Re: Residual density around iron

[Thomas Ursby <thomas.ursby@mbfys.lu.se>]

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Dear Alexander,

I have a possible explanation for the problem with the difference map,
but I didn't understand if there was a problem with the 2Fo-Fc map as
well?

In the "nfo-mfc_phicalc_map.inp" example file distributed with
X-plor 3.851 there is a typo. If nn=mm=1 (i.e. a difference map)
and SigmaA-weighting is used, then the centric reflections are set
to "mFo, PhiC" instead of "mFo-DFc, PhiC" on the following line:

      do (diff = combine(fom * ampl(fobs), phase(fcalc)) ) ( centric and
sel=1  ) 

(this is done since for 2Fo-Fc maps, the amplitude of the centric
reflections should be set to mFo to minimize model bias instead
of 2mFo-DFc as for acentric reflections, but for difference maps
the amplitudes should be mFo-DFc both for acentric and centric 
reflections).
This would generate spurious density features, but it doesn't seem
unreasonable to me that the largest feature would appear at the
strongest peak in the real map.

To calculate a difference map (not 2Fo-Fc !) change:

      do (diff = combine($nn * fom * ampl(fobs) - $mm * dd *
ampl(fcalc), phase(fcalc)) )   
         ( acentric and sel=1 ) 
      do (diff = combine(fom * ampl(fobs), phase(fcalc)) ) ( centric and
sel=1  ) 

to:

      do (diff = combine($nn * fom * ampl(fobs) - $mm * dd *
ampl(fcalc), phase(fcalc)) )   
         ( sel=1 ) 


Thomas


-- 
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  Thomas Ursby

Molecular Biophysics		Tel: (+46) 46 222.45.13
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