[sharp-discuss] Re: Heavy Atom Negative Density

[Clemens Vonrhein]

Dear Paul,

> Thanks for the response. I guess it's pretty obvious now you've said it -
> however, I have a few questions, and excuses!

No need for excuses ;-) After all, you're trying something fairly
fancy there ...

> 1) The Os and Hg derivative data have really weak anomalous signals (hence no use
> of anomalous data), so why would not including the Fe positions in these datasets
> have such a big impact?

It's not the fact that the Fe have no real anomalous signal: excluding
them from the set of chemical sites (C-sites) in these compounds means
that the isomorphous difference between your reference (in-house) and
e.g. the Os is seen as

   (F_protein          + F_osmium) - (F_protein + F_iron)  [1]

where it should be

   (F_protein + F_iron + F_osmium) - (F_protein + F_iron)  [2]


    F_protein = unperturbed native structure factor: no heavy atoms
    F_iron    = your modelled Fe sites
    F_osmium  = your modelled Os site

> 2) I don't understand what you mean by residual maps not using phase. I thought
> residual maps were:
> 
> |Fph - Fp|exp[i.phi(best)]

These are Difference Fourier maps. Sometimes, people call 'double
difference Fourier maps' also 'residual maps'

  | Fph - (Fp+Fh) | exp[i.phi(best)]

because they show sites that are not yet in the model for Fh. That's
the reason why we most of the time call our maps 'residual maps' too -
although the politically correct name would be 'log-likelihood
gradient' maps. So these maps are real space objects of the remaining
log-likelihood gradient - no phase involved at all. If you're familiar
with the 'double difference Fourier' maps (see e.g. the CCP4 fft doc)
than these maps are very similar: positive 'density' where you have to
put something and negative 'density' where your model has to removed.

Cheers

Clemens

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