Loading ...
Sorry, an error occurred while loading the content.

Can I refine 4-fold twinned data in cns?

Expand Messages
  • Lukacs, Christine
    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,
    Message 1 of 3 , Oct 1, 2009
    • 0 Attachment

      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 Lukacs, Ph.D.
      Senior Principal Scientist
      Roche

      This message is intended for the use of the named recipient(s) only and may contain confidential and/or proprietary information. If you are not the intended recipient, please contact the sender and delete this message. Any unauthorized use of the information contained in this message is prohibited.

       

    • Kay Diederichs
      ... 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
      Message 2 of 3 , Oct 1, 2009
      • 0 Attachment
        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
        --
        Kay Diederichs http://strucbio.biologie.uni-konstanz.de
        email: Kay.Diederichs@... Tel +49 7531 88 4049 Fax 3183
        Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz

        This e-mail is digitally signed. If your e-mail client does not have the
        necessary capabilities, just ignore the attached signature "smime.p7s".
      • 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 3 of 3 , Oct 2, 2009
        • 0 Attachment
          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
        Your message has been successfully submitted and would be delivered to recipients shortly.