Hi Bart,
I agree with the building strategy you propose, but at some point it stops
helping and a bit more attention to detail is needed. Reciprocal space
refinement doesn't seem to do the fine details. It always surprises me how much
atoms still move when you real-space refine a refined model, especially the
waters. I admit this is not a fair comparison.
High resolution data helps, but better data makes it tempting to put too little
effort in optimising the model. I've seen some horribly obvious errors in
hi-res models (more than 10 sigma difference density peaks for misplaced side
chains). At the same time there are quite a lot of low-res models that are
exceptionally good.
Cheers,
Robbie
> Date: Thu, 28 Oct 2010 16:32:04 -0600
> From: bart.ha...@ualberta.ca
> Subject: Re: [ccp4bb] Against Method (R)
> To: CCP4BB@JISCMAIL.AC.UK
>
> On 10-10-28 04:09 PM, Ethan Merritt wrote:
> > This I can answer based on experience. One can take the coordinates from a
> > structure
> > refined at near atomic resolution (~1.0A), including multiple conformations,
> > partial occupancy waters, etc, and use it to calculate R factors against a
> > lower
> > resolution (say 2.5A) data set collected from an isomorphous crystal. The
> > R factors from this total-rigid-body replacement will be better than
> > anything you
> > could get from refinement against the lower resolution data. In fact,
> > refinement
> > from this starting point will just make the R factors worse.
> >
> > What this tells us is that the crystallographic residuals can recognize a
> > better model when they see one. But our refinement programs are not good
> > enough to produce such a better model in the first place. Worsr, they are
> > not
> > even good enough to avoid degrading the model.
> >
> > That's essentially the same thing Bart said, perhaps a little more
> > pessimistic :-)
> >
> > cheers,
> >
> > Ethan
> >
>
> Not pessimistic at all, just realistic and perhaps even optimistic for
> methods developers as apparently there is still quite a bit of progress
> that can be made by improving the "search strategy" during refinement.
>
> During manual refinement I normally tell students not to bother about
> translating/rotating/torsioning atoms by just a tiny bit to make it fit
> better. Likewise there is no point in moving atoms a little bit to
> correct a distorted bond or bond length. If it needed to move that
> little bit the refinement program would have done it for you. Look for
> discreet errors in the problematic residue or its neighbors: peptide
> flips, 120 degree changes in side chain dihedrals, etc. If you can find
> and fix one of those errors a lot of the stereochemical distortions and
> non-ideal fit to density surrounding that residue will suddenly
> disappear as well.
>
> The benefit of high resolution is that it is much easier to pick up and
> fix such errors (or not make them in the first place)
>
> Bart
>
> --
>
> ============================================================================
>
> Bart Hazes (Associate Professor)
> Dept. of Medical Microbiology& Immunology
> University of Alberta
> 1-15 Medical Sciences Building
> Edmonton, Alberta
> Canada, T6G 2H7
> phone: 1-780-492-0042
> fax: 1-780-492-7521
>
> ============================================================================
