PeptideShaker tries to map the detected peptides for a given protein onto the PDB structure of the protein using Jmol. If multiple PDB structures exist for a protein, it is up to the user to select the desired structure. If there are more than one chain in the structure, the user also decides which of the chains to use.
Note that the amino acid sequence covered by the PDB structure is (almost) always shorter than the complete protein
sequence. The overlap and the sequence coverage obtained is shown for each chain in the PDB Chains table.
Due to the often limited coverage provided by the PDB structure, not all peptides can be mapped to the structure. The
peptides that can be mapped are annotated with PDB in the Peptides table to the lower left and shown in
green on the 3D structure model. The currently selected peptide is shown in blue.
By default the structure rotates slowly around the structure's y-axis. The feature can be turned on or off
from the menu in the upper right corner of the structure panel.
On the same menu there are also options for choosing between two different structure model types, and an
option for turning on/off the modification labels.
To manually rotate the structure simply left click it and drag it in the wanted direction. Zooming is achieved either by holding down middle mouse key and dragging up or down, or by the use of the scroll wheel. Moving the structure is done by double clicking and dragging the left mouse button.
Additional interaction with the structure is achieved by right clicking in the structure panel. For further details on how to modify the structure see Jmol. Jmol is an open-source Java viewer for chemical structures, here used to display protein structures.
For additional information about the PDB structure click the link in the PDB Matches table.