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If you are lucky enough to have 4-fold NCS, then you can carry out 4-fold
iterative NCS averaging which should allow you to get a superb map in
which to build an initial model.
The procedure works well for molecular replacement phases AS LONG AS you
use the MR phases once and only once (to compute an initial e.d. map) and
do not use them afterwards (i.e. no phase recombination).
This is what I would do first. Perhaps even (your twinning fraction is
quite high and the resolution low) only real space refinement in the
4-fold averaged map.
Fred.
On Wed, 27 Sep 2006, Veronica Tamu Dufe wrote:
> Dear All
> I have a twinned data with a twin fraction of 0.467549. The resolution of the
> data is 3?. I have a molecular replacement solution from phaser and assigned
> the free R reflections using thin shells in shelxpro.
> Since I have 4 molecules per asu, I thought that refining it with the NCSY
> command in shelxl could circumvent the low resolution as suggested in the
> shelxl manual.
> I did a rigid body refinment with BLOC 1, AFIX 6 and AFIX 0 (after each
> chain). TWIN matrix and BASF using LS and removing the BUMP.
> I get the following :
> R1 = 0.3850
> Rfree = 0.4197
> wR2 = 0.7337
> for all data.
> When I do restraint refinement (ie coordinates and isotropic B-factors) using
> CGLS, removing the AFIX and BUMP, reducing the SIMU, and DEFS values I get a
> large difference (20) between Rfree and R1 indicating that the data is being
> overfitted. Using the default values for SIMU and DEFS does not help.
>
> Has anybody succeded in refining twinned data to this low resolution with
> shelxl and how can I get it to work in my case considering that I will use
> NCS?
> Thank you all in advance
> Veronica
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