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 <[log in to unmask]> 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
>
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