Good point, if you mis-assign a P2(1) space group as C222(1) because of
the twinning-generated apparent extra 2-fold symmetry then you could get
into such a situation.
If the P2(1) space group only has space for a monomer in the asymmetric
unit then Vm will point out the problem, but if the monoclinic cell
already has NCS then this can be tricky.
If the monoclinic cell has 2-fold NCS with pseudo-222 characteristics
then it may be almost impossible to detect twinning because the
twin-related reflections will be strongly correlated. As a result,
averaging the twin-related reflections will not affect the intensity
distribution and the twinning analysis will fail.
However, if the pseudo-symmetry deviates only slightly from
crystallographic symmetry, you may end up happily solving the structure,
with litle evidence that there even was a problem. The final structure
would be largely correct apart from areas where the pseudo-symmetry
deviates from true crystallographic symmetry.
Bart
Poul Nissen wrote:
> Check this paper below - a C222(1) space group (a=212, b= 300, c=575)
> frequently appearing as a merohedral twin P2(1) with apparent C222(1)
> symmetry was exactly a major problem in the H. marismortui 50S structure
> determination.
>
> Poul
>
> Ban N, Nissen P, Hansen J, Capel M, Moore PB, Steitz TA.
> <http://www.ncbi.nlm.nih.gov/pubmed/10476961?ordinalpos=6&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum>
> Abstract
> <http://www.ncbi.nlm.nih.gov/pubmed/10476961?ordinalpos=6&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum>
> Placement of protein and RNA structures into a 5 A-resolution map of the
> 50S ribosomal subunit.
> Nature. 1999 Aug 26;400(6747):841-7.
>
>
> On 03/04/2008, at 17.48, Bart Hazes wrote:
>
>> I just realized that this is an orthorhombic C222(1) space group. I
>> didn't check it up but unless two of the cell-dimensions are nearly
>> identical I think merohedral twinning is not possible for this space
>> group, because the symmetry of the unit cell shape is not higher than
>> the symmetry of the space group.
>>
>> Bart
>>
>> Eleanor Dodson wrote:
>>
>>> It is not really possible to detect twinning by the simple moment and
>>> cumulative distribution tests for data from a crystal with pseudo
>>> translation. As Bart says, twinning decreases the value of the
>>> moments, whilst pseudo-translation increases them, so the two effects
>>> tend to cancel out. There is a reference to the L test: J. Padilla &
>>> T. O. Yeates. A statistic for local intensity differences: robustness
>>> to anisotropy and pseudo-centering and utility for detecting
>>> twinning. /Acta Crystallogr./ *D59*, 1124-30, 2003.
>>> <http://scripts.iucr.org/cgi-bin/paper?S0907444903007947>S They
>>> suggest using neighbouring reflections pairs to test . This can
>>> often overcome the problem associated with pseudo-translation.
>>> However it is quite sensitive to data quality.
>>
>>> See http://nihserver.mbi.ucla.edu/pystats/
>>
>>> Eleanor
>>
>>> Bart Hazes wrote:
>>
>>>> Hi Qiang,
>>
>>>>
>>>> A normal data set has a unimodal intensity distribution with a
>>>> predictable shape. When there is twinning the distribution remains
>>>> unimodal but becomes sharper and this is picked up in the twinning
>>>> analysis. When there is pseudo-translational symmetry, as you
>>>> indicate you have, then the intensity distribution becomes bimodal
>>>> with one set of reflections systematically strengthened and another
>>>> systematically weakened. This makes the whole distribution broader,
>>>> just the opposite of what twinning does, and therefore shows up as
>>>> "negative twinning" in the analysis.
>>
>>>>
>>>> Bart
>>
>>>>
>>>> Qiang Chen wrote:
>>
>>>>
>>>>> Hi all,
>>
>>>>>
>>>>> The data I am working on has a strong translation vector. The space
>>>>> group
>>
>>>>> is C2221 and resolution is 2.3 angstrom. There are two molecules per AU
>>
>>>>> with a pseudo-2-fold axis.
>>
>>>>> On the cumulative intensity distribution plot, the theor and obser
>>>>> curves
>>
>>>>> totally do not overlap. I did "detect_twinning" from CNS, and there
>>>>> is the
>>
>>>>> result:
>>
>>>>>
>>>>> <|I|^2>/(<|I|>)^2 = 3.2236 (2.0 for untwinned, 1.5 for twinned)
>>
>>>>> (<|F|>)^2/<|F|^2> = 0.6937 (0.785 for untwinned, 0.865 for twinned)
>>
>>>>> Does the result mean my data is not twinned?
>>
>>>>>
>>>>> Any suggestion will be highly appreciated.
>>
>>>>> Thank you!
>>
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>>>>>
>>>>
>>>>
>>
>>
>> --
>>
>> ==============================================================================
>>
>> Bart Hazes (Assistant Professor)
>> Dept. of Medical Microbiology & Immunology
>> University of Alberta
>> 1-15 Medical Sciences Building
>> Edmonton, Alberta
>> Canada, T6G 2H7
>> phone: 1-780-492-0042
>> fax: 1-780-492-7521
>>
>> ==============================================================================
>>
>
--
=============================================================================
Bart Hazes (Assistant Professor)
Dept. of Medical Microbiology & Immunology
University of Alberta
1-15 Medical Sciences Building
Edmonton, Alberta
Canada, T6G 2H7
phone: 1-780-492-0042
fax: 1-780-492-7521
=============================================================================
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