On Thursday 26 August 2010 11:56:39 am Hailiang Zhang wrote: > Hi, > > I want to refine B factors for several residues only (all the other B > factors and all coordinates fixed, I know it sounds weird but there is a > reason to try that).
Maybe you could tell us what this reason is? > Is there anyway CCP4 can do this? Thanks for any suggestions! Suggestion 1) Calculate structure factors for the entire rest of the model. Include these as F_partial contributing to the refinement of a model containing only your residues of interest. In this refinement, refine only the B terms. Caveat: I think you will encounter problems with how to handle the bulk solvent correction. Perhaps that must be included in F_partial also, and omitted from the subsequence mini-refinement. Suggestion 2) - Place your residues of interest in a single TLS group. - Do not assign any other atoms or residues to a TLS group. - Refine the entire model using refmac in TLS refinement mode. Choose 5 or 10 cycles of TLS refinement, but 0 cycles of coordinate/Biso refinement. Disregard all output other than the refined TLS description for the B factors in your residues of interest. - Use TLSANL to expand the TLS parameters back to individual Biso if you like. > > Best Regards, Hailiang > -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
