Table 2.

Results from different programs for difficult structure pairs

pair	PDB ID	PDB ID	Chimera	TOPOFIT	CE	CE/MA
1	3chy	2fox	88/2.2	19/0.7	108/3.6	93/2.6
2	2aza A	1paz	79/2.0	72/1.7	84/2.9	81/2.4
3	1cew I	1mol A	73/1.9	73/1.6	81/2.3	78/1.9
4	1cid	2rhe	90/2.0	69/1.5	97/2.9	88/1.9
5	1crl	1ede	184/2.5	143/1.9	219/3.8	183/2.3
6	2sim	1nsb A	257/2.6	207/2.0	275/3.0	266/2.5
7	1ten	3hhr B	82/1.3	81/1.4	87/1.9	85/1.6
8	1tie	4fgf	73/2.2	88/1.6	116/2.9	105/2.1
9	2snv	5ptp	118/2.3	83/1.8	130/3.1	118/2.4
10	1gp1 A	2trx A	89/1.8	96/1.6	64/5.2	54/2.7

Results are of the form N/RMSD, where N is the number of residue pairs matched and RMSD is the corresponding alpha-carbon root-mean-square deviation. Chimera: results from using MatchMaker and then Match -> Align with default settings, as reported under MM-default in Table 1. TOPOFIT [31] results were obtained using the web server [35]. CE [26] results were obtained using the web server [34] with default settings. CE/MA: equivalences obtained by using Match -> Align with cutoff 5.0 angstroms on the superpositions from CE.