[phenixbb] refinement problem

[Nathaniel Echols]

On Tue, Sep 30, 2014 at 8:21 AM, Sneha Rangarajan <rsneha at umd.edu> wrote:

>  I have a 1.9A dataset for a single chain Fv-peptide complex that shows
> psedomerohedral twin operators in Xtriage (1 in p212121, 3 in p21 and 7 in
> p1).
>

Standard warning: don't worry about twin operators unless you have unusual
intensity statistics - the mere fact that your lattice is compatible with
twinning does not mean that anything is wrong.  What does the final verdict
in Xtriage say?  (By the way, the new version in the nightly builds
provides much clearer feedback.)

 Although most programs (in CCP4) identify the best SG to be p212121, MR
> cannot find a solution with p212121 due to packing clashes.
>

Although it's possible that you have pseudosymmetry, I think this is
ultimately the core problem - no matter what space group you try, the MR
solution is incomplete, and probably for the same reason.  My guess is that
the conformation of the search model is significantly different (either
locally or globally) than that of the crystallized molecule.  If it's a
homologous structure (not the same protein), try running Sculptor first to
trim off the parts that don't agree.  If it's the same protein, either try
cutting it into individual domains and searching for those, or trim off
extended loops manually.  I would use P212121 symmetry if possible, but it
doesn't hurt to try MR in all of the space groups for now.

If you want to send us the files separately to help at phenix-online.org, we
may be able to give a more specific answer.

-Nat
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