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Hi Raji: Just to make this clear; sorry if I mispresented anything. In both cases the variables are minimum -- only rigid body refinement and nothing else. i.e. rigid.inp in CNS and "refi type rigid" in refmac. Weikai On Thu, May 18, 2006 3:59 pm, Raji Edayathumangalam wrote: > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > > I've done some crude comparisons for a couple of different structures > and ended up with differences in the range of ~1% between the programs. But > during the comparison, the refinement protocol in CNS included > minimization, b-group/individual and playing with no. of cycles (for same > structure from Refmac minus TLS) before the program honed in on similar > values. > > I am not sure the rigid body refinement output in CNS (if that's what > you meant) can be directly compared with Refmac output and 'might' explain > the differences in the R-factors. Did you try some more refinement in CNS > to see if the 5% difference decreases/disappears? > > Someone pl. correct me if you think CNS rigid body equals (in > theory/philosophy) Refmac refinement routine. > > Raji > > > > > > [EMAIL PROTECTED] wrote: >> *** For details on how to be removed from this list visit the *** >> *** CCP4 home page http://www.ccp4.ac.uk *** >> >> >> >> >> Hi All: >> >> >> I have two questions for the bulk solvent model: >> >> >> 1. Maybe I missed this in reading the manual, but in Refmac is there a >> way of inputting an mask to define the bulk solvent? Or it is always >> done automatically using the keyword SOLVENT? >> >> 2. Is the bulk solvent model in Refmac somehow different from that in >> CNS? For one of my low resolution data to 7A, the bulk solvent model in >> Refmac seems to behave much better than that in CNS. I only use rigid >> body refinement and there is no TLS refinement in Refmac. So in this >> case, maybe the major difference of R factor using these two programs >> would come from the bulk solvent models (maybe also the scaling of Fc >> to Fobs, or maximum likelyhood, etc.?). Anyway the R factors differ by >> 10% >> using the two different programs (40% in CNS vs. 30% in Refmac) when >> both have a bulk solvent model. If I turn off bulk solvent estimation >> in CNS, the R factor drops by 5% (i.e. now R=35% in CNS). >> >> Regards, >> >> >> Weikai >> >> >> >> >
