Hi Ian: Thanks a lot! I have 2 questions:
(1). Can I say the X-ray weighting is optimal when it yields the smallest Rfree, meanwhile RMS-Z(bonds) is smaller than "0.85 - 0.146*resolution" (angles also maybe)? (2). Why RMS-Z(bonds) should be lower than that for low resolution data and higher for high resolution? Or why high-resolution can allows more outliers? Thanks again for that! Best Regards, Hailiang > To give credit where it is due I should perhaps have explained that > the formula for RMS-Z(bonds) that I quoted was derived from an > analysis of re-refinements from the PDB-REDO project > (http://www.cmbi.ru.nl/pdb_redo), not from the PDB itself. PDB-REDO > itself uses the LLfree optimisation method that I referred to briefly. > > Cheers > > -- Ian > > On Tue, Sep 21, 2010 at 9:42 PM, Ian Tickle <ianj...@gmail.com> wrote: >> Hi Hailiang >> >> The short answer is that the optimal X-ray weighting factor minimises >> Rfree, or better -LLfree. >> >> However this is tricky to carry out in practice since it means you >> have to run several jobs adjusting the weight manually each time to >> find the optimum. Also, ideally the same procedure should be >> performed for the B weighting factor, but this adds yet another >> dimension to the problem, and I suspect most people just go with the >> default B weighting factor (though strictly speaking its optimum value >> is resolution-dependent). >> >> Another somewhat easier way in practice is to adjust the weight to get >> a particular target value for RMS-Z(bonds), however you still have the >> problem of choosing that optimal target value. The median value of >> RMS-Z(bonds) over the whole PDB is about 0.5 so you could use that for >> everything, though ideally the value should be lower than that for low >> resolution data and higher for high resolution. I use this >> empirically-derived formula obtained by fitting the RMS-Z(bonds) >> values in the PDB to a straight line with resolution: >> >> RMS-Z(bonds) = 0.85 - 0.146*resolution >> >> though this is probably valid only in the resolution range 3.5 to 1 >> Ang, since the number of structures outside that range is too small to >> get a meaningful fit. I'm sure others have different opinions on >> this. >> >> One problem with the 'WEIGHT MATRIX' value is that the optimum is >> resolution-dependent, i.e. the optimum value for a low-resolution >> dataset is quite different from that for a high-resolution one. The >> 'WEIGHT AUTO' option is much better in this respect as the optimum >> value is much less resolution-independent. The default weight value >> for 'WEIGHT AUTO' is 10 but I find this much too high, and I always >> reset it to 'WEIGHT AUTO 2.5' as a first attempt. >> >> Cheers >> >> -- Ian >> >> On Tue, Sep 21, 2010 at 8:54 PM, Hailiang Zhang <zhan...@umbc.edu> >> wrote: >>> Hi all: >>> >>> I have a question about deciding an ideal "Weight matrix" value in >>> REFMAC. >>> When I change it from 0.1 to 0.001, the bond distance rmsd changes from >>> 0.075 to 0.008, while the R changes from 0.26 to 0.33 (resolution >>> 3.2A). >>> Now I am not sure what is the best balance based on these numbers. Are >>> there any references or empirical values? Thanks! >>> >>> Best Regards, Hailiang >>> >> > >
