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Re: [ccp4bb] twinned? |
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CCP4bb navigationCCP4bb <-- 2008 <-- April 2008 <-- 03 April 2008Subject: Re: twinned? From: Bart Hazes bart {- dot -} hazes {- at -} UALBERTA {- dot -} CA Date: 2008-04-03 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. > > Abstract > > 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. >>> >>> 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! >> >>>>> >>>>> The information transmitted in this electronic communication is >>>>> intended only >> >>>>> for the person or entity to whom it is addressed and may contain >>>>> confidential >> >>>>> and/or privileged material. Any review, retransmission, >>>>> dissemination or other >> >>>>> use of or taking of any action in reliance upon this information by >>>>> persons or >> >>>>> entities other than the intended recipient is prohibited. If you >>>>> received this >> >>>>> information in error, please contact the Compliance HelpLine at >>>>> 800-856-1983 and >> >>>>> properly dispose of this information. >> >>>>> >>>>> >>>> >>>> >> >> >> -- >> >> ============================================================================== >> >> 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 ============================================================================== CCP4bb navigationCCP4bb <-- 2008 <-- April 2008 <-- 03 April 2008 |
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