In crystallography, one frequently encounters the situation where a section is unknown but there is evidence that the polypeptide segment is actually connected. Suppose the chain has the sequence Tyr, Ala, Glu, Lys, Ile, Ala, Ala, Ala, Glu, Asp, Gly, Gly, Gly, and two of the innermost alanines are missing. To generate an appropriate molecular structure, one should follow the example below:
segment
name="PROT"
chain
link pept head - * tail + * end
first prop tail + pro end
first nter tail + * end {* Note that the C-terminus is *}
{* missing. *}
sequence TYR ALA GLU LYS ILE ALA end
end
chain
link pept head - * tail + * end
last cter head - * end {* Note that the N-terminus is *}
{* missing. *}
sequence GLU ASP GLY GLY GLY end
end
end
In a real case, one might want to read the sequence
from the coordinate file, which would require splitting
the original coordinate file into two files containing
the two known sections of the chain.