[phenixbb] Twinning Refinement

Nathaniel Echols NEchols at lbl.gov
Thu Mar 25 22:50:02 PDT 2010

On Mar 25, 2010, at 10:13 PM, Joseph Brock wrote:
> Shell Lower Upper Average      Average     Norm. Linear Square
>  limit    Angstrom       I   error   stat. Chi**2  R-fac  R-fac
>       50.00   4.09  7648.3  1498.7 182.7 1.030  0.376  0.424
>   All reflections   1588.3   269.2    41.9  1.350  0.400  0.444

Aside from what Peter said: aren't these R-sym values are far too high for the symmetry (or indexing) to be correct?  Or is this allowed when twinning is present?  If Scalepack is throwing away that much data, this is also telling you that something else is wrong.  I'd start back at the indexing step and re-process in P1, then follow the rest of Peter's suggestions starting from step 2.2 (MR).  Also, I'd recomment trying labelit.index (included in any Phenix distribution after 1.5) on the raw images, because it may notice something that the conventional indexing programs miss.

As a general rule, you can't always assume that the symmetry will always be the same from crystal to crystal - identical proteins may form completely different crystal lattices depending on crystallization condition or ligand binding or freak chance.


Nathaniel Echols
Lawrence Berkeley Lab
NEchols at lbl.gov

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