some comments below.
On Sat, 9 Jul 2016 09:40:25 -0400, wtempel <[log in to unmask]> wrote:
>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}
hmm I don't understand that. If SPACE_GROUP_NUMBER is 3, then the cell parameters are 37.7 126.2 40.7 90.0 117.7 90.0, and there is only one two-fold axis.
How come pointless finds three 2-folds ? The above looks what you get in Pmmm.
>
>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?
"3" gets selected ("*") because its number of unique reflections is lowest among those possibilities with Rmeas less than 2*8.6 . This is a very simple rule that often works well.
That Rmeas in "21" (C222) is 18.4 (i.e. significantly higher than 12.6) may be consistent with the fact that the refmac-assigned twin-ratio is high but not 0.5. If it were perfect twinning, then Rmeas should be as good in C222 as in P2.
>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?
I would assume that the twin fraction that the L-test suggests should be close to what refmac comes up with.
> 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?
sounds like a somewhat remote possibility to me; it at least requires that the DNA is straight and parallel to one of the cell axes.
best,
Kay
>
>
>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
>> >>
>> >
>>
>
|
