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<[log in to unmask]> 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
>>
>
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