The default output for REFMAC
Missing Data: For those reflections where the FP are missing, mFo is set
equal to dFc. Hence the terms become FWT=dFC and DELFWT=0.0.
the Rfree reflections are counted as "missing" hence there shouldnt be
any bias intoroduced towards those Fobs assigned as free I dont think..
Of course all maps use the PhiCalc so there is inevitably bias towards
to current model..
eleanor
On 05/23/2011 11:03 PM, Pavel Afonine wrote:
Hailiang,
r-free reflections should not participate in refinement, regardless whether
it is real or reciprocal space one, done with machine driven minimizers or
your hands moving atoms in Coot. Period. The issue of correcting the
map appearance for missing data (resolution or completeness) is relevant but
different. Removing the data is noticeable, but most of the time putting
aside test set is not critical for map appearance (given that reflections
are selected randomly and do not exceed a reasonable fraction of available
data); and when it is critical, the cross validation should be done
differently anyway.
So the answer to your question is: every time you compute a map not just to
enjoy its appearance but to use it to improve your model, do not include
test flagged reflections into it.
Pavel.
On Mon, May 23, 2011 at 1:02 PM, Hailiang Zhang<[email protected]> wrote:
Hi,
I have a preliminary question. I understand Rfree reflection sets are
never used during automatic refinement, but, when generating the real
space density maps, do we have to exclude Rfree columns? Any references
will also be greatly appreciated!
Best Regards, Hailiang
