Hi Ian,
If you read my post carefully, and know the naming conventions, you will
see that the mtz naming convention and mtz labels are those that are
provided by Phenix...
I was aware that there will be differences (I was assuming minor ones -
in terms of map appearance) to the proper coefficients when using other
refinement software.
So I believe you !
Fred.
Ian Tickle wrote:
> Hi Fred
>
> You have to be careful here because believe it or not, not all
> programs output the same coefficients for 'minimal bias' maps, so
> depending on which program Hailiang is using for SF
> calculation/refinement he may or may not get the right answer! You
> are assuming the difference map coefficient is (mFo-DFc) for both
> acentrics & centrics so you are expecting to calculate:
>
> 3mFo-2DFc = (2mFo-DFc) + (mFo-DFc) for acentrics
> 2mFo-DFc = Fo + (mFo-DFc) for centrics
>
> However as I have been at pains to point out on numerous occasions the
> correct difference map coefficient is 2(mFo-DFc) for acentrics (i.e. 2
> times half the peak height from an acentric mFo-DFc map), and
> (mFo-DFc) for centrics (i.e. 1 times the full peak height from a
> centric mFo-DFc map). This fact tends to be obscured if you think of
> it as Fo+(Fo-Fc) instead of Fc+2(Fo-Fc), which was my real objection
> to thinking of it in the way Pavel suggested.
>
> In fact the last time I checked (recently) neither Refmac nor Buster
> got it right (details on request!) - not only that but they get it
> wrong in different ways: at least they are inconsistent with what in
> my view are the correct coefficients, which is based on my
> understanding of Randy Read's 1986 paper, and no-one has yet provided
> me with a rationale for the formulae used by Refmac & Buster. The
> CCP4 version of Sigmaa now gets it right, but that's only because I
> recently fixed it myself. I can't speak for phenix.refine, I suspect
> it gets it completely correct, since Pavel is on the case! So I think
> the safest CCP4 approach is to use Sigmaa to recalculate the map
> coefficients, then use FFT to combine them. This will require
> something like the following input to FFT:
>
> LABIN F1=FWT F2=DELFWT PHI=PHIC
> SCALE F1 1 0 F2 0.5 0
>
> (check the FFT doc!)
>
> in other words:
> 3mFo-2DFc = (2mFo-DFc) + 0.5*(2(mFo-DFc)) for acentrics
> 1.5mFo-0.5*DFc = Fo + 0.5*(mFo-DFc) for centrics
>
> Note that this gives the coefficient 1.5mFo-0.5DFc for centrics, not
> 2mFo-DFc as suggested in your paper (sorry I couldn't see the
> rationale for that choice). Again this becomes much clearer if you
> write 3mFo-2DFc as Fc + 3(mFo-DFc) i.e. 3 times half height (= 1.5
> times true height), so to be consistent the centric coefficient should
> also be 1.5 times true, or Fc + 1.5(mFo-DFc). I think it's important
> to get the centric reflections right (particularly in tetragonal and
> cubic space groups!) because obviously the centric phases tend to be
> better determined than the acentric ones.
>
> Cheers
>
> -- Ian
>
> On Fri, Jul 30, 2010 at 9:24 AM, Vellieux Frederic
> <[log in to unmask]> wrote:
>
>> Hi,
>>
>> You take the output mtz from the refinement program (let's assume it's
>> called refine_1.mtz).
>>
>> Command line mode:
>> sftools
>> read refine_1.mtz col 1 2 3 4 # assuming the mtz contains H K L 2FOFCWT
>> PHI2FOFCWT FOFCWT PHI2FOFCWT
>> cal col 3FO2FCWT col 1 col 3 +
>> set types
>> F
>> P
>> F
>> P
>> R F
>> write 3fo2fc.mtz col 5 2 3 4
>> quit (or stop, can't remember which)
>>
>> That's it...
>>
>> Fred
>>
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