[phenixbb] Only one solution in AutoMR with very negative LLG

Edward A. Berry BerryE at upstate.edu
Wed Mar 16 11:06:29 PDT 2011

Zhang yu wrote:
> Yes, I rescaled my data to C2 (186.38, 103.16, 295.88,  90.00, 98.79,
> 90.00), and AutoMR found a solution. After refinement, the R went down
> to ~0.38, and the electron density fits well with my model except some
> flexible parts. Although there is a small crash between symmetry related
> molecules, due to the flexible feature of that domain, I don't think it
> is a problem.
> But the index confused me a lot. When I try to re-index my space group
> in HKL2000. The initial Index always suggests
> P1 (103.32, 185.24, 291.75, 97.55, 90.18, 90.48 )  Distortion Index  0.00%
> P2 (186.38, 103.16, 295.88,  90.00, 98.79, 90.00)  Distortion Index  0.22%
> (they are basically the same)
> while HKL2000 couldn't index the data to correct C2, the only C2 it
> found is
> C2 (592.23, 103.32, 185.24,  90.00, 97.52, 90.00) Distortion index 4.11%
> the unit cell looks twice bigger than current one, and it has quite
> unacceptable distortion index. It couldn't be refined. (Extremely high
> chi square and mosaicity)
> So, I just rescaled the integrated data (P2) to C2. The statistics of
> scale is OK, and there is no obvious violation.
> Could someone tell me why HKL2000 couldn't find the correct C2 SP?
I am confused also. Your C2 cell is the same as the P2 cell. Since operators other
than translation are the same in the two SG's it should scale as well in C2,
that doesn't prove anything.
But now half the spots that were predicted in P2 will be systematically absent.

If they are really absent, the space group could be C2 ("the observed pseudo
translationals are crystallographic"), but in that case denzo
would not have offered the primitive cell it did.

If they are very weak, it could be translational pseudosymmetry masquerading
as C2, but then the space group would be P2 or p2(1).


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