[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [ccp4bb]: unmeasured data in map-calculations

***  For details on how to be removed from this list visit the  ***
***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***

Jan Abendroth wrote:
> My data set is quite incomplete in the highest resolution shell. When I
> calculate maps with the cns script model_map the sigmaA-weighted
> fofc-map (mFoDFc) has many "unreasonable" peaks at 3sigma-level. When I
> make cns to take Fc for the unmeasured Fo's the sigmaA-weighted fofc-map
> shows much fewer and much more reasonable peaks, simply this map becomes
> significanly better.
> This seems to make sense, but what is the physical/mathematical reason
> for this?
> How treats cns unmeasured hkl's in the "normal" mode in difference maps?
> Is there a related ccp4-option in refmac/fft?

My 2 cents worth, and perhaps the experts will also forgive me in the spirit 
of the season:

fft has keyword fillin which causes it to substitute Fc for Fo in nFo-mFc maps.

If this is not done, any map calculation program has little option but to 
omit the unobserved reflections, which is equivalent to setting them to zero,
which I think might account for your inexplicable peaks.

The philosophy of fillin is that the Fc is a better estimate of the
unobserved reflection than is zero, so will give a better map. But beware
of model bias! You will get the most beautiful map, with absolutely no
peaks that don't make sense, when you have zero completeness and use fillin:
2Fc-Fc = Fc so you are making an Fc/PHIc map. The Fourier transform 
is reversible and you will get back exactly the density of your model.

If you are doing density modification it is very important to use fillin
according to I. Rayment- Otherwise you are solving for the best set of 
phases consistent with the flat solvent, the NCS, AND A VALUE OF ZERO
FOR ALL THE MISSING REFLECTIONS. If you use fillin the value of missing F's
gets dragged along by neighboring reflections in reciprocal space, just as 
the phases of all reflections do, and when you go back and measure the
missing reflections they often come out close to the value of Fc from DM 
with fillin (again according to Rayment).