Dear All, I really appreciate your nice explanations!
On Fri, Dec 16, 2016 at 12:08 PM, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote: > > 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 <alexlee198...@gmail.com> 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? >> >> >> >
