[phenixbb] Does PHENIX exclude Rfree reflections in maps?

Edward Berry BerryE at upstate.edu
Fri Oct 2 21:37:44 PDT 2009

Joe Krahn wrote:

> For density modification, it may be possible to converge on a good map 
> if both missing and test reflections use "Fcalc" fill-in values from the 
> previous density-modified transformation. Maybe the people who could not 
> get good results without the test reflections used a DM method that 
> reset missing values to zero on every cycle.

Those suggestions would be supported by results in:
Rayment, I.  Molecular replacement method at low resolution: optimum 
strategy and intrinsic limitations as determined by calculations on 
icosahedral virus models. Acta Crystallogr. A 39, 102–116 (1983).
(Perhaps this is the paper B. Shaanan was thinking of?)

The authors used what is now called "fill-in" for the missing
reflections, and they also tried intentially omitting reflections
and using the fillin (Fcalc) values at each cycle. They found when this 
was done the resulting F's approached the actual unused experimental
values with cycles of averaging.  If they did not fillin the missing 
values the averaging suffered, because in effect they were forcing those
reflections to zero.


NCS averaging can be seen as a numerical method for solving the M.R.
equations, i.e. finding a set of phases that is consistent with the
observed amplitudes and the known symmetry.  NCS averaging with 5%
of reflections omitted is finding a set of phases consistent with the
known symmetry and observed working reflections *AND* with all of the
free refections having amplitude zero (which is probably not the set of
phases you want).

For example suppose you started with perfect data and perfect phases,
and agreement with the NCS operators is very good. Now you make a 2Fo-Fc
map with the test set omitted, i.e. replaced by zero. The missing sine
waves do not in general obey the NCS, so each omitted one introduces
asymmetry in the map-to-be averaged. Averaging then restores the
symmetry, but with slightly different density values. Fc for the next
round is calculated from the averaged map, and the omitted reflections
will in general have non-zero value. If these Fc values are taken for
the next round, by fill-in, they may eventually converge to the true
values and the map will be correct. If they are rezeroed at each round,
the only way for the process to restore symmetry is by modifying the
phases of all the other reflections to obtain a symmetrical density wich
is different from the correct one obtained with all the reflections.

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