Here is an example of an alignment for input for the program "Geometrical Core".

Note that the names of sequences should be of the form:
PDBcode_Chain[_Model]

>1PER_L
SISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKTK-RPRFLPELASALGVS
VDWLLNGT
>1PER_R
SISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKTK-RPRFLPELASALGVS
VDWLLNGT
>1ADR_A_1
LMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCS
PDYLLKGD
>1ADR_A_2
LMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCS
PDYLLKGD