id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
437	OpenMM hangs and uses all system memory, tug atom mouse mode	Tom Goddard	Tom Goddard	"Using the tug mouse mode on Mac OS 10.11 and 10.12 frequently at the first atom tug attempt ChimeraX hangs and very quickly uses all system memory (about 2 Gbytes / second).  For example, opening 1gcn and adding atoms

open 1gcn
addmissingatoms #1

then use tug mouse mode.  I believe this happens when their is very bad geometry.  The addmissingatoms uses PDBFixer which adds atrocious geometry.  I've attached a file where it put GLN 3 HG2 and HG3 atoms exactly on top of each other, which is probably the cause of the hang for this case.  Each run of PDBFixer generates different results -- some randomization is involved.

This bug is particularly serious as it disables the Mac if ChimeraX is not force quit within 30 seconds or so, after which it is very difficult to force quit because the machine becomes unresponsive."	defect	closed	major		MD/Ensemble Analysis		fixed						all	ChimeraX