Yes. that is how it should be done. if you have a map then you convert them to
Fourier coefficients directly using Fourier transformation.
Only for some particles density maps are positive everywhere. X-ray particles
are one of them.
For neutron and electron scattering maps could be negative as
EM maps are electron potential maps, fundamentally different from electron
density maps in X-ray crystallography.
You might also want to check the Protein Science paper by
Jimin Wang & Peter Moore, 2017
http://onlinelibrary.wiley.com/doi/10.1002/pro.3060/abstract
EM maps are electron potential
This is discussed, for example, here:
http://www.pnas.org/content/114/12/3103
Also, here I calculated the distribution of map values (scaled in r.m.s.)
for four groups of atoms: main-chain atoms, side-chain oxygen atoms of ASP
and GLU (negatively charged OD1, OD2, OE1, OE2), side chain atoms of
I would say so yes, but Garib is the expert on this - I'm only repeating
what he told me!
Cheers
-- Ian
On 15 March 2018 at 14:41, Eleanor Dodson wrote:
> So if I calculate "structure factors" from a map do I just use the map as
> is with the negative values
Hi Eleanor
Electron scattering factors can be negative for negative ions, particularly
at low d*. For a low-resolution map it means that the electric potential
is the opposite sign to what you expected. It's why you often don't see
ASP & GLU side-chains in low resolution EM maps.
Cheers
--
I am pig-ignorant about these ,, but this example has negative values as
well as positive..
What does this mean? I thought a well phased map would be pretty well all
positive..
Eleanor