[phenixbb] Educative Tool Idea
pafonine at lbl.gov
Tue Sep 13 17:17:28 PDT 2011
>>> In the meantime if you have ccp4 installed, sfall will calculate the
>>> structure factors, which you could display as above or with ccp4.
>> phenix.fmodel does this too - it will also include bulk solvent. I'm
>> not sure if this is important for the intended use; I wouldn't expect
>> reflections from a fake small-molecule crystal to be visually similar
>> to those of real macromolecular crystals anyway.
> This kind of exercise i good for educational purposes.
> For example make a model with 5 atoms, say alanine arbitrarily
> placed in a p1 cell. Now make an "omit" model whier one atom
> is missing. Calculate Fc and PhiC from both and combine them
> to make a map in various ways, using resolution 0.5 so each atom
> makes a peak. Does the omitted atom really show upat half-height
> in the Freal-PhiC and Fc-Phi-real maps? full height in the
> 2Fo-Fc map?
> Or switch it and say 4 atoms is the real structure,
> 5 is the model- does the extra atom disappear in the 2Fo-Fc map
> and show up negative in the Fo-Fc? (OK, the last two are obvious
> and don't need demonstrating)
> Or explore the limits of resolution imposed by the smoothness
> of atomic orbitals: calculate Fc at successively higher and
> higher resolution, use sfcheck to calculate the optical resolution,
> and explain why it doesn't go below about 0.5 A, and what happens
> if you give all the atoms B-factors around 80.
That's exactly how I did most of the slides (that show maps) here:
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