On 10 Aug 2007, at 18:59, Pavel Afonine wrote:
Hi Mike,
the best is to do both in a loop:
for cycle in cycles:
- do real space refinement;
- do reciprocal space refinement
Well - thats what we all do - right ?
The real space refinement can be done either with the tools from
Chapman at al,
or interactively by the user or by (here I go again ... ) ARP/wARP or
Resolve etc etc.
In all cases we fit the model to the map ... only the tools differ.
Although I would be tempted to suggest some general reading to Mike
[EMAIL PROTECTED] [1]
(there is one copy of Blundell and Johnson available at Amazon for
1239.64$, quite a bargain)
the most simple minded way to think of it is that in real space you
fit a piece of model to a piece
of density locally. In reciprocal space the data from the entire
molecular model is fitted
to the entire diffraction dataset at the same time. The argument
about phases I think you know it,
so I will not diatribe on this. ;-)
Also, there are no more than 2-3 MAD experimental phase-sets out
there (all in very high resolution)
that can claim that the phases derived from them are as accurate as
the phases from the refined model.
Thus even if you let aside all of the rest of the theory, the phases
we 'measure' these days are not that good.
Also, usually we think of 'excellent' phases that come from density
modification. Thats already modeling ...
Finally, I think the vast majority of structures are still from
molecular replacement, and thus you don't have good phases by
definition.
A.
[1] Why don't people subscribe to ccp4 from their real institute
email addresses ?
PS Is nobody reading Nature these days or no-one likes a good
argument about crystallographic models any more in this bb ?
Have a look at this very nice paper:
Acta Cryst. (1999). D55, 835-845 Critical initial real-space
refinement in the structure determination of arginine kinase
G. Zhou, T. Somasundaram, E. Blanc, Z. Chen and M. S. Chapman
and other "real space refinement" related papers by M. S. Chapman
et al.
Pavel.
Mike S wrote:
Dear CCP4 experts,
Recently, I was debating a colleague on the pros/cons of
refinement done in reciprocal space compared to refinement in real
space.
I always thought reciprocal space refinement was preferable since
measured amplitudes will be more accurate than calculated phases
(unless good experimental phases are available). My colleague
argued that with sigmaA and maximum-likelihood methods, calculated
phases are much "better" than they were in the past and the two
refinement techniques are equivalent in terms of robustness. He
said the reason most software hasn't switched entirely to real-
space refinement is due to computational issues.
Please help enlighten me. All comments/diatribes welcome.
Thanks,
Mike
