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 >> >
