Dear Rajan,
You could also use the CCP4 program LSQKAB (Kabsch, 1976):
First superimpose domains 1 of the two conformational states. Then take this first overlay as the starting position and superimpose domains 2. The log file of LSQKAB should give the angle in going from the first to the second superposition.
Best regards,
Navdeep
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On Sun, Mar 02, 2014 at 10:22:47PM +0530, 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*
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Navdeep S. Sidhu
Departments of Structural Chemistry
& Neuropediatrics
University of Goettingen, Germany
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