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Re: [cnsbb] Can I refine 4-fold twinned data in cns?

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  • Jonathan Elegheert
    Hi Christine, maybe this is worth looking at if you want to solve it through CNS; /Acta Cryst./ (2005). D*61*, 613-621 /Escherichia coli/ MltA: MAD phasing and
    Message 1 of 3 , Oct 2, 2009
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      Hi Christine,

      maybe this is worth looking at if you want to solve it through CNS;

      /Acta Cryst./ (2005). D*61*, 613-621


      /Escherichia coli/ MltA: MAD phasing and refinement of a
      tetartohedrally twinned protein crystal structure

      The authors adapted the CNS 'data_detwin' module to account for the
      tetartohedral twinning. The modified files can be found in the IUCr
      electronic archive (http://journals.iucr.org/services/earchive.html ;
      reference: WD5026).

      This paper describes something similar and uses the files from the above
      paper;

      /Acta Cryst./ (2007). D*63*, 206-220


      Structure of triosephosphate isomerase (TIM) from
      /Methanocaldococcus jannaschii/

      This is a detwinning strategy however, and refining against the twinned
      experimental data with the correct twin operator(s) is preferable. I
      don't know how Refmac5 handles this, it could be the easier option though.

      HTH,

      Jonathan

      --
      Jonathan Elegheert
      Ph.D. Student

      Unit for Structural Biology & Biophysics
      http://www.lprobe.ugent.be/xray.html

      Lab for Protein Biochemistry and Biomolecular Engineering
      Department of Biochemistry & Microbiology
      Ghent University, Belgium

      e-mail: jonathan.elegheert@...



      Kay Diederichs schreef:
      > Lukacs, Christine schrieb:
      >>
      >>
      >> Hi –
      >>
      >>
      >>
      >> I have a dataset that seems to be perfectly twinned – 4 times.
      >>
      >>
      >> Long story short:
      >>
      >> Apparent space group of P6122 gives MR solution, one molecule in AU,
      >> beautiful ligand density; but R-factors stuck in the high 30s –low 40s.
      >>
      >> I ran through the twinning manipulations (in ccp4) to try P6, P312,
      >> and P321. Statistics show perfect twinning, but no luck with
      >> refinement.
      >>
      >> So I went back to P3 - now I get a solution in P31, four molecules
      >> in the AU, and four twin operators with fractions of 0.25 each. R
      >> factors finally drop and the maps look good.
      >>
      >>
      >>
      >> I would like to take this into CNX now. Can I specify more than one
      >> twin operator in the various input files (make_cv_twin.inp,
      >> detwin_perfect.inp, and anneal_twin.inp)?
      >>
      >>
      >> If someone can help and would like more details, I am happy to take
      >> this off-line.
      >>
      >>
      >>
      >> Thanks
      >>
      >> Christine
      >>
      >>
      >
      > Christine,
      >
      > I'd say you can consider yourself lucky that the latest version of
      > refmac5 can deal with tetartohedral twinning which you seem to have.
      >
      > AFAICT neither CNS nor phenix.refine support that kind of calculation.
      >
      > HTH,
      >
      > Kay
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