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 maps, fundamentally different from electron density maps in X-ray crystallography. All the best, Steve On Thu, Mar 15, 2018 at 12:09 PM Pavel Afonine <pafon...@gmail.com> wrote: > 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 < > 0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> 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 >> > > -- Steve Chou
