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CCP4BB  October 2011

CCP4BB October 2011

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Subject:

Re: Optimisation of weights

From:

Ian Tickle <[log in to unmask]>

Reply-To:

Ian Tickle <[log in to unmask]>

Date:

Fri, 14 Oct 2011 11:30:26 +0100

Content-Type:

text/plain

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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
for concern.

Cheers

-- Ian

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.
>
> Cheers
>
> -- 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?
>>
>> Cheers
>>
>> -- Ian
>>
>
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
>

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