id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
752	CIF/PDB I/O problems	Tristan Croll	Greg Couch	"I'm looking at a fairly large structure (4ljz) which has zinc ions in two chains (D and J). If I save this from ChimeraX as a mmCIF file and re-open it, chains D and J appear to be treated as ligands in their entirety - they're shown initially as sticks with CPK colouring rather than the VDW/colour by chain of the rest of the structure, and are not included in ribbon calculation.

If I try to open this mmCIF in Coot, it seems to interpret it as an empty structure. Phenix handles it without trouble and returns a PDB file. Loading that into ChimeraX reveals another piece of weirdness: if the PDB contains LINK records (between the zinc ions and surrounding cysteines) then everything is fine. If the LINK records aren't present, then for some reason all breaks in the peptide backbone become ligated with long bonds.

I can provide files if you like, but they're ~10MB apiece."	defect	closed	major		Input/Output		fixed		Eric Pettersen				all	ChimeraX