[phenixbb] right symmetry?

[Gabriela Guédez]

Hi Peter,

the maps are not so diffrent in p31 or p61.

L-test doesnt show twinning in p31 and the RvsR stats says it is not the
right symmetry.

The r-values I showed you before were calculated in rigid body refmac5.

The free r was assigned with freeRflag 5%. I used the command “
phenix.reflection_file_converter “ to create mtzs readable in phenix.

Now, i reran new refinements in phenix with the command phenix.refine my.mtz
my.pdb strategy=rigid_body selections.params twin_law=”” to compare with
refmac and now I get r-values with 1-2% different in all tested space
groups:

p6122 R = 0.3644, Rf = 0.3750
p61     R = 0.3546, Rf = 0.3527
p61     R = 0.3413, Rf = 0.3412 twin
p31     R = 0.3318, Rf = 0.3342 twin

p3121 R = 0.3584, Rf = 0.3494 twin

I should point out the point group of the molecule is 622, the same as the
lattice symmetr, could it be some ncs operators are being misespecified as
crystallographic giving rise to the high symmetry?... isit twinning along z
as you said and the 2-fold NCS is considered crystallographic?

Thanks again,

Gabriela








On Tue, Jan 5, 2010 at 3:49 PM, Peter Zwart <phzwart at gmail.com> wrote:

> my bet would be p31 twinned (i guess along the z axis, right?).
> your model needs some work though ....
>
> How did you choose a free r set? I hope phenix did it for you.
>
> P
>
>
>
> 2010/1/5 Gabriela Guédez <gguedez at gmail.com>:
> > Hi Peter,
> >
> > thanks.
> >
> > here the Rvalues after rigid body refmac:
> >
> >                   R          Rfr
> > P6122      0.371    0.377
> > P61          0.361    0.369
> > P31          0.337    0.338  twin
> > P3121      0.376    0.378  twin
> > P321        no solution
> >
> >
> > Now, RvsR stats in P3121 are as following:
> >
> > R_abs_twin observed data   : 0.155
> > R_abs_twin calculated data  : 0.372
> >
> > "Twins with RPS" (Lebedev, Vagin, Murshudov 2006, Acta Cryst. D62,83-95).
> >
> > But the refinement doesnt look better than P31.
> >
> > Thanks again. Cheers,
> >
> > Gabriela
> >
> >
> > On Sat, Jan 2, 2010 at 5:45 PM, Peter Zwart <phzwart at gmail.com> wrote:
> >>
> >> Hi Gabriela,
> >>
> >> Can you give us some more info? What are the excat r-values in all space
> >> groups?
> >>
> >> How does the refinement in p321 or p312 look?
> >>
> >> Cheers,
> >>
> >> Peter
> >>
> >>
> >> 2010/1/2 Gabriela Guédez <gguedez at gmail.com>:
> >> > Hi Phenixbb,
> >> >
> >> > I have a data that indexes in P6122, also P61 and P31. Data analysis
> in
> >> > phenix.xtriage says no twinning is suspected according to the L-test.
> >> >
> >> > However, after MR and twin RB refinement, the model improves from
> P6122
> >> > or
> >> > P61 to P31 5% Rfacs and 0.5 the FOM.
> >> >
> >> > I thought the data might have RPS and twinning not detected with the
> >> > L-test.
> >> > So, i ran xtriage to compute the RvsR statistics using the
> >> > obs_and_calc.mtz
> >> > file and the results were:
> >> >
> >> >
> >> > in P61
> >> > R_abs_twin observed data   : 0.112
> >> > R_abs_twin calculated data : 0.047
> >> >
> >> >
> >> > in P31
> >> > R_abs_twin observed data   : 0.117
> >> > R_abs_twin calculated data : 0.139
> >> >
> >> > "misespecified crystal symmetry", according to Lebedev, Vagin,
> Murshudov
> >> > et
> >> > al 2006, Acta Cryst. D62,83-95.
> >> >
> >> > I would like to know a test that tells me the right symmetry.
> >> >
> >> > I appreciate your help. Thanks,
> >> >
> >> > Gabriela
> >> >
> >> > _______________________________________________
> >> > phenixbb mailing list
> >> > phenixbb at phenix-online.org
> >> > http://phenix-online.org/mailman/listinfo/phenixbb
> >> >
> >> >
> >>
> >>
> >>
> >> --
> >> -----------------------------------------------------------------
> >> 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
> >> -----------------------------------------------------------------
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> >
> >
> >
> > --
> > ----------------------------------------------------------------------
> > Gabriela Guédez R.
> > gabriela.guedez at bzh.uni-heidelberg.de
> >
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
> >
> >
>
>
>
> --
> -----------------------------------------------------------------
> 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
> -----------------------------------------------------------------
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>



-- 
----------------------------------------------------------------------
Gabriela Guédez R.
gabriela.guedez at bzh.uni-heidelberg.de
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