[phenixbb] right symmetry?

[Peter Zwart]

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
>> >
>> > _______________________________________________
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>> > 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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> 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
-----------------------------------------------------------------