The following are tools developed by the Joint Center for Structural Genomics group (2000-2015) at SSRL. They are no longer being maintained, but are available for as long as they run.

Find ligands in PSI structures: Ligand Search Server
Perform QC check on your structure: QC Check
Check out a target for Refinement or QC: RefQC Check      (For JCSG users only: requires password authentication)
Building of missing residues in electron density map gaps: Xpleo Server