Re: [ccp4bb]: Monoclinic twinning?

["Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>]

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matthew.c.clifton.1 wrote:
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> 
> Hi all,
> I may have come across an example of monoclinic twinning in my data that
> appears to be orthorhombic.
> 
> The story:
> I am working on a MAD data set that appears to be in the space
> group P21221. However, upon running the data through SOLVE, the electron
> density maps are very difficult if not impossible to follow even though
> the data set was to 2.4 angstroms. I thought that I had the wrong space
> group and I proceeded to process the data as monoclinic.
> 
> During the indexing of the data as P2, a strange problem occurred. DENZO
> had problems with the identification of the correct lattice (they varied
> between data sets taken from the same crystal in the exact same
> orientation).
> 
> Example indexing in P2:
> Peak_minus data set 57.38 91.51 112.37 90 90.24 90
> Inflection_minus data set 91.53 57.4 112.36 90 90.24 90


  This isnt so strange - since the angles are all near 90 degrees, it is 
easy to choose any of the three as the unique two fold..
Since DENZO will not accept a "target" cell, you can easily get the 2nd 
data set indexed differently from the first.
There is a little ccp4 program axissearch which tabulates alternative 
reciprocal lattice lengths which you sometimes need to help decide on 
how to reindex, but here it is pretty obvious to change hkl to kh-l for 
the inflection.. Or as you say - select extra peaks and hope DENZO will 
find something consistent..
But why do you think the peak is correct and the inflexion not, rather 
than the other way round.

Twinning is something different - it can occur wherever there are two 
possible crystal axes of equal length.Often when it occurs in in 
monoclinic cells, a and a+c are almmost equal. But that doesnt seem to 
be the case here.
Can the data be processed equally well as Pmmm as for P2/m?

> 
> The data from the inflection wavelength could be "corrected" such that it
> found the same lattice as the Peak_minus data set by adding ~200 more
> peaks to the indexing, but it changed the unit cell parameters to:
> 57.15 91.36 111.06 90 91.04 90
> 
> Following this, I decided to investigate the possibility of twinning. I
> ran the data through the CNS program detect_twinning where it output the
> following information:
> <|I|^2> / (<|I|>)^2 = 1.6711 (average value over all bins, where 2.0 is
> untwinned and 1.5 is for twinned).
> (<|F|>)^2 / <|F|^2> = 0.8602 (average value over all bins, where 0.785 is
> untwinned and 0.865 is twinned).
> 
> When the data was processed through TRUNCATE, the Cumulative Intensity
> Distribution looked almost exactly like the example given on the CCP4
> website for a twinned crystal. The data appears to be clean with no large
> streaked reflections or the presence of a secondary lattice.
> 
> Is the data truly twinned? If so, how is this happening geometrically? (I
> am having a hard time drawing a picture of this). The only example I can
> find that is similar is an abstract from the bioinformatics-structure
> conference in Jerusalem, Israel from November 17-21, 1996 (HiPIP II
> structure to 1.7 angstroms resolution from a twinned monoclinic crystal).
> Any suggestions on how to proceed from here would also be helpful.
> 
> If not, why is all the data indicating that it may be twinned?
> 
> Any suggestions or input would be appreciated.
> 
> Thanks in advance,
> Matt
> 


  One thing you also need to consider is to look at the native 4A 
patterson - if there is a large off origin peak indicating a pseudo 
translation the cumulative intensity distribution can be misleading, 
although the moments will actually be higher than the normal 2, not lower.

>