[phenixbb] Target function for refinement in case of Pseudo-translational symmetry

Varun Bhaskar varun.rsb at gmail.com
Mon Sep 29 04:38:45 PDT 2014


I collected a dataset for a binary complex (72kDa size) to 3.62A resolution
which could be processed in P32 2 1 space group.  Data quality analysis
with phenix.xtriage showed a presence of Pseudotranslational symmetry
(Non-origin peak in the patterson with 60% intensity  at 0.33, -0.33,
-0.013). I determined the structure with MR. I have 6 copies in ASU. I
tried Zanuda for SG validation and this looks like the right space group.

For refinement when I use Maximum likelihood (ML) as the target function,
my Rfactor/Rfree is around 31.3/32 but when I change it to Least square
(LS) my Rfactor/Rfree drops to 27.3/29.8. The map quality after ML or LS
refinement looks  very similar for most of the molecule, except for few
places where the map from ML has slightly better features.

I read people use LS instead of ML only in the case of twinning but I am
not sure if it could also be used in the case of PST.  Would the use of LS
as the target function for refinement be right in this case?

Thanks in advance

Best Regards
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