[sharp-discuss] Re: Heavy Atom Negative Density

Clemens Vonrhein vonrhein@globalphasing.com
Wed, 30 Jan 2002 12:30:06 +0000


Paul,

I'm a bit puzzled ... and have some questions:

> I am having trouble trying to find out why I am getting negative density
> for Fo(phic) maps calculated in SHARP.

How did you calculate these maps? Through the interface or by hand
(using FB/PHIB from eden.mtz)? Are these directly from SHARP or
after solvent flattening?

Do you get negative density on the sites (all, some?) or around the
sites?

If it's electron density maps we're talking about (before or after
solvent flattening): have you tried the inverted hand?

> I managed to pull out possible Fe sites from a residual map using
> the anomalous signal from the peak wavelength (phases taken from
> data using just 1 Fe in the previous round).

The residual maps don't really use phases, so I assume that you used
the residual maps (preferably ANO since it's MAD) from your single
site MAD to find additional sites.

> The refined occupancies and B factors seem okay (~1.0 and 10.0),
> and the FOM is okay (~0.35 to 3.0A for acentric reflections) - but the
> denisty only looks good at -5 sigma.

Most important: what do the residual maps look like? Are these fairly
flat? 

How did you treat your f'/f'' values: if from a (good) fluorescence
scan you probably kept them fixed. A look at the ANO residual maps for
each wavlength then is a good test to see if these values are resonable.

Cheers

Clemens

PS: there is even the possibility of a problem wiht your anomalous
differences being (F-) - (F+) instead of (F+) - (F-) ...

-- 

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