Table 2. Matching related EM maps. Systema DnaB.DnaC complex [25] DnaB.DnaC complex [26] GroES-ADP7-GroEL-ATP7 [27] GroES-ATP7-GroEL [28] GroES-ADP7-GroEL-ATP7 [27] GroEL-ATP7 [27] GroES-ATP7-GroEL [28] GroES-ATP7-(single-ring)GroEL [29] ATP-TClpB mutant [10] ADP-TClpB [10] AMPPNP-TClpB [10] ADP-TClpB [10] AMPPNP-TClpB [10] ATP-TClpB mutant [10] TFIID-closed [30]b TFIID-open [30] apo-ORC [31]b ATP-ORC [31] Ribosome 80S [32]b Ribosome 40S [32] Matching & Docking EM Maps EMDB code and resolution (A˚ ) w and g No. of matches and correct matches with score.210000 Rank of highest ranking false match 1023, 42.2 1017, 26.0 1046, 23.5 1180, 7.7 1046, 23.5 1047, 14.9 1180, 7.7 1286, 10.4 1244, 11.2 1242, 16.7 1243, 12.1 1242, 16.7 1243, 12.1 1244, 11.2 1194, 33.0 1196, 35.0 1252, 34.0 1253, 34.0 1093, 18.3 1092, 25.3 1.7 3.75 2.8 2.11 2.6 2.35 3.2 1.79 2.9 2.22 2.9 2.25 3.0 2.22 1.7 5.12 1.7 5.26 2.4 3.69 277 38 57 27 21 18 915 29 145 89 84 72 12 12 1 1 39 13 262 3 39 24 17 20 66 73 3 13 14 3 aThe first structure in each pair is the stationary object A and the second structure is the moving object B. bValues are given for matching with the lowest density cutoff for object A and highest cutoff for object B (see text). doi:10.1371/journal.pone.0003594.t002 the w ranges is 9.6 A˚60.8. The corresponding average calculated with w derived from the dependency graph in Figure 1 is 9.7 A˚61.3. It appears that the optimal w values modify the resolution of the EM map creating surfaces that are not resolution dependent. Virtual atoms with radius of 9.7 A˚ produce a surface that confers tolerance to small structural mismatches or to mis- positioning due to the stepwise scanning of the rotation-translation space. This result is very important in view of the wide resolution range of EM structures. The search volume in these simple tests, in which objects A and B are identical, consists of the outer part of the surface layer of object A, corresponding to the difference between the surface extensions applied to the two objects. The thickness of this layer, (w21)g, depends on the EM map resolution. Therefore, self- matching of the higher resolution EM maps, which often are presented at small grid intervals, leads to a shift of the highest scoring model at the identity orientation from the expected position (#3 grid steps). The best matching results are obtained when w.1 thus allowing some freedom for object B to move and adjust to object A. Matching related EM maps A more realistic test of the FitEM2EMIN algorithm was the matching of related EM maps, including matching of the same object determined at different resolutions, matching of partial structures and matching of different conformers. Optimal w ranges were reevaluated for five pairs of structures (see Table 1). Rotation-translation scans were performed employing several w values and ranges of optimal w were determined using the abovementioned criteria. The resultant w ranges for these five cases fit reasonably well to the regression line of w versus resolution obtained in the self-matching of EM maps, as shown in Figure 1. Ten pairs of related EM maps were used to test our matching algorithm and to demonstrate its performance. In one case, the EM maps of the complex between helicase DnaB and its DnaC loading partner, determined at very different resolutions (26 and 42.2 A˚) were matched [25,26]. Despite the large difference in resolution our algorithm ranked a correct match at the top. A false Figure 1. The dependency of the optimal w values on the resolution of the matched EM maps. The full circles depict the results of self-matching (for systems listed in Table 1). The hollow circles depict the results of matching of related EM maps (the average resolution is used here). The regression line (y = 20.0612x+3.7551; R2 = 0.78) is based only on the full circles. The error bars reflect the range of the optimal w. doi:10.1371/journal.pone.0003594.g001 PLoS ONE | www.plosone.org 3 October 2008 | Volume 3 | Issue 10 | e3594