Re: [ccp4bb] What makes the difference between 2 composite omit maps?
I am not aware of this point being explicitly made. Maybe somebody else
could point to the relevant reference?
However, the logic here is very simple:
(1) Take a model and generate from it Fc
(2) Calculate map with minimal rms error m*Fo*exp(i*phiCalc)
(3) This map is biased with respect to errors in the model
(4) To avoid this bias one can subtract a part of the model
(Fc*coefficient) from the above map
- the coefficient is chosen so electron density in the resulting map
does not change at the point where we added or subtracted an atom;
- conceptually the above procedure when we subtract an atom is the
composite omit map
- "does not change" means here: within first order approximation, we
ignore second order effects
- for sigmaA-weighted map this coefficient is D/2
(5) The subtraction gives: (m*Fo-D/2*Fc)exp(i*phiCalc)
(6) After multiplication by 2, we get (2m*Fo-DFc)exp(i*phiCalc)
Hailiang Zhang wrote:
Thanks! Can you refer me some documents about your following statements:
derivation of sigmaa-weighted 2mFo-DFc formula is by calculating Fourier
coefficients of the following map:
Rescaled composite omit map, where minimal structural element (of the size
about the resolution element) is being omitted and the starting point is
the map with coefficients m*Fo*exp(i*phiCalc)
It seems the above was not involved in Read's publications about SIGMAA.
Thanks again!
Hailiang
sigmaa-weighted 2mFo-DFc is the _COMPOSIT_OMIT_ map. There is no point in
calculating omit map of an omit map
A brief explanation: derivation of sigmaa-weighted 2mFo-DFc formula is by
calculating Fourier coefficients of the following map:
Rescaled composite omit map, where minimal structural element (of the size
about the resolution element) is being omitted and the starting point is
the map with coefficients m*Fo*exp(i*phiCalc)
BTW, composite omit map of a map with coefficients Fo*exp(i*phiCalc) is
simply Fo-1/2Fc map that after factor of 2 scaling becomes 2Fo-Fc map
Hi,
I want to calculate the sigmaa-weighted 2mFo-DFc composite omit map, and
tried the following 2 scripts:
(1)
./omit hklin ${f}.mtz mapout ${f}.map <
concerned about which one is more appropriate for the sigmaa-weighted
2mFo-DFc composite omit map.
(mFo is what I generated from the SIGMAA output)
Thanks for any suggestions!
Best Regards, Hailiang
Zbyszek Otwinowski
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.
Dallas, TX 75390-8816
Tel. 214-645-6385
Fax. 214-645-6353
Zbyszek Otwinowski
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.
Dallas, TX 75390-8816
Tel. 214-645-6385
Fax. 214-645-6353
--
Zbyszek Otwinowski
UT Southwestern Medical Center
5323 Harry Hines Blvd., Dallas, TX 75390-8816
(214) 645 6385 (phone) (214) 645 6353 (fax)
zbys...@work.swmed.edu
Re: [ccp4bb] What makes the difference between 2 composite omit maps?
Thanks! Can you refer me some documents about your following statements:
derivation of sigmaa-weighted 2mFo-DFc formula is by calculating Fourier
coefficients of the following map:
Rescaled composite omit map, where minimal structural element (of the size
about the resolution element) is being omitted and the starting point is
the map with coefficients m*Fo*exp(i*phiCalc)
It seems the above was not involved in Read's publications about SIGMAA.
Thanks again!
Hailiang
> sigmaa-weighted 2mFo-DFc is the _COMPOSIT_OMIT_ map. There is no point in
> calculating omit map of an omit map
>
> A brief explanation: derivation of sigmaa-weighted 2mFo-DFc formula is by
> calculating Fourier coefficients of the following map:
>
> Rescaled composite omit map, where minimal structural element (of the size
> about the resolution element) is being omitted and the starting point is
> the map with coefficients m*Fo*exp(i*phiCalc)
>
> BTW, composite omit map of a map with coefficients Fo*exp(i*phiCalc) is
> simply Fo-1/2Fc map that after factor of 2 scaling becomes 2Fo-Fc map
>
>> Hi,
>> I want to calculate the sigmaa-weighted 2mFo-DFc composite omit map, and
> tried the following 2 scripts:
>>
>> (1)
>> ./omit hklin ${f}.mtz mapout ${f}.map <> LABI FP=mFo FC=DFC PHI=PHIC
>> RESO 29.50 3.22
>> SCAL 2.0 -1.0
>> EOF
>>
>> (2)
>> ./omit hklin ${f}.mtz mapout ${f}.map <> LABI FP=FWT FC=FC PHI=PHIC
>> RESO 29.50 3.22
>> SCAL 1.0 0.0
>> EOF
>>
>> The output maps are just different, and I wonder why. I am also more
> concerned about which one is more appropriate for the sigmaa-weighted
> 2mFo-DFc composite omit map.
>>
>> (mFo is what I generated from the SIGMAA output)
>>
>> Thanks for any suggestions!
>>
>> Best Regards, Hailiang
>>
>
>
> Zbyszek Otwinowski
> UT Southwestern Medical Center at Dallas
> 5323 Harry Hines Blvd.
> Dallas, TX 75390-8816
> Tel. 214-645-6385
> Fax. 214-645-6353
>
>
>
> Zbyszek Otwinowski
> UT Southwestern Medical Center at Dallas
> 5323 Harry Hines Blvd.
> Dallas, TX 75390-8816
> Tel. 214-645-6385
> Fax. 214-645-6353
>
>
Re: [ccp4bb] What makes the difference between 2 composite omit maps?
sigmaa-weighted 2mFo-DFc is the _COMPOSIT_OMIT_ map. There is no point in
calculating omit map of an omit map
A brief explanation: derivation of sigmaa-weighted 2mFo-DFc formula is by
calculating Fourier coefficients of the following map:
Rescaled composite omit map, where minimal structural element (of the size
about the resolution element) is being omitted and the starting point is
the map with coefficients m*Fo*exp(i*phiCalc)
BTW, composite omit map of a map with coefficients Fo*exp(i*phiCalc) is
simply Fo-1/2Fc map that after factor of 2 scaling becomes 2Fo-Fc map
> Hi,
> I want to calculate the sigmaa-weighted 2mFo-DFc composite omit map, and
tried the following 2 scripts:
>
> (1)
> ./omit hklin ${f}.mtz mapout ${f}.map < LABI FP=mFo FC=DFC PHI=PHIC
> RESO 29.50 3.22
> SCAL 2.0 -1.0
> EOF
>
> (2)
> ./omit hklin ${f}.mtz mapout ${f}.map < LABI FP=FWT FC=FC PHI=PHIC
> RESO 29.50 3.22
> SCAL 1.0 0.0
> EOF
>
> The output maps are just different, and I wonder why. I am also more
concerned about which one is more appropriate for the sigmaa-weighted
2mFo-DFc composite omit map.
>
> (mFo is what I generated from the SIGMAA output)
>
> Thanks for any suggestions!
>
> Best Regards, Hailiang
>
Zbyszek Otwinowski
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.
Dallas, TX 75390-8816
Tel. 214-645-6385
Fax. 214-645-6353
Zbyszek Otwinowski
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.
Dallas, TX 75390-8816
Tel. 214-645-6385
Fax. 214-645-6353
[ccp4bb] What makes the difference between 2 composite omit maps?
Hi,
I want to calculate the sigmaa-weighted 2mFo-DFc composite omit map, and
tried the following 2 scripts:
(1)
./omit hklin ${f}.mtz mapout ${f}.map <
