Edward A. Berry wrote:
Hailiang Zhang wrote:
Hi there:
I found that the grid values in the map file generated by CCP4-fft
generally has a mean value of ~0, and of course there will be lots of
negative values. This apparently is not the real physics, since the
electron density has to be positive everywhere (hope I am right). Can
somebody give me any hint how to convert the fft map file which has mean
value of 0, to a more physically meaningful map which has positive
densities everywhere? (I thought about offsetting the whole map by the
minimum negative values to make everything positive, but I doubt it is
right).
Best Regards, Hailiang
Actually taking the minimum value as zero might be a good approximation,
as long as the resolution is high enough so there are gaps in the protein
too small to be solvent-filled but large enough to be resolved from
surrounding density.
Maps from FFT will always have average value zero unless you include the
0,0,0 reflection: the transform is a sum of sin and cos terms, all of
which have
zero value when integrated over the unit cell, except the cos(0.X) term.
So any linear combination of these terms will average to zero if it doesn't
include the zero order term.
The 0,0,0 reflection is hard or impossible to measure because it gets
mixed up with the undiffracted beam. But it is easy to calculate, because
the integral of unity against the electron density is just the average
electron density times the volume, or the total number of electrons.
So if you know the total number of electrons in the unit cell,
you can divide by the unit cell volume to get the average
electron density (OK, I guess that is obvious) and add it to the
zero-average FFT map. This assumes the map is on an absolute scale,
which won't be quite true, so your idea of offsetting the minimum
to zero may be more satisfactory.
Ed
Ed is right, of course. Just remember to include ALL the electrons
in the unit cell - both those of the protein and those of the solvent,
ordered and disordered.
Dale Tronrud
