Hi, Peter,
I have tried to carry out MR in P3. It turned out that P31 is the right one.
After MR, I refined it
using Phenix.refine with or without twin law. The result is as following:
Twin law R Rfree
Twin fraction in phenix.refine
None 0.3869
0.4080 none
-h,-k,l 0.2828
0.3584 0.16
h,-h-k,-l 0.2829
0.3575 0.50
-k,-h,-l 0.2833
0.3587 0.15
(The structure was refined against dataset @20.0~2.8 A)
I am wondering why there is no difference under different twin laws. How can
I determine the
real twin law and the real twin fraction? Thanks very much.
best regards,
Yingjie
On Thu, Oct 16, 2008 at 9:42 PM, Peter Zwart <[EMAIL PROTECTED]> wrote:
> if possible try and solve it in P3(n) and take it from there.
>
> This data you show now might be 'overmerged'.
> Also, the fact that the data is twinned doesn't really matter at this
> point. The most important bit is to get the space group right, or at
> least not too high so you can solve it.
> When the spacegroup is too low, model information can be very helpfull.
>
> Peter
>
>
>
>
>
> 2008/10/16, Eleanor Dodson <[EMAIL PROTECTED]>:
> > People dont read the CCP4 documentation on twinning! Grrr
> > PG P3 can have 3 twinning operators; and these are:
> > k,h,-l ( or symm equiv) - if this is a crystallographic operator the PG
> > becomes P321
> > -h,-k,l (or symm equiv) - if this is a crystallographic operator the PG
> > becomes P6
> > -k,-h,-l (or symm equiv if this is a crystallographic operator the PG
> > becomes P31 2
> >
> > The second moment test is not too badly affected if you get the PG wrong
> (
> > some centric reflections are flagged as acentric, but these are usually a
> > small % of the total)
> >
> > Neither is the l test, but this is easily disturbed by problems with
> the
> > data
> >
> > However the H-test, or the Britten test and some others look at
> > correlations between possibly twinned intensities, and there if you have
> the
> > wrong point group, they can be very misleading..
> >
> > From the information you have provided I would guess the PG is P321 but
> I
> > need the TRUNCATE plots to be happy about saying that; they give some
> > feeling for data quality.
> > Eleanor
> >
> >
> > Yingjie Peng wrote:
> >
> > > Hi,
> > >
> > > I tried to processed it as P321. It seemed that it might be right. The
> > > Rmerge increased
> > > just a little. Then I used phenix.xtriage and sfcheck to check it. The
> > > results are as following:
> > >
> > > phenix.xtriage:
> > >
> > > Twinning and intensity statistics summary (acentric data):
> > >
> > > Statistics independent of twin laws
> > > - <I^2>/<I>^2 : 2.084
> > > - <F>^2/<F^2> : 0.827
> > > - <|E^2-1|> : 0.666
> > > - <|L|>, <L^2>: 0.400, 0.227
> > > Multivariate Z score L-test: 9.082
> > > The multivariate Z score is a quality measure of the given
> > > spread in intensities. Good to reasonable data are expected
> > > to have a Z score lower than 3.5.
> > > Large values can indicate twinning, but small values do not
> > > necessarily exclude it.
> > >
> > >
> > > Statistics depending on twin laws
> > >
> > -----------------------------------------------------------------
> > > | Operator | type | R obs. | Britton alpha | H alpha | ML alpha |
> > >
> > -----------------------------------------------------------------
> > > | -h,-k,l | M | 0.461 | 0.102 | 0.065 | 0.022 |
> > >
> > -----------------------------------------------------------------
> > >
> > > Patterson analyses
> > > - Largest peak height : 4.288
> > > (corresponding p value : 0.98768)
> > >
> > >
> > > The largest off-origin peak in the Patterson function is 4.29% of the
> > > height of the origin peak. No significant pseudotranslation is
> detected.
> > >
> > > The results of the L-test indicate that the intensity statistics
> > > are significantly different than is expected from good to reasonable,
> > > untwinned data.
> > > As there are twin laws possible given the crystal symmetry, twinning
> could
> > > be the reason for the departure of the intensity statistics from
> > normality.
> > > It might be worthwhile carrying out refinement with a twin specific
> target
> > > function.
> > >
> > >
> > > sfcheck:
> > >
> > > Pseudo-translation is not detected.
> > > Minimal estimated error : 0.0864
> > >
> > > Perfect twinning test <I^2>/<I>^2 : 2.0191
> > >
> > > Partial Twinning test:
> > > -h,-k,+l
> > > Polar angles: 0.00 0.00 180.00
> > > Alpha(twin fraction),Npair,Ior,Tol : 0.148 118812 2 0.000
> > >
> > >
> > > Then, what should I do? I did not deal with any twinning dataset. Any
> > > comments and suggestions
> > > will be greatly appreciated. Thanks!
> > >
> > > Yingjie
> > >
> > >
> > >
> > > On Thu, Oct 16, 2008 at 12:24 AM, Eleanor Dodson
> > <[EMAIL PROTECTED]>wrote:
> > >
> > >
> > >
> > > > I should have said - most likely explanation is point group is reall
> > P321
> > > >
> > > > Eleanor
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > > 2008/10/15, Eleanor Dodson <[EMAIL PROTECTED]>:
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > > I cant follow this very well.
> > > > > > Try SFCHECK as well which will do the same tests and give a
> > differently
> > > > > > formatted output..
> > > > > > or TRUNCATE which gives you plots of these stats v resolution..
> > > > > >
> > > > > > <I^2>/<I>^2 : 2.351 This is higher than the expected value of 2
> > for
> > > > > > untwinned data. (1.5 for perfectly twinned data)
> > > > > > However it can be distorted by non-crystallographic translation,
> > but you
> > > > > > dont seem to have that..
> > > > > > Or by experimental errors and you need to inspect it in
> resolution
> > > > > > ranges
> > > > > > to detect that - assuming your low res data is more accurate than
> > the
> > > > > > high
> > > > > > res.
> > > > > >
> > > > > > Eleanor
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > Yingjie Peng wrote:
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > > Dear guys,
> > > > > > >
> > > > > > > I have collected a dataset with the sg as P31. I ran
> > pehnix.xtriage to
> > > > > > > analyse the data with
> > > > > > > following result:
> > > > > > >
> > > > > > > Twinning and intensity statistics summary (acentric data):
> > > > > > >
> > > > > > > Statistics independent of twin laws
> > > > > > > - <I^2>/<I>^2 : 2.351
> > > > > > > - <F>^2/<F^2> : 0.788
> > > > > > > - <|E^2-1|> : 0.766
> > > > > > > - <|L|>, <L^2>: 0.446, 0.270
> > > > > > > Multivariate Z score L-test: 3.358
> > > > > > > The multivariate Z score is a quality measure of the given
> > > > > > > spread in intensities. Good to reasonable data are expected
> > > > > > > to have a Z score lower than 3.5.
> > > > > > > Large values can indicate twinning, but small values do not
> > > > > > > necessarily exclude it.
> > > > > > >
> > > > > > >
> > > > > > > Statistics depending on twin laws
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > ------------------------------------------------------------------
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > > | Operator | type | R obs. | Britton alpha | H alpha | ML
> alpha |
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > ------------------------------------------------------------------
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > > | -h,-k,l | M | 0.460 | 0.043 | 0.039 | 0.022
> |
> > > > > > > | h,-h-k,-l | M | 0.054 | 0.423 | 0.459 | 0.478
> |
> > > > > > > | -k,-h,-l | M | 0.476 | 0.042 | 0.043 | 0.022
> |
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > ------------------------------------------------------------------
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > > Patterson analyses
> > > > > > > - Largest peak height : 4.693
> > > > > > > (corresponding p value : 0.95672)
> > > > > > >
> > > > > > >
> > > > > > > The largest off-origin peak in the Patterson function is 4.69%
> of
> > the
> > > > > > > height of the origin peak. No significant pseudotranslation is
> > detected.
> > > > > > >
> > > > > > > The results of the L-test indicate that the intensity
> statistics
> > > > > > > behave as expected. No twinning is suspected.
> > > > > > > Even though no twinning is suspected, it might be worthwhile
> > carrying
> > > > > > > out
> > > > > > > a refinement using a dedicated twin target anyway, as twinned
> > structures
> > > > > > > with
> > > > > > > low twin fractions are difficult to distinguish from
> non-twinned
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > structures.
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > > The correlation between the intensities related by the twin law
> > > > > > > h,-h-k,-l
> > > > > > > with an
> > > > > > > estimated twin fraction of 0.42 %
> > > > > > > is most likely due to an NCS axis parallel to the twin axis.
> This
> > can be
> > > > > > > verified by
> > > > > > > supplying calculated data as well.
> > > > > > >
> > > > > > >
> > > > > > > Is it perfect twinning or partial twinning? I am supposed to do
> MR
> > with
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > this
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > > dataset.
> > > > > > > What should I do next with this dataset? Thanks very much.
> > > > > > >
> > > > > > > Best regards,
> > > > > > >
> > > > > > > Yingjie
> > > > > > >
> > > > > > >
> > > > > > > Yingjie PENG, Ph.D. student
> > > > > > > Structural Biology Group
> > > > > > > Shanghai Institute of Biochemistry and Cell Biology (SIBCB)
> > > > > > > Shanghai Institute of Biological Sciences (SIBS)
> > > > > > > Chinese Academy of Sciences (CAS)
> > > > > > > 320 Yue Yang Road, Shanghai 200031
> > > > > > > P. R. China
> > > > > > > 86-21-54921117
> > > > > > > Email: [EMAIL PROTECTED]
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > > >
> > > > >
> > > >
> > > >
> > >
> > >
> > >
> >
>
>
> --
> -----------------------------------------------------------------
> P.H. Zwart
> Beamline Scientist
> Berkeley Center for Structural Biology
> Lawrence Berkeley National Laboratories
> 1 Cyclotron Road, Berkeley, CA-94703, USA
> Cell: 510 289 9246
> BCSB: http://bcsb.als.lbl.gov
> PHENIX: http://www.phenix-online.org
> CCTBX: http://cctbx.sf.net
> -----------------------------------------------------------------
>
