Editing SecStrAnnotator:OneToOne (section)

===Arguments===

* <code><span style=color:green>DIRECTORY</span></code> is the directory containing all the input files. The output files will also be saved to this directory. 
* <code><span style=color:green>TEMPLATE</span></code> describes the template protein domain in one of the following formats: <code><span style=color:green>PDB</span></code> or <code><span style=color:green>PDB</span>,<span style=color:green>CHAIN</span></code> or <code><span style=color:green>PDB</span>,<span style=color:green>CHAIN</span>,<span style=color:green>RANGES</span></code>. The whole argument must be written without spaces. Examples: 
** <code>1og2</code> (structure 1og2, chain A by default)
** <code>1og2,B</code> (chain B)
** <code>1og2,B,100:400</code> (residues 100–400 of the chain B)
** <code>1og2,B,:400</code> (residues up to 400 of the chain B)
** <code>1h9r,A,123:183,252:261</code> (residues 123–183 and 252–261 of the chain A)
* <code><span style=color:green>QUERY</span></code> describes the query protein domain and uses the same format as <code><span style=color:green>TEMPLATE</span></code>.

Keep in mind that the chains and residues are numbered according to the label_* numbering scheme in mmCIF file format (i.e. chain identifier is <code>label_asym_id</code>, residue number is <code>label_seq_id</code>).