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
==============================================================================
