Electron densities and other maps in YASARA
For the majority of (not too old) PDB files determined by X-ray crystallography, the RCSB provides not only the structure factors, but also the corresponding electron densities for download. This is especially handy in case you are hypotizing about the functional role of some residues in your favorite protein, and want to check if the side-chain rotamer in the PDB file is strongly supported by the experimental data, or maybe somewhat more flexible in reality (i.e. smeared out in the electron density).
YASARA makes this kind of analysis trivial: when you download a PDB file from the RCSB at File > Load > PDB file from Internet, you can choose to include the electron density right away, and show it as a surface or wireframe at a given sigma contour level. Alternatively, you can import electron densities, electrostatic potentials and any other map in several supported formats (DSN6, Gaussian Cube, Delphi, YASARA table). YASARA turns the data into a 3D table (1D and 2D tables are also possible), which you can then manipulate, save in a different format, and visualize in countless ways. Six styles useful for electron densities are shown on the right side. For other types of maps, useful styles include points, transparent densities, crosses, planes, surfaces and 2D contours.