Dear Rajan, you can superpose the two domains, e.g. with Coot. Coot will display the transformation matrix and maybe even the angle and axis of rotation. If the latter is not the case, you can extract the angle and axis from the transformation matrix (one of the eigenvalues and eigenaxes, I suppose).
Best, Tim On 03/02/2014 05:52 PM, rajan kumar wrote: > Dear all, > > sorry for off topic question. My protein is composed to two domains > connected by a flexible linker and shows large domain motion with large > RMSD value of 9.0 A* difference with respect to the initial structure, > when simulated for 20 ns. As the first domain doesn't shows any RMSD change > when superimposed to initial structure but the other domain moves > significantly. so my question is how i could be to calculate the angle of > motion in degree of the flexible domain with respect to the initial > structure after superimposition. > thank you all in advance > > Regards > > *Rajan kumar choudhary* > *Senior Research Fellow* > *Department of Atomic Energy(Govt.Of India)* > *ACTREC TATA Memorial Center * > *Kharghar Navi-Mumbai* > *Mumbai-410210* > *India* > -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
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