Hi Robbie,
yes, the apparently larger radius of convergence in real space
refinement impresses me, too. Therefore, I usually do local real space
refinement after manually correcting errors, either with Moloc at lower
resolution or with Coot at higher resolution, prior to reciprocal space
refinement.
If I recall correctly, real space refinement was introduced by Robert
Diamond in the 60s long before reciprocal space refinement. In the 90s
Michael Chapman tried to revive it, but without much success, as far as
I know. With the fast computers today, maybe the time has come again for
real space refinement ...
Best regards,
Dirk.
Am 29.10.10 08:03, schrieb Robbie Joosten:
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
>
> ============================================================================
--
*******************************************************
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail: kostr...@genzentrum.lmu.de
WWW: www.genzentrum.lmu.de
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