Did not knew about that trick !
But I second that a well made script (i.e. not my homemade one) included in
software for paired refinement would be a great addition.
On Thu, 8 Nov 2018 at 20:13, Georg Mlynek <georg.mly...@univie.ac.at> wrote:
> Dear Frank,
>
> pdb_redo webserver does. However you have to cheat to provoke it: The
> resolution remark in the PDB has to be 0.10A beyond what it was used
> before. You can use also use the command line version of pdb-redo to tweak
> settings for your calculation (the expert option).
>
> However it would be nice to have the option also in ccp4 and phenix. Doing
> this without a script is painful.
>
> Br, Georg.
>
> Am 11/8/2018 um 17:52 schrieb Frank von Delft:
>
> Does any refinement software automatically do the CC* resolution
> exploration ("paired refinement") that Kay did in the original paper? Now
> that *would* be fantastically useful.
>
>
> On 08/11/2018 12:44, Pavel Afonine wrote:
>
> Clément,
> I'm guessing this is because it isn't clear what CCwork/CCfree can tell
> you that Rwork/Rfree can not. Needless to say we all more or less have a
> good idea about what the ok values for Rwork, Rfree and Rfree-Rwork (as
> function of resolution) while it is much less clear (to me at least) when
> it comes to CCwork/CCfree.
> I think phenix.refine used to report CCwork/CCfree in some releases but I
> removed it as useless.
> All the best,
> Pavel
>
> On Thu, Nov 8, 2018 at 8:16 PM Clement Degut <
> 000026de0a160250-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Hi all,
>>
>> This probably have already be discussed, but can't find trace of it :
>> Is there any reason I am not aware of that refinement software (thinking
>> of both phenix and refmac) do not output CC work / free ?
>> We all accepted CC 1/2 for resolution cut (whether it's 30 or 10 %) which
>> tend to lead to high Rfree ( last shells having very poor phases), at least
>> high overall R free in regard to the majority same resolution structures as
>> they been refined with I/sig > 3.
>> Which in return push people to cut resolution AFTER refinement which
>> obviously drastically decrease the R free and catapult your structure from
>> worst of the PDB to best of the PDB. It should never be done but it is
>> nonetheless.
>> How to blame a "non expert" to do that when changing the resolution from
>> 1.49 to 1.5 change your Rfree by 2% (yes it exaggerated but you get the
>> idea).
>> Now it seems to me -but I may be very wrong as I am far from expert in
>> the arcane math of these- that CC work and free would be more agnostic to
>> this resolution cut off problem, as we compare it to the CC* value anyway ?
>> thought it will never start to be used if refinement software don't output
>> it as a standard (not talking about completely replacing Rfree here as it
>> is obviously useful).
>> Would CC work/free be a bad appreciation of the refinement process ?
>>
>> Thanks
>>
>> Clément
>>
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