On Tue, 10 Jul 2018 22:08:48 +0100, Eleanor Dodson
wrote:
...
> In general if you have NCS your Free R
>values tend to be lower than expected..
>Eleanor
>
... and with tNCS, the Rwork / Rfree values tend to be higher than expected.
Kay
FreeR flags are a bit of a pain - there is the number you should select,
then how to compensate for non-crystallographic symmetry and putative
twinning.
Vilmos has written a useful Rfree assignment tool which covers possible
twinning problems. It selects FreeR flags for the highest Laue symmetry
I’ll also add for completeness, that (in Phenix at least) by default a total of
2000 reflections will be selected at most - meaning if you have a lot of
reflections the total percentage selected will be substantially less than 10%
or even 5%.
> On Jul 10, 2018, at 7:44 AM, Pavel Afonine
It's important to remember that free-R reflections are not only used to
calculate Rfree, but also are used in calculation of m and D scales in
2mFo-DFc and mFo-DFc maps, as well as in likelihood-based refinement
targets. The fact is that you need to have a sufficient amount of free-R
reflections
and calculates the average R-free and R-complete if your test set
cannot be made larger than 500 reflections.
Cheers,
Robbie
> -Original Message-
> From: CCP4 bulletin board On Behalf Of ???
> Sent: Tuesday, July 10, 2018 10:03
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb
The precision or significance of rfree depends on the number of reflections
used to calculate it. No fixed rule for percentage exists. Tickle & Brunger
have elaborated on this. References pp 625 in bmc. Depending on how many
data overall you have and can set aside, for an overall rfree uncertainty
Dear all
I am confusing the choose of free R-flags recently. Rfactor means calculatted
from reflection not used in refinement,so what's big the difference between
different percentage of R-flags,like it's about 5% in ccp4 -refmac, while it is
10% in phenix-refinement,what's the difference
