On 10-10-29 12:03 AM, Robbie Joosten wrote:
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type="cite">
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.
Does the water move back to its old position if you follow up the
real-space refinement with more reciprocal refinement. If so, the map
may not have been a true representation of reality. Basically what I
was implying is that if the required model changes "details" are such
that they fall within the radius of convergence then the atoms should
move to their correct positions; unless something is keeping them from
moving such as an incorrectly placed side chain that causes a steric
conflict. Fix the incorrect side chain and your "details" will take
care of themselves. I don't imply that I can always spot an easy error
to fix and sometimes end up rebuilding several different ways in the
hopes that one will resolve whatever was the problem. If that doesn't
happen at some point you need to give up, especially if it does not
affect a functionally important region. I do think it is good practice
to point out regions in the model that are problematic and have never
had reviewers complain about that if it is clear you made the effort to
get it as good as possible given the data.
[log in to unmask]"
type="cite">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.
Can't blame the data for that, in the end each person (and supervisor)
need to take responsibility for the models they produce and deposit.
Same applies to sequence data bases that are full of lazy errors. If
humans are involved both greatness and stupidy are likely outcomes.
Bart
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type="cite">
Cheers,
Robbie
> Date: Thu, 28 Oct 2010 16:32:04 -0600
> From: [log in to unmask]
> Subject: Re: [ccp4bb] Against Method (R)
> To: [log in to unmask]
>
> 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
>
>
===========================================================================
--
===========================================================================
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
===========================================================================
