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.
