DM will be most helpful to you if you are as unbiased as possible to begin with. I *think* that DM right after MR is about as biased as DM after MR after a round of Refmac post-MR (given that MR these days includes rigid body refinement anyway) but I would be very curious to hear what the resident theoreticians have to say about this, in terms of actual mathematics.
The maximum benefit you can get from DM will come through if you also include NCS averaging (if you have NCS of course). Nowadays you can try a number of nice DM routines - and don't forget Resolve - each offering somewhat unique advantages. You should also carefully estimate actual solvent content, and other pre-set parameters since they will have considerable effect on the quality and meaningfulness (unbiased information content?) of the resulting maps. Incidentally, it is always good to have a few practical indicators of bias removal e.g. to delete a residue in a search model and then see it come back in post-DM maps or to observe difference density near parts of the search model that differ in the actual structure. Artem www.harkerbio.com "Speed of a cheetah, strength of a bear and tenacity of a divorce lawyer" On Fri, Dec 16, 2016 at 2:44 PM, 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? > > >
