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
<mailto: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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