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Re: [ccp4bb] twinned? |
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CCP4bb navigationCCP4bb <-- 2008 <-- April 2008 <-- 03 April 2008Subject: Re: twinned? From: Poul Nissen pn {- at -} MB {- dot -} AU {- dot -} DK Date: 2008-04-03 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. 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. >> 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! >>>> >>>> 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 > > = > = > = > = > = > = > = > = > ====================================================================== > CCP4bb navigationCCP4bb <-- 2008 <-- April 2008 <-- 03 April 2008 |
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