id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
827	Structure file I/O issues	Tristan Croll	Eric Pettersen	"Simple-but-important one first: mmcif_write.py currently crashes due to a reference to `atoms.occupancy` rather than `atoms.occupancies` at line 91.

Another issue on loading: if a residue has all its atoms but the geometry is ""aggressively"" bad, ChimeraX will sometimes miss a bond. This is cropping up for me when I use Coot's ""Add hydrogens using Refmac"" command. It's the only currently-available hydrogen-addition tool I know of that (a) the majority of existing structural biologists will have, and (b) provides all the hydrogens necessary for OpenMM to work (including N-terminal hydrogens). Unfortunately, apart from those advantages it's *really* bad. It seems to work OK at adding hydrogens to a ""perfect"" high-resolution structure, but at lower resolution it doesn't seem to even attempt to provide decent geometry for some hydrogens, and a handful will end up 2-3 Angstroms away from the atom they should be bonded to! I guess they rely on subsequent refinement to fix them - and OpenMM's minimiser can pull them into line in a snap. But, in these cases I inevitably run into a handful of residues where ChimeraX has failed to form a heavy atom-hydrogen bond on loading, leading to the simulation failing to launch.

I presume ChimeraX has some form of geometric test to decide whether or not to form a given bond when loading a structure. I don't think this is advisable, to be honest - or at least, there should be a ""permissive"" bond that forms all bonds according to the residue dictionary definitions for each residue, no matter what the geometry. Bad geometry happens for all sorts of reasons, after all."	defect	closed	major		Input/Output		fixed						all	ChimeraX