Hi Fred But then what you suggested won't work if I'm right about phenix correctly writing 2(mFo-DFc) for acentrics and (mFo-DFc) for centrics in the FOFCWT column (as does CCP4 Sigmaa in the DELFWT column), since you will get:
(2mFo-DFc) + 2(mFo-DFc) = 4mFo-3DFc for acentrics mFo + (mFo-DFc) = 2mFo-DFc for acentrics - not exactly what you expected! Of course I could be wrong about phenix, but I was under the impression that Pavel had all this sorted out - I guess we have to wait for the USA to wake up! What you suggested will actually do what you expected with a Refmac MTZ file (except the labels don't match) which contains (mFo-DFc) for both acentrics and centrics, but not with Buster which outputs 2(mFo-DFc) in both cases - you see what I mean about inconsistency! Cheers -- Ian On Fri, Jul 30, 2010 at 12:36 PM, Vellieux Frederic <frederic.velli...@ibs.fr> wrote: > 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 >> <frederic.velli...@ibs.fr> 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 >>> >
