Partial structure mask bulk solvent parameters. If you use simple scaling then mask solvent is still on. You can turn it off by "Calculate the contribution of from the solvent region"
To turn Babient's bulk solvent you need to use Babinet's scaling instead of simple. I hope it helps regards Garib On 29 Dec 2011, at 21:08, Bernhard Rupp (Hofkristallrat a.D.) wrote: > Dear Refmac developers group, > > I am trying to understand a small detail in the refmac log listing. In the > bulk > > solvent section just below the restraint table (I use monitor MANY in > general): > > ----------------------------------------------------------------------------- > > Overall : scale = 0.891, B = -0.266 > > Partial structure 1: scale = 0.375, B = 24.388 > > Overall anisotropic scale factors > > B11 = -0.39 B22 = 0.09 B33 = 0.33 B12 = -0.00 B13 = 0.48 B23 = 0.00 > > ----------------------------------------------------------------------------- > > > Is the listing indeed containing the flat bulk solvent model (‘simple model’ > in refmac gui, SOLVENT YES) k and B in the first 2 lines? > > > If so, I am curious > > a) what exactly is ‘Overall’ versus ‘partial structure’? What is the > relative magnitude of the scale and B telling me in each case? > > b) would it not be useful to have it reported in the PDB header? > > All I find there is the anisotropic B scaling matrix and a mean (overall) B > value (of unspecified origin – how exactly is that computed?) > > REMARK 3 B VALUES. > > REMARK 3 FROM WILSON PLOT (A**2) : NULL > > REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.711 > > > Explanation/intuition would be much appreciated. > > > Best regards, BR > > ----------------------------------------------------------------- > > Bernhard Rupp > > 001 (925) 209-7429 > > +43 (676) 571-0536 > > hofkristall...@gmail.com > > b...@hofkristallamt.org > > http://www.hofkristallamt.org/ > > ------------------------------------------------------------------ > > Old and treacherous will beat young and skilled every time > > ------------------------------------------------------------------ > > PS: The doc leaves me a little confused because SCAL type SIMP would imply > > KB = K0*exp(-B0*s^2) (Simple Wilson scaling) > > i.e. K1 = 0 > > while BULK (Babinet) which I did not specify > > KB = K0*exp(-B0*s^2) * (1- K1*exp(-B1*s^2)) > > gives me 2 Ks and Bs. > > So I conclude that ‘overall’ and ‘partial’ lines do not list Babinet ks and > Bs (the B is also too small for that) > > Garib N Murshudov Structural Studies Division MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
