The Fit3D webserver implements the JavaScript-based Protein Viewer from Marco Biasini . The zoom level can be controlled with the mouse wheel. You can manipulate the point of view by pressing the middle mouse button or by holding down the Shift-key. To center the point of view double click with the left mouse button.

One against one alignment for a single match found by Fit3D. The green ball-stick structure represents the query motif. Residues of the query motif are labeled in green, whereas the corresponding match is labeled in black on gray background.

One against all alignment for the query motif against all matches found by Fit3D. The residues of the query motif are labeled in green.

Global alignment of the query motif source structure (green) with a structure where a match occurred (grey). The superimposition is based on the matching residues of the query and the target structure. Hence, non-homologous structures can be easily recognized to verify whether a match occurred due to global structural similarity or convergent evolution.