It must be the same complete model that you refined previously, I
doubt that it will give the correct answer if you leave out the waters
for example.
You say "there was quite a difference". Could you be more specific:
what were the values of the weights, R factors and RMSZ(bonds/angles)
before and after weight optimisation?
Cheers
-- Ian
On Fri, Oct 14, 2011 at 8:42 AM, <[log in to unmask]> wrote:
> 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 <[log in to unmask]> wrote: -----
>
> To: [log in to unmask]
> 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, <[log in to unmask]> 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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