This isnt the sort of thing a refinement program does. Refinement starts from the model you provide - uses that to generate phases and the appropriately weighted difference map to alter the input coordinates. So that map is used in the close environment of a the model, so solvent flattening is not an important option. ( There is an element of these in the choice of scale between Fobs and Fcalc but it isnt explicit. ]
NCS averaging is useful, but it is done by imposing NCS on the refined models. However if you want to do automated rebuilding using BUCCANEER or Arp/Warp it may be worth first generating phases by a good many cycles of REFMAC, then using PARROT to impose ncs symmetry and solvent flattening, then beginning the rebuild cycles with these phases. This approach is provided in CCP4I2 Eleanor On 16 December 2016 at 19:44, Alex Lee <[email protected]> wrote: > Hi All, > > I am using CCP4i 7.0.0.025 linux version. I am wondering if Refmac5 > automatically does density modification (e.g. solvent flattening, NCS, > etc..) in the refinement after I put a solution coordinate from Phaser MR > molecular replacement and the experiment data (MTZ file)? If Refmac5 does > not do density modification automatically, is it better that first doing a > density modification (CCP4i DM or Pirate) after molecular replacement > (input the solution coordinate file and mtz map generated by Phaser MR), > and then building structures and finally do the Refmac5? > > >
