[phenixbb] structure factor labels in phenix.refine

Nathaniel Echols nechols at lbl.gov
Fri Nov 8 09:59:57 PST 2013

On Thu, Nov 7, 2013 at 3:50 PM, Ryan Spencer <rspencer at uci.edu> wrote:

> I have found that phenix.model_vs_data does not deal well with a perfect
> twin data set. The refined data is:
>                 r_work=0.2013 r_free=0.2298 (in PDB file)
>                 r_work=0.2815 r_free=0.3006 (from phenix.model_vs_data)
> There is one merohedral twin operator: -h-k,k,-l (48%) and 6 very small
> (<1.0%) pseudo-merohedral twin operators.

Yes, the automatic twinning detection is one of the weak points of the
current Table 1 program (and the enhanced MolProbity validation in Phenix);
a more flexible approach will be available soon.  However, if you have a
case where you're certain the structure is twinned (and these R-factors do
support that hypothesis) but Phenix is missing it, we'd be interested in
seeing the model and data.  It may just be a limitation of the twinning,
but occasionally our code trips on corner cases, or it could be something
stranger misdiagnosed as twinning.

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