[phenixbb] twin axis for p21

Anastassis Perrakis a.perrakis at nki.nl
Tue Nov 25 23:42:54 PST 2008

Hi -

I admit I might be preaching the wrong gospel here, but the easiest  
thing to do in such cases
is to try Zanuba at the YSBL server. You did most things manually  
but giving to that web server the high symmetry data and model,
it will try systematically all other low symmetry choices and report  
back. Pretty much what
you have done but more systematically. Zanuba does not do twin  
refinement for now.

btw, I am not 100% confident, but I wonder if the twin fraction in the  
two out of three
P21 you are trying is around 50% which could be consistent with a real  
two fold in that case?
And the 'real' one less twinned?

Good luck !


On 26 Nov 2008, at 0:36, HUA YUAN wrote:

> Dear Colleagues,
> I'd like to share with you with a twinning puzzle that's been
> troubling me for a while.
> I have a ~2.2 A data merged in p212121 space group with unit cell:
> 41.8300  117.4490  134.4840   90.0000   90.0000   90.0000
> Translational NCS was detected but structure solution was able to be
> obtained by phased molecular replacement as we have a Au derivative
> data set. Obtaining experimental phase or MR alone didn't work.
> However, with this model and data set, the refinement didn't work
> (with R-free ~40% or higher if with more cycles).  Different twinning
> tests have been carried out and no sign of twinning.  All possible
> p222 space groups have been tried but no luck or even worse.
> Considering that translational symmetry and perfect twinning may make
> things deceiving, the data was merged into p21 and a twin-refinement
> was performed in phenix.refine.  After 3 cycles of rigid-body and
> group ADP, a R-free of ~30% was obtained and the output map looks OK.
> It looks like we got it.  But then things get interesting when we
> tested other two axis as the p21 unique axis.  With all the three
> choices plus corresponding twin-refinement, we could get a similar
> R-free (30%).  Besides, the three maps all look OK except for one
> missing some side chains.
> Then the structure was solve in p1 and Xtriage was used with the hope
> that one axis would stand out.  However, the RvsR for all three axis
> are almost the same.  Did I miss anything here?  Of course, we could
> pick up the one axis we like best and get the structure solved ^---^.
> However, this puzzle would eat me alive for a very long time.
> Best,
> Hua _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb

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