[sharp-discuss] Native Fe in SHARP phasing

[Edward Berry]

Thanks, Clemens,
I think my example corresponds to your second case, MIRAS. All compounds,
including the native which is first, contain the irons (we don't have any 
good way to get rid of them without denaturing the protein!). But the 
irons are declared as heavy atoms in all compounds (in order to use their
anomalous signal) so it would be sensible for the calculated native 
structure factors to not contain them. 

In this case would it be sensible to construct a native map from
FPnat, PHIsha, FOMsha if I want to see density for the irons?
(merging my native with the sharp output file to get FPnat
in the same mtz.) The columns in my sharp output files are labeled
differently: FPsha, no FBsha) and I haven't seen this "Phase Improvement 
and Interpretation" control panel, presumably because we haven't upgraded 
to SOLVE 2 yet. 

Ed

Clemens Vonrhein wrote:
> 
> 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
> >
> > _______________________________________________
> > sharp-discuss mailing list
> > sharp-discuss@globalphasing.com
> > http://www.globalphasing.com/mailman/listinfo/sharp-discuss
> 
> --
> 
> ***************************************************************
> * Clemens Vonrhein, Ph.D.          vonrhein@GlobalPhasing.com
> *
> *  Global Phasing Ltd.
> *  Sheraton House, Castle Park     Tel: +44-(0)1223-353033
> *  Cambridge CB3 0AX, UK           Fax: +44-(0)1223-366889
> *--------------------------------------------------------------
> * BUSTER Development Group      (http://www.globalphasing.com)
> ***************************************************************