Hi, If there is a hinge motion between the two domains, then allowing for this will give you a much better starting model. As Klaus suggested, you may just be able to do rigid body refinement of the two domains. However, it is also possible to place the two domains separately in Phaser, by putting the two domains in separate PDB files, defining an ENSEMBLE with each of these PDB files, then searching for both of them in the same job. In the ccp4i GUI, you can specify an additional ensemble by clicking the Add ensemble button, and you can add another component to search for in the same job by clicking the Add another search button.
I hope that answers the question you were asking! Best wishes, Randy Read On 2 Dec 2013, at 04:11, Prem Prakash <prem...@gmail.com> wrote: > Dear All, > > The density obtained after molecular replacement using phaser at 2.5 Angstrom > and then used buccneer for autobuilding of the model. I am not getting > reasonable R value (it is 38.5 %) but the figure of merit is 0.629. > > As My protein has two domains. So is it possible to fragment the individual > domain and then again perform the molecular replacement. How it will improve > my phase more and how R-factor will be reduced ? > > Please help and direct me in proceeding in a right way, and if possible > provide a protocol for doing that. Thank you > > With kind regards > > ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
