W568 Nucleic Acids Research, 2009, Vol. 37, Web Server issue DaliLite (21) format, the table of atom correspondences and a PyMol (22) script that shows the pairs of surface points that generated the superimposition of the second structure onto the ﬁrst. Below, the results page (Figure 4) presents a Jmol visu- alization of the two superimposed structures, and a table containing the correspondences between the atoms of the two structures with the same atomtype and closer than 2.5 A˚ after the superimposition. Each pair of correspond- ing atoms can be visualized in spaceﬁll by clicking on its check box in the right-hand column of the table. (All the corresponding atoms can be simultaneously selected by clicking at the top of this column.) There is also a side- by-side view of the two structures where the regions that Figure 4. Alignment obtained from the comparison between the binding sites of 1atp, chain E and of 1csn, chain A. The table on the left shows the atom correspondences. When a box is checked, the relative pair of atoms is shown in spaceﬁll. Figure 5. Side-by-side view of 1atp, chain E and 1csn, chain A. The atoms that belong to the solution are colored following a gradient from the N-terminal (yellow) to the C-terminal (red). For each structure, the residues that belong to the solution are colored according to the colors in the Jmol visualization.