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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 ARG and LYS (positively charged NH1, NH2, NZ), and all other side-chain atoms. Clearly side-chain oxygen atoms of ASP and GLU have indeed systematically weaker density: http://cci.lbl.gov/~afonine/tmp/fig.png First picture: all maps from EMDB of resolution 3A or better. Second picture: all maps from EMDB of resolution 3-4A. All the best, Pavel On Thu, Mar 15, 2018 at 7:17 AM, Eleanor Dodson < [log in to unmask]> wrote: > 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 >