id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
5954	Add Phenix douse tool to add waters	Tom Goddard	Eric Pettersen	"As part of the Phenix R24 grant we will be allowing ChimeraX to call Phenix tools.  The first one we are trying is phenix douse which places water molecules in a give cryoEM map near an atomic model.  Douse returns a new atomic model with all the original atoms plus some waters added.  We will make a command and a gui interface for this.  It will assume the user has installed Phenix and should allow the user to specify the phenix location if it cannot be found automatically.

Pavel Afonine on the Phenix team developed douse and will work with us on this.

We want the ChimeraX tools to invoke Phenix tools via a REST service so that it can get JSON return values (file paths, error messages, calculated numeric quantities) without having to parse the typical command-line output from phenix tools.  Billy Poon has developed an initial REST server for phenix that we can use to call douse, and other tools."	enhancement	closed	high		Structure Editing		fixed		Zach Pearson Tom Goddard				all	ChimeraX