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You may also access the mapping directly from your scripts using a URL of the form: http://www.bioinf.org.uk/cgi-bin/pdbsws/query.pl?plain=1&qtype=ttt&id=iii&chain=ccc&res=rrr
The fields in the URL are as follows:
|plain=1||This causes the CGI script to generate plain parsable text rather than HTML|
|all=yes||This causes a full alignment to be printed|
|qtype=ttt||ttt is the query type which may be pdb, ac, or id|
|id=iii||iii is the PDB code, SwissProt identifier, or UniProt accession|
|chain=ccc||ccc is the chain label used only when the query type is PDB|
|res=rrr||rrr is the PDB residue identifier, or the residue number in the UniProt entry|
The results are returned in the form:
|RESID:||PDB residue id|
|PDBAA:||Amino acid present in the PDB file|
|UPCOUNT:||Residue number in the UniProt sequence|
|UPAA:||Amino acid present in the UniProt file|
|START:||First residue in the PDB chain (if known)|
|STOP:||Last residue in the PDB chain (if known)|
|ERROR:||Error message (if any - database connectivity)|
The RESID: PDBAA: UPCOUNT: and UPAA: fields will only be provided if a residue number has been used in the search.
Two Perl modules are provided to make this easier from within your code