[phenixbb] output of labelit.check_pdb_symmetry

"Weiergräber, Oliver H." o.h.weiergraeber at fz-juelich.de
Thu Jul 12 08:44:14 PDT 2012


I am using labelit.check_pdb_symmetry in order to evaluate a crystal structure with sg P21 (2 copies/asu) and all angles indistinguishable from 90 degs for potential higher (i.e. orthorhombic) symmetry. Comparison of refinement statistics clearly indicates that the most likely scenario is perfect pseudomerohedral twinning of a true P21 crystal (Rfree=0.21). Accordingly, labelit.check_pdb_symmetry reports a striking discrepancy between Rsymop(Iobs) and Rsymop(Icalc): 8 % vs 31 %, i.e. there is an additional (apparent) 2-fold symmetry in the data which cannot be explained by the model.
In an attempt to force a solution for comparison and visualization purposes, I have increased the r_symop_tol parameter to 0.35; the program starts to evaluate possible space groups with fTF, yielding scores (these are correlation coefficients, right?) way above 90 %. Still, in the end it reports there are no higher symmetry solutions.

Why is this? Does the program check for the contrast between the best solution and the others? Changing peak_cutoff to a "discriminative" value did not help...

Best regards,

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