[phenixbb] output of labelit.check_pdb_symmetry

Nicholas Sauter nksauter at lbl.gov
Thu Jul 12 10:44:35 PDT 2012


peak_cutoff only changes the tolerance on the fTF correlation coefficient;
however the program is probably still not finding a solution with a
reasonable weighted phase-difference score Phi(g).  The tolerance for
this (default=0.25) can be increased with the score_tol= command line
argument.  You can send me your output file offlist for a closer look.


On Thu, Jul 12, 2012 at 8:44 AM, "Weiergräber, Oliver H." <
o.h.weiergraeber at fz-juelich.de> wrote:

> Hello,
> 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,
> Oliver
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Nicholas K. Sauter, Ph. D.
Computer Staff Scientist, Physical Biosciences Division
Lawrence Berkeley National Laboratory
1 Cyclotron Rd., Bldg. 64R0121
Berkeley, CA 94720-8118
(510) 486-5713
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