As usual, I'd recommend the program Dyndom which is available from CCP4i.
This will identify domain borders + hinge regions as well.
Best, Matthias
-----------------------------------------
Dr. Matthias Zebisch
Division of Structural Biology,
Wellcome Trust Centre for Human Genetics,
University of Oxford,
Roosevelt Drive,
Oxford OX3 7BN, UK
Phone (+44) 1865 287549;
Fax (+44) 1865 287547
Email [email protected]
Website http://www.strubi.ox.ac.uk
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On 3/2/2014 4:52 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*
