Dear Smith,
when you expand to P1, pointless should suggest the space group you
expanded from, unless you fiddled with the data after expansion.
Regards,
Tim
On 07/01/2015 04:43 AM, Smith Liu wrote:
> If both the PDB and mtz for the pdb have been assigned to P1 space group for some reason, can this lead to Rwork higher than Rfree during refinement?
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> If after converting my PDB and mtz to P1 space group, and I have forgotten what is the original space group for my PDB and mtz before conversion to P1 space group, is any method which can recover the original space group for my PDBand mtz, so that in the following refine Rwork would be lower than Rfree?
>
>
> Smith
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> At 2015-07-01 01:55:22, "Eleanor Dodson" <[log in to unmask]> wrote:
>
> I suppose if I was the referee for this structure and your FreeR is so close to the Rfactor I would ask you to ensure you had the right space group - is the 6 fold NCS actually 2 fold NCS with a crystallographic 3 fold..
> Cases occur where R32 is indexed as C2..
>
>
> Certainly if the Rfree set is assigned randomly to reflections which are symmetry equivalents then you see this phenomena of Rfree = Rfactor
>
>
> Eleanor
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>
> On 30 June 2015 at 18:26, Gerard Bricogne <[log in to unmask]> wrote:
> Dear Wolfram,
>
> I have a perhaps optimistic view of the effect of high-order NCS
> on Rfree, in the sense that I don't view it as a "problem". People
> have agonised to extreme degrees over the "difficulty" of choosing a
> free set of reflections that would produce the expected gap between
> Rwork and Rfree, and some of the conclusions were that you would need
> to hide almost half of your data in some cases!
>
> I think it is best to remember that the idea of cross-validation
> by Rfree is to prevent overfitting, i.e. ending up with a model that
> fits the amplitudes too well compared to how well it determines the
> phases. In the case of high-order NCS (in your case, the U/V ratio
> that the old papers on NCS identified as the key quantity to measure
> the phasing power of NCS would be less than 0.1!) the phases and the
> amplitudes are so tightly coupled that it is simply impossible to fit
> the amplitudes without delivering phases of an equally good quality.
> In other words there is no overfitting problem (provided you do have
> good and complete data) and the difference between Rfree and Rwork is
> simply within the bounds of the statistical spread of Rfree depending
> on the free set chosen.
>
> You are lucky to have 6-fold NCS, so don't let any reviewer
> convince you that it is a curse, and make you suffer for it :-) .
>
>
> With best wishes,
>
> Gerard.
>
> --
>
> On Tue, Jun 30, 2015 at 12:58:44PM -0400, wtempel wrote:
>> Hello,
>> my question concerns refinement of a structure with 6-fold NCS (local
>> automatic restraints in REFMAC) against 2.8 A data. The size of my free set
>> is 1172 selected in thin resolution shells (SFTOOLS) and corresponding to
>> 4.3 % of reflections.
>> A refmac run of 10 cycles of TLS and 10 cycles of CGMAT starts out at
>> Rfree/Rcryst 0.271/0.272. After the 10th TLS cycle I have 0.227/0.224. Yes,
>> Rfree < Rcryst. At the end of CGMAT I have 0.2072/0.2071.
>> I understand that NCS stresses the independence assumption of the free set.
>> Am I correct in believing that Rfree *may* be smaller than Rcryst even in
>> the absence of a major mistake? My hope is that the combined wisdom of
>> ccp4bb followers can point out my possible mistake, suggest tests that I
>> may perform to avoid them and, possibly, arguments in defense of a
>> crystallographic model with Rfree < Rcryst.
>> Many thanks,
>> Wolfram Tempel
>
>
> --
>
> ===============================================================
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> * Gerard Bricogne [log in to unmask] *
> * *
> * Global Phasing Ltd. *
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>
>
--
--
Dr Tim Gruene
Institut fuer anorganische Chemie
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