[phenixbb] about low resolution refinement

Pei-Chun Lin pclin at hotmail.com
Sat Oct 16 17:15:29 PDT 2010


I have the similar problem when I am working on refining my low resolution model (3.5 Ang).

One component of my protein complex represents a beta-sandwish structure, and the conecting loops between beta-strands are disordered.

After refinement, the beta-sheets were disrupted.
What do you suggest about this problem.


Date: Sun, 10 Oct 2010 16:48:57 -0700
From: pafonine at lbl.gov
To: qunwan1 at gmail.com; phenixbb at phenix-online.org
Subject: Re: [phenixbb] about low resolution refinement




    I am refining a low resolution data. According to
      sigma vs. resolution, my resolution is 4.7A. 

    not sure what is "sigma vs. resolution" but hope you made the right


    Because there are four identical molecular per
      asymetric unit, I can use positional refinement. There are about
      65% alpha-helices in the structure, so I want to use secondary
      structure restrain. Does phenix has this restrain in the


    Sorry for missing documentation on this subject.


    First of all, get the latest version of PHENIX (the one you have is
    very old):




    Then (once you have the latest), yes, you can use secondary
    structure restraints. 


    phenix.refine model.pdb data.hkl


        so phenix.refine automatically determines secondary structure
        and applies the restrains. Note, GIGO principle applies, that is
        if your input model is distorted then it's unlikely that the
        procedure will figure out the secondary structure correctly.


        To make it a less black-box, you can run


        phenix.secondary_structure_restraints model.pdb >


        and then check (and edit if necessary) the ss_restraints.params file, and then run
        phenix.refine as following:


      phenix.refine model.pdb data.hkl
    main.secondary_structure_restraints=true ss_restraints.params


        I hope Nat comments more if I missed something.


        Let me know if you have any other questions.


        Good luck!






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