On Wednesday, 13 May, 2015 18:17:04 Chen Zhao wrote:
> Hi Ethan,
Sorry, I'm coming in late on this so I might have missed an
earlier explanation of exactly what programs are involved.
> Yes. My question was simply whether it calculates the statistics
^^^^
> from completely unmerged intensities and just compare say h,k,l with -h,-k,l
> (or -h,-k,-l and h,k,-l) if there is a 2-fold? Although I believe so...
What is "it"?
If you mean the tables in IDXREF.LP, they only report the fit of points
to a particular lattice. They do not compare the intensities of
potential symmetry mates. Quoting from the program output:
Note, that reflection integration is based only on orientation and metric
of the lattice. It does not require knowledge of the correct space group!
Thus, if no such information is provided by the user in XDS.INP,
reflections are integrated assuming a triclinic reduced cell lattice;
the space group is assigned automatically or by the user in the last
step (CORRECT) when integrated intensities are available.
If you mean the output from a later run of pointless/aimless,
so far as I know it applies the symmetry operation being tested
to all reflections, which means that Friedel/Bijvoet pairs are
not compared. But I could be wrong on that point.
> And what is a good number? Is 20 % OK? What about 30 % and even higher?
Still refering to output from pointless/aimless, the crucial point is not
the absolute number but rather how the agreement for the symmetry operation
being tested compares to the agreement for the identity operation.
For example, here is the output for a lousy data set with a real 2-fold:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Scores for each symmetry element
Nelmt Lklhd Z-cc CC N Rmeas Symmetry & operator (in Lattice
Cell)
1 0.806 6.97 0.70 17852 0.516 identity
2 0.919 7.67 0.77 21302 0.486 *** 2-fold k ( 0 1 0) {-h,k,-l}
[snip]
Laue Group Lklhd NetZc Zc+ Zc- CC CC- Rmeas R- Delta
ReindexOperator
1 P 1 2/m 1 *** 0.919 7.30 7.30 0.00 0.73 0.00 0.50 0.00 0.1
[-h,-l,-k]
2 P -1 0.081 -0.69 6.97 7.67 0.70 0.77 0.52 0.49 0.0
[h,-k,-l]
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
In this case the program reports a 0.91 likelihood that the Laue
group is P2 even though the Rmeas is horrible.
Ethan
> Thanks a lot,
> Chen
>
>
> > On May 13, 2015, at 6:07 PM, Ethan A Merritt <merr...@u.washington.edu>
> > wrote:
> >
> >> On Wednesday, 13 May, 2015 17:51:59 Chen Zhao wrote:
> >> Hi all,
> >>
> >> I am sorry about this question which I should have figured out earlier. For
> >> point group determination, does the Rmeas consider Fridel pairs
> >> differently?
> >
> > A Friedel pair consists of the [hkl] and [-h-k-l] reflections.
> > This pairing is independent of space group.
> > So the agreement or lack of agreement between Friedel pairs is
> > not informative about selection of point group or space group.
> >
> > You may be thinking of a Bijvoet pair, which consists of
> > [hkl] and the Friedel mate of some symmetry equivalent of [hkl]
> > within a particular spacegroup.
> >
> > But even in the presence of anomalous scattering I think that
> > Bijvoet pairs are expected to agree with each other better than
> > with a reflection not related by point group symmetry.
> >
> >> (although I think it should be...) This is because I saw a
> >> derivative dataset collected at peak (from a demo) whose Rmeas is quite
> >> high (>50 %) for all the space groups tested (including P1). However, the
> >> native dataset has only <10 % Rmeas. Should I worry about the derivative
> >> dataset? There seems to be multiple lattices in both datasets based on
> >> IDXREF.
> >>
> >> You inputs are really appreciated!
> >>
> >> Sincerely,
> >> Chen
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
