Interrogate the mapping from your scripts
31.01.20 REST Access
The URI for REST access has changed (again!) The URI is now:
http://www.bioinf.org.uk/servers/pdbsws/query.cgi?plain=1&qtype=ttt&id=iii&chain=ccc&res=rrr
You may access the mapping directly from your scripts
using a URI of the form:
http://www.bioinf.org.uk/servers/pdbsws/query.cgi?plain=1&qtype=ttt&id=iii&chain=ccc&res=rrr
The fields in the URI are as follows:
| Field | Meaning |
|---|---|
| plain=1 | This causes the CGI script to generate plain parsable text rather than HTML |
| plain=2 | This causes the CGI script to generate JSON output 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 |
For example:
http://www.bioinf.org.uk/servers/pdbsws/query.cgi?plain=1&qtype=pdb&id=1yqv&chain=y&res=24
http://www.bioinf.org.uk/servers/pdbsws/query.cgi?plain=1&qtype=pdb&id=1yqv
http://www.bioinf.org.uk/servers/pdbsws/query.cgi?plain=1&qtype=pdb&id=1yqv&all=yes
http://www.bioinf.org.uk/servers/pdbsws/query.cgi?plain=1&qtype=id&id=LYSC_CHICK
http://www.bioinf.org.uk/servers/pdbsws/query.cgi?plain=2&qtype=ac&id=P03952&res=400
Results
The results are returned in the form:
| Keyword | Meaning |
|---|---|
| PDB: | PDB code |
| CHAIN: | chain label |
| RESID: | PDB residue id |
| PDBAA: | Amino acid present in the PDB file |
| AC: | UniProt accession |
| ID: | UniProt identifier |
| 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.
Perl Modules
Two Perl modules are provided to make this easier from within your code