Dear CCP4ers,
I really would sharpen the structure factors, not only the electron
density maps. The simple reason is: if sharpening emphasizes enough
information at higher resolution to help interpreting the electron
density maps, refinement will also benefit from this information.
Of course, the mean B-factor of the refined structure will be lower by
the sharpening B-factor, but since B-factor sharpening is usually done
with lower resolution data, the Wilson B-factor is usually very high,
and thus far, I didn't run into problems with B-factors crashing at the
lower limit.
The sharpening B-factor can easily reach values in the -100s A**2, not
only -10 to -50 A**2. Axel Brunger has published several papers about
how to estimate a good sharpening B-factor (a recent one with references
is Brunger et al. Acta Cryst D65, 128-133). He usually describes map
sharpening, but B-factor sharpening of structure factors seems to be
done routinely for virus structures in Steve Harrisons lab.
One word of caution: the B-factor sharpening should be correctly
described not only in the publication but also in the PDB deposition (if
refinement was done against sharpened structure factors, the refinement
statistics can only be reproduced using these structure factors). The
original structure factors can be easily reproduced by applying back the
negative sharpening B-factor.
Best regards,
Dirk.
Am 26.02.11 01:09, schrieb Garib N Murshudov:
I would not sharpen structure factors before refinement. It may cause problems
with B value refinement (a lot of B values may stuck around 2 or minimum B).
One must remember that not all atoms in crystal have same Bvalue. There is a
distribution of Bvalues.
However maps can be sharpened after refinement. It can be done directly in coot
(I hope this version of coot is now widely available). Or if you are using
refmac for refinement you can use:
mapc sharpen # regularised map sharpening. Bvalues and regularisation
parameters are calculated automatically
or
mapc sharpen<Bvalue> # regularised map sharpening with specified Bvalue
or
mapc sharpen<Bvalue>
mapc sharpen alpha<value=0.1> # regularisation paramater. alpha=0 is simple
sharpening.
I am sure other programs have similar options. (I know CNS has and it has been
used successfully by many people)
regards
Garib
P.S. These options available from refmac v5.6 available from;
www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac5.6_linux.tar.gz
On 25 Feb 2011, at 23:57, Dima Klenchin wrote:
At 05:39 PM 2/25/2011, Pete Meyer wrote:
Or could anyone suggest a program that would be of help?
CAD scaling with a scale factor of 1.0 and negative B-factor (isotropic or
anisotropic) should do the trick. I haven't had much luck with density
sharpening (at least at ~4-5 Angstroms), but others have apparently had some
success with it.
Alternatively, CCP4i task Run FFT does the job:
1. Take MTZ from Refmac output
2. Run FFT to create simple map with SigmaA-weighted phases (i.e., PHWT label).
3. In Infrequently used options, "Apply B-factor scaling to F1", specify
negative B-factor scaling value, usually within -10 to -50.
- Dima
--
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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
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