Table 4.

Computational tools used in the validation and analysis of cryo-EM density maps

Function	Program Name (Reference)
Segmentation	Amira (Visage Imaging, GmbH)
	Avizo (VSG, France)
	Chimera (Pettersen et al., 2004)
	CoDiv (Volkmann, 2002)
	EMAN (Ludtke et al., 1999; Tang et al., 2007)
	Segger (Pintilie et al., 2010)
	VolRover (Baker et al., 2006)
Rigid body fitting	Chimera (Pettersen et al., 2004)
	CoFi (Volkmann and Hanein, 1999)
	DockEM (Roseman, 2000)
	EMFit (Rossmann, 2000)
	Foldhunter (Jiang et al., 2001)
	Mod-EM (Topf and Sali, 2005)
	Situs (Wriggers et al., 1999)
	UROX (Siebert and Navaza, 2009)
Flexible fitting	DireX (Schröder et al., 2007)
	Flex-EM (Topf et al., 2008)
	MDFF (Trabuco et al., 2009)
	NMFF (Tama et al., 2004)
	NORMA (Suhre et al., 2006)
	Yup.scx (Tan et al., 2008)
	Situs (Rusu et al., 2008)
SSE Identification	Helixhunter (Jiang et al., 2001)
	Sheetminer/Sheetracer (Kong and Ma, 2003; Kong et al., 2004)
	SSEHunter (Baker et al., 2007)
Modeling	Coot (Emsley and Cowtan, 2004)
	EM-IMO (Zhu et al., 2010)
	Gorgon (Baker et al., 2011)
	Modeller (Topf et al., 2006; Topf and Sali, 2005)
	O (Jones et al., 1991)
	Rosetta (Baker, 2006; DiMaio et al., 2009)
Visualization	Amira (Visage Imaging, GmbH)
	Avizo (VSG, France)
	Chimera (Pettersen et al., 2004)
	PyMol (DeLano Scientific LLC, USA)
	VMD (Humphrey et al., 1996)