for a less-discernable reason.

It's great (and really quite impressive) that AddH is able to infer hydrogenation based on geometry alone, but I also think it needs a mode that sticks to strict dictionary definitions for each residue. Bad geometry is an unfortunate fact of life (albeit a problem that one would hope is reducing with time), and depending on the use-case the current behaviour of AddH risks making geometry errors worse rather than helping to fix them."	defect	closed	major		Structure Editing		fixed						all	ChimeraX