Visualize Electron Density Maps For Bound Ligands
View sigma-weighted 2m|Fo|-d|Fc| electron density "mini-maps" for bound ligands using the JSmol 3D View. This feature is available for ligands with more than one atom (ions excluded) in PDB entries with structure factor data. Different sigma values can be selected.
The feature can be accessed from an entry's Structure Summary page in the Small Molecule's section or from the bottom of the 3D View page.
Electron density mini-map for Retinoic Acid in PDB ID 1CBS at sigma level 1. In this example, the ligand fits well into the density.
Electron density mini-map for Thymidine-5'-Phosphate in PDB ID 3HW4 at sigma level 2. Electron density is only available for part of the ligand.
Electron Density (JSmol) button from the Structure Summary page for PDB entry 1CBS.
Options to view different ligands and mini-maps and to change sigma levels appear under the JSmol viewer for PDB entry 1PRC.