[phenixbb] Simulated annealing composite omit map conversion

Dale Tronrud det102 at uoxray.uoregon.edu
Sat Oct 8 23:27:50 PDT 2011

On 10/8/2011 7:27 PM, Nathaniel Echols wrote:
> On Sat, Oct 8, 2011 at 7:20 PM, Yuri<yuri.pompeu at ufl.edu>  wrote:
>> Thats simple enough... Do I have any control over grid  ( make a tighter
>> looking mesh for publication)
> grid_resolution_factor will set this - 0.33 is the default.  The
> spacing between grid points is this number times d_min.  I wouldn't
> recommend going much lower than 0.25, otherwise it risks misleading
> the reader into thinking that the map is more precise than is actually
> the case.

    "more precise than is actually the case"?  I don't understand this.
A map has precision to infinitely fine spacing.  The sampling grids we
choose are the artifacts - the courser the grid the worst the representation.
The prismatic points and spikes of a coarsely sampled map are aliasing
artifacts.  A smoothly varying surface is an accurate representation of
the continuous density function.

    You should contour your maps at whatever "fineness" it takes to get
rid of the sharp bends of the contours.  I routinely contour at 6 times
the resolution (which confusingly enough is "3" in Coot).  The practical
upper limit is that you usually want to be able to "see" though the
contours so the sampling rate becomes tied to the line width.

    A finely sampled map does not look "fabricated", it looks like proper
electron density.

Dale Tronrud

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