Re: [ccp4bb] Transferring a Free R set.

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Transferring a Free R set.
From: Mark Wilson mwilson13 {- at -} UNLNOTES {- dot -} UNL {- dot -} EDU
Date: 2008-12-18

Next message:
Subject: Re: Transferring a Free R set.
From: "Alun R {- dot -} Coker" A {- dot -} Coker {- at -} MEDSCH {- dot -} UCL {- dot -} AC {- dot -} UK
Date: 2008-12-18

Subject: Re: Transferring a Free R set.
From: "Edward A {- dot -} Berry" BerryE {- at -} UPSTATE {- dot -} EDU
Date: 2008-12-18

Alun R. Coker wrote:
> Hi All,
>
> I have been in the habit of transferring my initial free R assignments
> to any new data sets or to isomorphous data sets such as substrate
> complexes. Although theoretically this is necessary to obtain a valid
> free R many of my colleagues maintain that this is completely
> unnecessary in practice. Does anyone on the list have a view on this or
> has anyone tested to see if it makes any difference.
>
> Alun.

While leaving the theory to the experts, I'll suggest a test to answer
the question in an individual case. Try refining your old model against the new
data, keeping the same Free set against which the model has (not) been refined.
If the values of R and R-free are essentially the same, initially and perhaps
through rigid body refinement, then it would have been alright to pick a new
free-R set. The model is no more biased toward the working reflections (of the new
dataset) than the free. The "noise" in the new dataset is completely independent
from the noise in the old dataset that was being "overfit" by the working reflections.

If there is a significant gap initially, with Rfree > Rwork, then there is some
systematic error (difference) between the model and the data, which carries over
to the new dataset, which the refinement program is partially able to fit without
improving the model as measured by the free reflections. in this case it may be
important to keep the same Free-R set, although if the model will undergo
significant rebuilding and refinement the bias may be "shaken out" before the end.

Still, the pragmatic answer would be "just do it".
I don't think any reviewer will give you trouble for using the same free-R set.

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Transferring a Free R set.
From: Mark Wilson mwilson13 {- at -} UNLNOTES {- dot -} UNL {- dot -} EDU
Date: 2008-12-18

Next message:
Subject: Re: Transferring a Free R set.
From: "Alun R {- dot -} Coker" A {- dot -} Coker {- at -} MEDSCH {- dot -} UCL {- dot -} AC {- dot -} UK
Date: 2008-12-18