Dear George,
thanks a lot! I see the point, that in reciprocal space refinement one
could refine directly against the observed intensities and sigmas. But
in principle, one could do iterative real space refinement, structure
factor and intensity calculation for refinement statistics and weights,
calculation of an improved electron density map (but that requires Fs
again ...), and so forth until some convergence criterion is met. I
wonder, which refinement scheme is more efficient.
The missing reflections in map calculation is something that we have to
live with, and unless the data are severely incomplete, I must admit,
that I don't worry too much.
The twinning problem is really severe! Here, I don't see how this could
be done in a clever way in real space.
Interesting discussion ...
Best wishes,
Dirk.
Am 29.10.10 10:41, schrieb George M. Sheldrick:
Dear Dirk,
There are good reasons why real space refinement has never become popular.
With reciprocal space refinement, you refine directly against what you
measured, taking the standard uncertainly of each individual intensity
into account. In this context I was pleased to read in CCP4bb that REFMAC
will soon be refining against intensities (like SHELXL). Then the
assumptions made (e.g. no distortion of the expected intensity distribution
by e.g. NCS or twinning) and even 'bugs' in (c)truncate will no longer
matter. If for some reason a reflection wasn't measured, then simply
leaving it out it does not invalidate a recoprocal space refinement.
The same applies to reflections that are reserved for Rfree.
In contrast, the electron density is only theoretically correct if all
reflections between 0,0,0 and infinity are included in the Fourier
summation, For a twin it is even worse, because we don't know how to
partition the difference between Fo^2 and Fc^2 between the twin
components. None of the attempts to work around these problems are
entirely convincing. Maps and real space refinement are invaluable in
the intermediate stages of model building and correction, but the
final refinement should be performed in reciprocal space.
Best wishes, George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582
On Fri, 29 Oct 2010, Dirk Kostrewa wrote:
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
--
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Bart Hazes (Associate Professor)
Dept. of Medical Microbiology& Immunology
University of Alberta
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phone: 1-780-492-0042
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*******************************************************
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
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*******************************************************
--
*******************************************************
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
*******************************************************
