VHELIBS, a validation helper for ligands and binding sites
The Validation HElper for LIgands and Binding Sites (VHELIBS) is software that aims to ease the validation of binding site and ligand coordinates for non-crystallographers. It is written in java and can be downloaded from github here. I have not tested it extensivey but on my cursory look it seems to work fine under Mac OS X, provided you have installed java.
Using a convenient graphical user interface, it allows one to check how ligand and binding site coordinates fit to the electron density map. VHELIBS can use models from either the PDB or the PDB_REDO databank of re-refined and re-built crystallographic models. The user can specify threshold values for a series of properties related to the fit of coordinates to electron density (Real Space R, Real Space Correlation Coefficient and average occupancy are used by default). VHELIBS will automatically classify residues and ligands as Good, Dubious or Bad based on the specified limits. The user is also able to visually check the quality of the fit of residues and ligands to the electron density map and reclassify them if needed.
To start the application simply double-click on the icon, and then enter a PDB code (or you can load a list from a file) the analysis takes a few mins so if you are planning to examine a list of structures you may want to set it running overnight. The results can then be examined in the viewer which is uses JMOL.
It all seems pretty intuitive. In the view above the ligand atoms are purple and the associated electron density red, the protein atoms are white and a dubious area of associated electron density is shown in yellow.
You can read more details here Journal of Cheminformatics 2013, 5:36 doi.