[phenixbb] Educative Tool Idea

Edward A. Berry BerryE at upstate.edu
Tue Sep 13 17:10:15 PDT 2011

Nathaniel Echols wrote:
> On Tue, Sep 13, 2011 at 4:31 PM, Edward A. Berry<BerryE at upstate.edu>  wrote:
>> 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.

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