The alignment and the list of templates are used by MODELLER to derive several slightly different models automatically. This stage is straightforward and is described in the tutorial (Section 1.8). However, do check the log file for error messages by searching for the `_E>' string. Usually, the representative model is that which has the lowest value of the molecular pdf. If the models are constructed by the standard procedure, this value is reported in the log file as well as in the REMARK record of the output PDB files with the models.