Maybe it is worth recalling some ancient discussions, involving Real
Space R factors as defined by Alwyn Jones and Gerard Kleywert.
If I remember properly, they give an "Rfactor" between the density in an
ATOMMAP generated from a model, but with truncated B factors and the
density in the map underconsideration - an exptly phased one, a 2mFO
-DFC or whatever.
This requires that the electron densities are more or less on the same
scale, and gave good Real Space R factors for atoms with low B factors,
and high ones for wrong residues, disordered residues, and those with
high B factors
The CC is meant to avoid problems of scale - the ATOMMAP is calculated
taking the b factors into account, so gives a reasonable CC for
correctly placed atoms with high b factors. However theoretically a
residue with occupancies =0.00 which lies in a totally empty part of the
map under consideration could still give a resonable CC .
As Pavel says, it is a very blunt tool which can mislead but also help
you pinpoint errors.. I have found it most useful when trying to select
the best phasing procedure..
Eleanor
Pavel Afonine wrote:
> Hi Hailiang,
>
> On 5/25/10 8:14 PM, Hailiang Zhang wrote:
>> Have seen the real-space correlation used widely judging the map quality.
>> Generally or empirically, in order to say an map (area) has "good"
>> quality, how large should the real space correlation coefficient be? Say,
>> is 0.8 good enough on a residue base? Any references about this will be
>> greatly appreciated!
>
> why don't you just familiarize yourself with the map CC values computed
> per atom or per residue, for a few different structures at different
> resolutions? It might take you a few hours but from that point on you
> will have some reference between the map CC values and actual map
> appearance. phenix.model_vs_data or phenix.real_space_correlation can
> compute all these values for you.
>
> I did it at some point to educate myself and never regretted about the
> time I spent doing this -:)
>
> Pavel.
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