A handy way to do what Paul suggests is the Zanuda server at York
which will try refinement in all lower symmetries ...
From the first email though two things are unclear:
1. How good was the Phaser solution (eg z-score?) ?
2. Did you only try rigid body fitting as you wrote? (I find regid
body after Phaser frankly useless)
Anyway, what I would do would be to:
a. get the latest version of refmac before doing anything else, and do
full XYZB refinement, not rigid body, with tight NCS restraints
b. if that does not drop Rfree to say below 45%, submit to Zanuda to
check symmetry as Poul suggests - do that anyway in fact!
c. if zanuda gives lower symmetry, reprocess your data in lower
symmetry, run Phaser again, run refmac again, check for twining
Maybe I will go now on preaching the wrong gospel for this BB,
but Buster and/or Phenix are extremely useful at that resolution range.
I must say that Buster sometimes has been really impressive in our
hands.
A.
On 3 Oct 2010, at 9:09, Poul Nissen wrote:
Try a lower symmetry, e.g. P21 or P1 with one or two octamers in the
asymmetric unit (well, unit cell for P1), but you already know your
packing so no problem solving it.
It can sometimes be very subtle and your model refinement will be
the most sensitive test for the correct space group - so don't be
misled by seeming perfect scaling in orthorhombic.
Poul
On 03/10/2010, at 04.56, Jack Russel wrote:
Hi all,
I have collected a data at 2.9 Å and the solved the structure
using phaser . the space group comes to be P2 21 21. There are 4
molecules in Assymetric unit and an octamer is generated according
to the symmetry. But after repeated rounds of rigid body refinement
with REFMAC5 and model building with coot the R factor had been
struck at 40% and R free at 50%.
So my first question is whether my solution after phaser is
correct. And if it is how can i lower the R factor and Rfree.
The second question is it possible to have such a large difference
between R factor and R free.
Thanks in advance
