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Annealing before complete model building!

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  • i_m_subh
    Hi, I have built an almost complete model with some refinement but I am still unable to build two small loops (5-6 residues)using coot or O even after some
    Message 1 of 2 , Aug 3, 2008
      Hi,
      I have built an almost complete model with some refinement but I am
      still unable to build two small loops (5-6 residues)using "coot" or
      "O" even after some refinement.
      I want to do annealing and energy minimization with CNS.I was
      wondering that will it help if I use my current incomplete model for
      annealing and minimization to get a better electron density for
      further model building?
      Or is it always required to build the complete model first and then
      proceed with minimization and annealing to get the best/publishable model?

      Thanks for your suggestions.

      Subhendu
    • Leo Chavas
      Dear Subhendu -- ... It might help your modeling, but I quite sure it will not make the density of the loops appear, or at least not completely. Have you tried
      Message 2 of 2 , Aug 3, 2008
        Dear Subhendu --

        On 4 Aug 2008, at 06:44, i_m_subh wrote:
        I have built an almost complete model with some refinement but I am
        still unable to build two small loops (5-6 residues)using "coot" or
        "O" even after some refinement.
        I want to do annealing and energy minimization with CNS.I was
        wondering that will it help if I use my current incomplete model for
        annealing and minimization to get a better electron density for
        further model building?

        It might help your modeling, but I quite sure it will not make the density of the loops appear, or at least not completely. Have you tried to add water molecules? You might try to refine further your model to have better phases, and then the density for those loops will appear. Also, what you might want to try is to add one residue only from each end of the missing loop, then run annealing, and check if any density appeared. If so, then repeat the process until your loop is completed. If not, it just means either it is unstructured completely, or that it has been cleaved somewhere in the purification process.

        Or is it always required to build the complete model first and then
        proceed with minimization and annealing to get the best/publishable model?

        just a short comment: you don't want to have a "publishable" data (well, you do want to publish, obviously...) but rather a "biological meaningful" data. If the fact to have the loops unbuilt is biologically meaningless, then I'd start to worry. But is it the case?... 

        HTH

        Kind regards.

        -- Leo --
        ------------------------------------------------------------
        Chavas Leonard, Ph.D. @ home
        Research Associate
        Marie Curie Actions Fellow
        ------------------------------------------------------------
        Faculty of Life Sciences
        The University of Manchester
        The Michael Smith Building
        Oxford Road
        Manchester Lancashire
        M13 9PT
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        Tel: +44(0)161-275-1586
        http://personalpages.manchester.ac.uk/staff/leonard.chavas/


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