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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 endIn 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.
Xplor-NIH 2024-09-13