id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
2074	Next steps: building into density	Tristan Croll	Eric Pettersen	"A lovely example I came across the other day:

{{{
open 3esu structureFactors true
view /F:1140; cofr center
delete /F:1145,1140,1246,1372,1371,1311,1310
}}}

What's there is clearly a HEPES molecule from the buffer, which was obscured by an overzealous water-picking algorithm adding waters to most of the peaks. In the near-term future, I'd really like to start providing tools for the the user to build into density like this (as well as waters, ions, and the peptide/nucleic acid chain itself, of course).

A few things that would make this much easier:

- Python access to residue templates (#1682) 

- The map segmentation tool from Chimera. The more the target density can be isolated from its surroundings, the easier everything should become.

From there, the rest should be mostly straightforward. Fetch the template from the CCD, add the residue from the template, do some initial rigid-body fit and perhaps some degree of (non-MD) flexible docking, then settle into place using a simulation (initially in isolation from the surroundings if appropriate)."	enhancement	closed	moderate		Structure Editing		fixed		Tom Goddard Greg Couch				all	ChimeraX