First (in an automated way) the DNA segment selected in the main window is scanned for transcription factor binding sites (TFBS) from the Transfac Database. Then a search of structures in the PDB database from candidates with higher scores is performed. Only PDB structures with the Transcription factor bound to single DNA double helices are appropriate for the analysis. Either when no suitable TFBS are found (figure on the right hand side) or the user wants to add/remove annotated TFBS is there the possibility to edit the dialog box. The user must then Save the information and continue.