The Tool Buttons
The PDB viewer is a light-weight feature for displaying the 3D structures contained in a PDB file.
The figure can be rotated around all axes by using the mouse.
If a cross-linker has been selected (from the main window), the menu entry "theoretical cross-link distances from PDB" can be used to
generate in-silico cross-link maps. These show the distance between each reactive residue in the protein(s) in Angstrom. The colours show
whether a particular crosslink is within reach for the selected cross-linker (green) or not (red).

You can use this feature to help you decide on a cross-linker before you set up the actual experiment.
The second page of the PDB viewer displays
information on each residue in the pdb file, and its
position in the XYZ planes.
The generated in-silico cross-link map is
shown automatically in the cross-link
heatmap tool window.

Notice that you an also load pdb files from
here, and create in-silico cross-link
heatmaps.