First the stats for POINTLESS with XDS_ASCII.HKL (CORRECT with
SPACE_GROUP_NUMBER=
3):
Nelmt Lklhd Z-cc CC N Rmeas Symmetry & operator (in
Lattice Cell)
1 0.913 9.30 0.93 50862 0.039 identity
2 0.915 9.23 0.92 93951 0.045 *** 2-fold l ( 0 0 1) {-h,-k,l}
3 0.916 9.21 0.92 93677 0.050 *** 2-fold k ( 0 1 0) {-h,k,-l}
4 0.915 9.24 0.92 96828 0.045 *** 2-fold h ( 1 0 0) {h,-k,-l}
Interestingly, CORRECT.LP with SPACE_GROUP_NUMBER= 0 and unspecified
TEST_RESOLUTION_RANGE:
SPACE-GROUP UNIT CELL CONSTANTS UNIQUE Rmeas
COMPARED LATTICE-
NUMBER a b c alpha beta gamma
CHARACTER
5 72.0 37.7 126.2 90.0 90.1 90.0 1372 12.0
3617 39 mC
5 37.7 72.0 126.2 90.0 90.0 90.0 1325 13.0
3664 29 mC
1 37.7 40.6 126.2 89.9 90.0 62.4 2499 8.6
2490 31 aP
21 37.7 72.0 126.2 90.0 90.0 90.0 738 18.4
4251 38 oC
* 3 37.7 126.2 40.7 90.0 117.7 90.0 1303 12.6
3686 34 mP
1 37.7 40.6 126.2 90.1 90.0 117.6 2499 8.6
2490 44 aP
Why did xds prefer “3” over “5”, which has a lower Rmeas?
Jacob asked about the refmac-assigned twin ratio:
Twin operator: H, K, L : Fraction = 0.519; Equivalent operators: -H, K, -L
Twin operator: -H, -K, H+L: Fraction = 0.481; Equivalent operators:
H, -K, -H-L
Is it reasonable to compare these values with the L-test ratio? It may be
relevant that the crystal includes a significant (> 50% of macromolecular
non-H atoms) DNA double helix component. Could the DNA exert a
translational pseudo-symmetry effect on the intensity ratios and mask a
truly higher twin ratio?
On Sat, Jul 9, 2016 at 2:19 AM, Kay Diederichs <
[log in to unmask]> wrote:
> On Fri, 8 Jul 2016 17:14:42 -0400, wtempel <[log in to unmask]> wrote:
>
> >Hello all,
> >expanding this thread, and keeping Garib’s paper in mind, how would my
> >colleagues proceed in the following case:
> >1.8 Å data can can be merged in space group C2221 with an Rmeas of 5%. The
>
> it pays off to look very closely how well it can be merged. E.g. only if
> the twin fraction alpha is high (say, >0.4) you get the same good Rmeas in
> the apparent (wrong) high-symmetry space group as in the correct
> low-symmetry space group. For your low twin fraction, I would expect that
> merging in P21 gives a better Rmeas than in C2221. In case you use XDS,
> maybe you want to use higher resolution data to do that comparison - adjust
> TEST_RESOLUTION_RANGE ! Pointless automatically finds the appropriate
> resolution range for the comparison, and gives very detailed information
> about how well the data support each symmetry element. So please post here
> what you get - for a true orthorhombic crystal you should get something like
>
> *******************************************
>
> Analysing rotational symmetry in lattice group P m m m
> ----------------------------------------------
>
> <!--SUMMARY_BEGIN-->
>
> Scores for each symmetry element
>
> Nelmt Lklhd Z-cc CC N Rmeas Symmetry & operator (in
> Lattice Cell)
>
> 1 0.941 9.62 0.96 175778 0.054 identity
> 2 0.942 9.61 0.96 227697 0.053 *** 2-fold l ( 0 0 1) {-h,-k,l}
> 3 0.942 9.61 0.96 225738 0.053 *** 2-fold k ( 0 1 0) {-h,k,-l}
> 4 0.942 9.61 0.96 225139 0.053 *** 2-fold h ( 1 0 0) {h,-k,-l}
>
> In this case all symmetry operators are as good as the identity operator,
> so it is true crystallographic symmetry (or the twinning is perfect, but
> this is what the L-test would tell you).
>
> HTH,
>
> Kay
>
> >L-test suggests a twin ratio of 0.13 and Rwork/Rfree hover around
> 0.44/0.48
> >with an essentially complete structure. After expansion to P21, and
> >twin-aware assignment of free flags, Rwork/Rfree are 0.24/0.29 without and
> >0.19/0.26 with twin refinement in refmac. The coordinates do not differ in
> >any obvious way between runs with or without twin refinement. Is this
> >sufficient evidence to rule out C2221? If so, how would readers of this
> >discussion forum decide which, if any, should become the “model of
> record”:
> >refined with or without the twinning option.
> >With best regards,
> >Wolfram Tempel
> >
> >
> >On Wed, Jul 6, 2016 at 9:05 AM, Kay Diederichs <
> >[log in to unmask]> wrote:
> >
> >> On Wed, 6 Jul 2016 09:13:22 +0100, Randy Read <[log in to unmask]> wrote:
> >>
> >> >Dear Zbyszek,
> >> >
> >> >I agree completely with your general point that there is a trend for an
> >> increasing number of people to adopt too-low symmetry, rewarded by lower
> >> R-factors in twinned refinement.
> >>
> >> Dear Randy,
> >>
> >> I wish you had not used the word "rewarded" - for Germans at least, it
> has
> >> no ironic or pejorative connotation. I hope people do not understand
> this
> >> as if you were endorsing this unfortunate practice. There are already
> too
> >> many structures being twin-refined "because it reduces the R-factors"
> (and
> >> I fell into this trap as well before reading Garib N. Murshudov (2011)
> >> "Some properties of crystallographic reliability index - Rfactor:
> effect of
> >> twinning" Appl. Comput. Math., V.10, N.2, 2011, pp.250-261
> >> http://www.ysbl.york.ac.uk/refmac/papers/Rfactor.pdf ).
> >>
> >> best,
> >>
> >> Kay
> >>
> >
>
