Hi, Looks like you have some density for same conformation as in A chain.
It could be you have two (or more) conformations for some parts of the structure in MolB. It is often tricky to sort out when you have two conformations for residues and map is ambiguous (and at 2.8A). I would rigid body fit chunks of residues (6-10 residues?) that have density in difference map - then prune back things with no density in difference map (delete residues and atoms on side-chains outside of density - with delete atom in coot). Then set occupancy of ‘new’ stuff to 0.3 and do a little tightly restrained refinement and calculate new maps (in my experience - if you set occupancy to 0.5 you are likely to get too much model bias - to see other conformation). Quite likely this will not help and it will still be ambiguous. [ Alternatively - If you solve another 50 structures of the same thing - in different space-groups/cells - you may find different conformations for the 'missing parts’ appear in a couple of structures - and then you may be able to better model them in MolB of this structure]. Ben On 2 Oct 2017, at 15:42, Vikram Dalal <vikram.dalal...@gmail.com> wrote: Hi all, I am solving a protein data of 2.6 A. It has two monomers in ASU. It has 377 residues. I have built residues 26 to 36 and 41 to 377 in A chain while B chain has model 42 to 129, 146 to 168 and 189 to 371. Current R factor and R Free is 23.2 and 28.5, respectively. I have attached electron density (fourier map at 1.0 contour and difference map at 2.5) figures for 130 to 145, 169 to 188 and C terminal region of B chain and superposed model of A chain is shown in green color. I have tried manually building missing residues of B chain according to A chain model, but R free increased to 29. Any suggestions will be highly aprreciated. Thanks & Regards, <C_terminal_of_B_chain.png><resid130_145_of _B_chain.png><residues_169_to_188_of_B_chain.png> Dr Ben Bax York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD ben.d.v....@gmail.com
