Rather hard to advise! Options are: a) The helical domain is wrongly positioned! b) There are scaling problems or swathes of missing data which can depress some parts of the electron density. If you use coot and reduce the contour level in this region, is anything sensible visible?
A useful test is to set the occupancy of some bulky residues to 0.00, repeat the refinement, then see whether you can see the missing atoms at some level in the map. Eleanor On 10 September 2014 03:20, Appu kumar <[email protected]> wrote: > Hello All, > > I am new to low resolution refinement parametrization and regularization. > Crystal diffracted with high anisotropy reaching to 3.5A in one direction > and 4.5A other direction. I am refining a structure at 3.9A resolution. > Protein has two domain connected trhough a linker and is packed as tetramer > in ASU. Refinement in phenix as well as in refmac leads to wipe away of > electron density in helical domain of protein leaving only blobs of > electron density while other domain have good amount of density after > refinement. I need your precious and valuable suggestion for proceeding > with refinement. > > Thanks in advance for your suggestion. > > Thank you > >
