It was actually a trigonal case with about 2.5 along a and b and 3.1
along c.
We were also skeptic, but ... it worked.
Eleanor Dodson wrote:
[log in to unmask]">What
resolution do you have?
I have always been a bit sceptical about this, since if nothing is
measured because of the anisotropy no sharpening will generate a term
..
The "free lunch" algorithm is certainly useful. We used this with
ACORN to correct phases at high resolution, setting all missing data to
the mean normalised value - ie All missing Es = 1, and that does help.
You can understand why.
And the same idea must help with any form of phasing - <F> is a
better estimate of the amplitude than F=0 and if there is some useful
phase info from density modification or density averaging then the maps
will improve.
But just sharpening unmeasured data - hmmmmm
eleanor
F.Xavier Gomis-Rüth wrote:
I think it is important to differentiate
between two stages: first, when you want to solve the structure, and
second, when you produce a final model
you're going to deposit with the PDB. In the first case, it has proven
useful for us lately in two cases to apply anisotropic scaling, be it
through the
Sawaya&Dickerson server or through XPREP, for getting useful
electron density maps. In the latter case the difference between
isotropic and
anisotropic scaling was as simple as a completely messy density vs.
clear regular secondary structure elements that are currently enabling
to (manually)
build a model. Once a complete model is obtained, (final) refinement
should be performed against the anisotropic, unmodified data as
refinement
programs such as refmac and cns properly account for data anisotropy
through appropriate anistropic scaling.
If you have concerns regarding fabricated data: Even more astonishing
is the "free-lunch" approach: you completely fabricate data up to 1.0A
resolution
and this apparently makes the difference between solving a structure
or not !
Maybe Isabel or George could comment on this.
Xavier
[log in to unmask] wrote:
Isn't automatically included fabricated
data for missing reflections a really bad idea for anisotropic data
where most reflections are "missing" at high resolution? Shouldn't
there be a big flashing red flag alerting the user to what's been done?
Phoebe
At 01:22 PM 3/26/2007, Edward A. Berry wrote:
Actually I was thinking of a somewhat
earlier paper:
Rayment,I. Molecular relacement method at low resolution:
optimum strategy and intrinsic limitations as determined
by calculations on icosahedral virus models.
Acta Crystallogr. A 39, 102 116 (1983).
But thanks for bringing the Caliandro et al. paper to my attention.
Thanks also to Fred. Vellieux for his comments, and to Pete Dunton
for explaining to me that while fft doesn't do fillin by default,
the 2MFo-DFc map coefficients from refmac5 do have fillin values
for the missing reflection, making model bias a problem when
many missing residues are included.
Now I understand Petrus's question.
Ed
Michel Fodje wrote:
You are probably referring to the
following works:
Caliandro et al, Acta Cryst. D61 (2005) 556-565
and Caliandro et al, Acta Cryst. D61 (2005) 1080-1087
in which they used density modification to calculate phases for
unmeasured reflections, and used the phases to extend the resolution by
calculating rough estimates unmeasured amplitudes. Using this technique
they actually could improve the electron density.
If I'm not mistaken, George Sheldrick has implemented this "Free Lunch"
algorithm in SHELXE.
/Michel
On Fri, 2007-03-23 at 08:05 -0800, Edward Berry wrote:
If instead you allow the missing F's
to "float", calculating them on each cycle from the previous map
using the fillin option, someone has shown (don't have the
reference handy at the moment) that the F's tend toward the true F's
(in the case that they weren't really missing but omitted as part
of the test).
Ed
---------------------------------------------------------------------------------------------------------------------------
Phoebe A. Rice
Assoc. Prof., Dept. of Biochemistry & Molecular Biology
The University of Chicago
phone 773 834 1723
fax 773 702 0439
http://bmb.bsd.uchicago.edu/index.html
http://www.nasa.gov/mission_pages/cassini/multimedia/pia06064.html
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