the electron-density map
The electron-density map is the final prize of a structure determination: a three-dimensional contour map showing where the electrons — and therefore the atoms — actually are inside the unit cell. Atoms appear as peaks, hills of density, and heavier atoms make taller hills because they carry more electrons. Reading it feels like reading a topographic map of the cell, with each summit marking an atom.
It is built by Fourier synthesis: rho(x, y, z) = (1/V) times the sum over all reflections hkl of F(hkl) e^(-2 pi i (hx + ky + lz)). Crucially this sum needs each reflection's full structure factor — both its amplitude |F| (which you measured) and its phase phi (which you did not). So the map can only be computed after you have solved the phase problem. Once you have, the peaks locate the atoms, and the volume under each peak counts its electrons, which identifies the element (a carbon peak integrates to about six electrons, an oxygen to about eight).
This map is precisely what people mean when they say a structure has been solved. From the atom positions you read off bond lengths and angles, and a difference map — the observed density minus the density calculated from your current model — highlights atoms you have missed or misplaced, guiding refinement. Be honest that quality depends on resolution: low-resolution data blur neighbouring atoms into merged blobs, so you fit a model to the map and refine, rather than simply reading off coordinates.
In a solved organic structure the electron-density map shows a hexagonal ring of six evenly spaced peaks — a benzene ring — each peak integrating to about six electrons, confirming they are carbon atoms, with the atoms 1.4 angstrom apart.
Atoms show up as density peaks; peak height and integral identify the element.
You cannot compute the map without the phases, so it comes after phasing, not before. And low resolution merges atoms into blobs — the map is fitted with a model, not read off atom by atom.