[sharp-discuss] Native Fe in SHARP phasing

[Clemens Vonrhein]

Ed,

that depends what kind of SHARP refinement you do. 

If it's SAD/MAD (i.e. a single compound with all heavy atoms declared)
the SHARP map (from FB/PHIB in eden.mtz or FBsha/PHIBsha in
eden_flat_*pc.mtz) will contain the heavy atoms in the map. However,
after solvent flattening the peak height of these atoms will be
significantly decreased - all density modification assumes to some
degree simple solvent/protein features and doesn't take heavy atoms
into account. You might be able to play with it to some extent using
the 'min/max density truncation in "protein" region' feature in the
'Phase Improvement and Interpretation Control Panel': adjusting the
'max' to 0.0 will leave all high peaks in the "protein" as they are.

If it's SIR(AS)/MIR(AS) with your native data as first
compound(reference) the SHARP map will NOT contain the Fe (or any
other heavy atoms declared in other compounds). 

But maybe you have even a more difficult setup
(MAD+native+derivative)? Could you specify this then?

Hope that helps.

Cheers

Clemens


On Wed, Jan 09, 2002 at 02:35:55PM -0800, Edward Berry wrote:
> A question about the SHARP output files eden*.mtz:
> If I use native irons of my protein for phasing (anomalous and 
> dispersive differences at different wavelengths) together with
> regular heavy atom derivatives, does the iron contribution get
> subtracted out before making the "native" protein mtz file F's 
> (FPsha and FPshasol)? If I want to make a map with the iron 
> density, should I use my native amplitudes together with 
> PHIshasol and FOMshasol?
> 
> Thanks,
> Ed
> 
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> sharp-discuss mailing list
> sharp-discuss@globalphasing.com
> http://www.globalphasing.com/mailman/listinfo/sharp-discuss

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