Background When preparing a PDB for analysis (eg docking or modeling) it is important to check the reported occupancies and b-factors. The occupancy is a fraction of atimic density at a given center. If there are two eqally occupied conformers both will have an occupancy of 0.5 - the normal value is 1 range 0-1. The *{B-Factor} is the mean-square displacement of atom from its position in the model - the normal range is 5-50.

One way of visualizing the occupancy and b-factor is by coloring the structure by these values. You can do this by clicking and holding on a representation button in the display panel and selecting Color-by.

As an example let us look at the crystal structure 1ATP

• Type in the PDB search tab 1atp and the structure will be displayed in the graphical display.
• Use the ICM workspace to undisplay everything except for the "e" subunit. You can do this by clicking in the blue boxes in the ICM Workspace.
• Display the "e" subunit in wire representation using the wire button in the display tab.
• Click and hold on the wire button and select Color-by B-Factor. Regions of high B-factor are colored red.