[ccp4bb]

[kavya]

Respected Sir,

Thank you for your clarification. I had adopted this
method recently. My doubt was if we have to optimize
these two parameters during refinement, should we have
the whole model along with water and ligands or only
protein with few water positioning is enough. The reason
why I am asking because there was quite a difference
when I refined the same structure without the optimization
and with optimization of these two parameters.

Thanking you
With regards
M. Kavyashree

-----CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> wrote: -----

    To: CCP4BB@JISCMAIL.AC.UK
    From: Ian Tickle
    Sent by: CCP4 bulletin board
    Date: 10/14/2011 12:34PM
    Subject: Re: [ccp4bb] Optimisation of weights

    Hi Kavya

    The resolutions of the structures mentioned in the paper were only
    examples, the Rfree/-LLfree minimisation method (which are actually
    due to Axel Brunger & Gerard Bricogne respectively) does not depend on
    resolution.

    If the structures are already solved & refined, you don't need to do
    any model building, it should be within the radius of convergence with
    the new weights - it's only a small adjustment after all.

    Cheers

    -- Ian

    On Fri, Oct 14, 2011 at 6:12 AM,  <ka...@ssl.serc.iisc.ernet.in> wrote:
    > Dear users,
    >
    > Can the optimization of the X-ray weighing factor
    > and B-factor (overall wt) as mentioned in the paper
    > Acta Cryst. (2007). D63, 1274–1281 by Dr.Ian Tickel,
    > be used for the refinement of the data sets beyond
    > the resolution range mentioned in the paper: 1.33 -
    > 2.55 Ang?
    >
    > Also the structures that were used to optimize these
    > parameters were already solved and refined, so when
    > we are solving a new structure to what extent does the
    > model has to be built before starting the optimization?
    >
    > Thanking you
    > With Regards
    > M. Kavyashree
    >
    >
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