Example: A Polypeptide Chain with an Unknown Section

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.