[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

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Phoebe A. Rice
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The University of Chicago
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