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. Author manuscript; available in PMC: 2010 Mar 10.

Published in final edited form as: Acta Crystallogr D Biol Crystallogr. 2006 Mar 18;62(Pt 4):398–409. doi: 10.1107/S0907444906002204

Fig. 2 — The relationships between relative rotations. {u}is the global coordinate frame which is arbitrarily placed. {A_i} and {B_i} are the coordinate frames attached to the i^th domain in the template and the target, respectively. Our goal is to calculate R_{B_i,B_j} the relative rotation between domains in the target, by using the rotations R_{u,A_i}, R_{u,A_j}, R_{A_i,B_i}, and R_{A_j,B_j}. One can obtain R_{u,A_i} and R_{u,A_j} from the structural details of the template conformation. One also can calculate R_{A_i,B_i} and R_{A_j,B_j} by converting the relative rotations H_{A_i,B_i} and H_{A_j,B_j} which are described in the global frame {u} into the relative rotations with respect to {A_i}local frame.