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

Pavel Afonine pafonine at lbl.gov
Mon Sep 29 08:36:30 PDT 2014

Hi Varun,

ideally this needs to be accounted for at the level of target function 
calculation, as explained here:
Intensity statistics in the presence of translational 
noncrystallographic symmetry. Read RJ, Adams PD, McCoy AJ. Acta Cryst. 
D69, 176-183 (2013).

In reality, this is not yet implemented for refinement.

It's not given that the minimum of ML coincides with the minimum of 
R-factor, so in general minimization of ML does not guarantee drop in 
R-factor, as explained here:


Also, the goal of ML-based refinement is not to obtain lowest R (as 
explained in link above).

I wonder what happens if after LS refinement you switch back to ML: do 
R-factors remain around 27.3/29.8 or they increase?


On 9/29/14 4:38 AM, Varun Bhaskar wrote:
> Hi,
> 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
> Varun
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