On Sunday, 17 March 2013, Pavel Afonine wrote:
> Hi Sonali,
>
> regarding isotropic vs anisotropic parameterization of your individual
> ADPs: apart from common sense and theoretical considerations, this is also
> in great part software dependent.
>
> I can't speak for other programs, but for phenix.refine I would say the
> rule of thumb is:
> - higher than 1.5A: refine macromolecule with individual anisotropic ADPs
> (the rest - isotropic);
I would place the expected resolution break-even point at more like
1.2 - 1.3 A. But that's only an expectation, not a rule to rely on.
You should justify anisotropic refinement of a structure on the basis
of its own particular model and measured data. Robbie Joosten has
already pointed out that you can use the PDB-Redo scripts to test
whether individual anisotropic ADPs are justified.
> - higher than 1.2A: all anisotropic (macromolelcule, water, ligands)
> - lower than 1.7A: all isotropic;
> - 1.5-1.7A is a grey area where there is only one single way to know for
> sure: try both (isotropic and anisotropic) and see which one works best.
> I realize "works best" is a broad term, but I would say Rwork, Rfree,
> Rfree-Rwork and values of refined anisotropic ADPs should be enough to make
> a decision.
Unfortunately, Rfree cannot be used reliably for this purpose.
Please see my "To B or not to B" Acta D paper from last year
for worked examples of why Rfree cannot be trusted in this case.
In particular, in the 1.5 - 1.7A region Rfree is likely to
indicate incorrectly that anisotropic refinement is OK, whereas
"peeking at the answer sheet" (i.e. using a known structure where
true atomic resolution data is available) demonstrates that the
anisotropic refinement is garbage even though Rfree is improved.
cheers,
Ethan
> If it's not a neutron data, H atoms should be always isotropic (kind of
> obvious, but mentioning it just in case..).
>
> Good luck,
> Pavel
>
> On Sun, Mar 17, 2013 at 1:06 AM, sonali dhindwal <
> sonali11dhind...@yahoo.co.in> wrote:
>
> > Dear All,
> >
> > We want little suggestion and knowledge regarding refinement of data in
> > Refmac. We have a data with resolution upto 1.5A. Overall redundancy of 5.5
> > and 3.7 in high resolution bin. and I over Sigma is also 21 overall and
> > 2.2 in last resolution bin.
> >
> > When we first did isotropic refinement we used automatic weighing term,
> > which gave good Rfree and Rfactor of 18.4 and 16.9 but high rmsBond and
> > rmsAngle of 0.027 and 2.5 respectively. We were able to improve rmsBond and
> > rmsAngle values by decreasing weighing term to 0.5.
> >
> > But when we do anisotropic refinement with weighing term of 0.5 it gives
> > Rfree, Rfactor and FOM of 16.8, 15.0 and 90.7 respectively. And rmsAngle
> > and rmsBond of 0.0074 and 1.25.
> >
> > Now, we want to know what should be the ideal values for rmsAngle and
> > rmsBond at such resolution. Secondly, if we can use anisotropic refinement
> > with such data.
> >
> > All your suggestions will be highly valuable.
> > Thanks in advance.
> >
> > --
> > Sonali Dhindwal
> >
> > “Live as if you were to die tomorrow. Learn as if you were to live
> > forever.”
> >
>
