[phenixbb] Twinning in data reduction and phenix.refine

Chen Zhao c.zhao at yale.edu
Fri Jul 11 08:15:11 PDT 2014

Dear all,

I am now dealing with a pseudo-merohedral twin (3.2 A, P1 twinned into C2),
and I have a couple of questions concerning the data reduction and

1) R-free flag in refinement
a) For twin refinement, I know the reflections related by the twin law
should have the same R-free flag. If I process my data in P1, and generate
the R-free flag by phenix.refine using the key word
xray_data.r_free_flags.use_lattice_symmetry=True, can phenix generate the
R-free flags considering the 2-fold point group symmetry and deal with the
twinning properly?
b) I read that the R-factor could go down to around 40% in twin refinement
in the presence of twinning even if the model is completely wrong. For my
understanding, this could be due to the fact that the reflections are
correlated by the twin law. If the R-free flags are chosen in the highest
lattice symmetry, will the R-free still suffer from this problem?

2) Twin fraction
In phenix.xtriage, the predicted twin fraction is about 30%. However, in
phenix.refine, the twin_fraction is always between 46% to 50%. Why could
this happen?

3) Data reduction
I am not very clear about this point, since I just started dealing
twinning. But what I am thinking is whether it is a good idea to merge the
Friedel pair in the presence of twinning. Since the two twin domains have
different hkl index if considering one as the reference, is the Friedel law
still valid? This might be a very simple mathematical problem.

I really appreciate your answers!

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