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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