Hi your X-ray weight of .08 seems very small, the optimal value is
normally in the range 1 to 4 (I usually set it initially at the
median, i.e. 2.5). But which weight keyword did you use "WEIGHT
MATRIX .08" or "WEIGHT AUTO .08" (the latter is I think undocumented,
so I'm guessing the first)? Anyway I would strongly advise the
latter: the difference is that the MATRIX weight is on a completely
arbitrary scale, whereas the AUTO weight is at least relative to the
theoretical value of 1 (even though the optimal value may not be 1 in
practice, at least your initial guess will be in the same ball park).
Note that what Refmac calls "automatic weighting" is not the same as
what X-PLOR, CNS & phenix call "automatic weighting" (at least that's
my understanding). "WEIGHT AUTO" in Refmac is the same as "WEIGHT
AUTO 10", whereas auto-weighting in X-PLOR corresponds to "WEIGHT AUTO
1" in Refmac. Not surprisingly these give quite different results!
The optimal B factor weight is also around 1, see the paper for typical values.
I'm still not clear precisely what you meant by ""there was quite a
difference". I don't see that big a difference between the 2 runs,
just a slight tightening up of the geometry. Are you saying you see
big differences in the refined co-ordinates? That would be a cause
On Fri, Oct 14, 2011 at 11:19 AM, <[log in to unmask]> wrote:
> Respected Sir,
> For one of the structures that I did optimisation
> had values - (resolution of the data - 2.35Ang)
> Before optimization- (Bfactor weight=1.0, X-ray Weight - auto)
> R factor 0.2362
> R free 0.2924
> -LLfree 7521.8
> rmsBOND 0.0160
> zBOND 0.660
> After optimisation- (B-factor weight=0.2, X-ray Weight - 0.08)
> R factor 0.2327
> R free 0.2882
> -LLfree 7495.7
> rmsBOND 0.0111
> zBOND 0.460
> Also can you tell me what is the limit for B-factor weight hat can be varied.
> Thanking you
> With Regards
> M. Kavyashree
> Sorry I just re-read your last email and realised and didn't read it
> properly the first time. But what I said still stands: you can of
> course try to optimise the weights at an early stage (before adding
> waters say), there's no harm doing that, but there's also not much
> point since you'll have to do it all again with the complete model,
> since adding a lot of waters will undoubtedly change the optimal
> weights. So I just leave the weight optimisation until the model is
> complete. As long as the initial weights are "in the same ball park",
> so that your RMSZ(bonds) is around 0.5 for typical resolutions (a bit
> lower for low resolution, a bit higher for very high resolution) it
> won't affect interpretation of maps etc.
> -- Ian
> On Fri, Oct 14, 2011 at 9:37 AM, Ian Tickle <[log in to unmask]> wrote:
>> It must be the same complete model that you refined previously, I
>> doubt that it will give the correct answer if you leave out the waters
>> for example.
>> You say "there was quite a difference". Could you be more specific:
>> what were the values of the weights, R factors and RMSZ(bonds/angles)
>> before and after weight optimisation?
>> -- Ian
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