id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
124	Preference so warnings don't show a dialog	Tom Goddard	Eric Pettersen	"Currently warnings that occur when opening a PDB or mmCIF file show a dialog and the user has to press Ok to continue.  This is not good when running a batch processing script.  Would like to have a command to make warnings go to the log without raising a dialog.  There might also be a preference setting for this.

The case I encountered was rendering 100 images of mmCIF file assemblies.  On 4aa7.cif I get two warning dialogs:

open mmcif:4aa7
Cannot find consistent set of bond orders for ring system containing atom C3 in residue R82 1454.B
Cannot find consistent set of bond orders for ring system containing atom C3 in residue R82 1454.A

also 4aaw.cif produced a warning dialog

open mmcif:4aaw
Cannot find consistent set of bond orders for ring system containing atom C3 in residue R84 1460.A

I'm running my script on the entire PDB (only 100 files as a test so far) so I can't practically click Ok to all these warnings.  The script is not run in nogui mode because it needs to render images.  Eric Pettersen suggested Python code could push its own exclusive logger to catch all the warnings.  In any case the above capability to suppress dialogs for warnings will be useful.
"	enhancement	closed	minor		Infrastructure		fixed						all	chimera