The second stage is to prepare a multiple alignment of all the structures and sequences in the family of interest. An initial structural alignment of the structures can be obtained by the MODELLER's MALIGN3D command. A very robust protein structure alignment program is CE [Shindyalov & Bourne, 1998]. It is usually better to include all the structures related to the representative PDB structures, as listed in the modlib/CHAINS_3.0_40_XN.grp file. Using the ALIGN2D, ALIGN or MALIGN commands, the multiple structural alignment can then be aligned as one block with all the related sequences. Unfortunately, in most cases, automatically derived alignments have to be manually edited to optimize the quality of the model derived from the alignment. This is the task for the next stage.