id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
1144	Bad geometry leaves histidine HE2 unbonded on PDB load	Tristan Croll	Eric Pettersen	"This is a fairly artificial situation, but nonetheless...

As a test of how well ISOLDE can recover from bad geometry, I created a deliberately badly distorted model (after adding hydrogens with AddH):

{{{
import numpy
m = session.models.list()[0]
m.atoms.coords += numpy.random.rand(*m.atoms.coords.shape)-0.5
}}}

If I save the resulting model as a PDB file and reload, the histidine HE2 atoms are no longer attached - I guess because the doubly-protonated His isn't in the dictionary of standard residues?"	defect	closed	minor		Input/Output		fixed						all	ChimeraX