Note: parameters are case insensitive. In the following examples
they are written in upper case for clarity.
|
Desired action | Working example | Comments |
To retrieve a list of all available PDB entries |
use the URL /oca-bin/ocaids?id=ALL |
|
To link to the Atlas page |
use /oca-bin/ocashort?id=1ACE |
It will retrieve the newest available ID (1ACE is obsolete) |
To retrieve an obsolete entry |
add the parameter obs=1
to send-pdb, as in this URL
/oca-bin/send-pdb?obs=1&id=1ACE |
|
To retrieve a gzip compressed PDB file |
use /oca-bin/send-x-pdb?id=4HHB |
|
Query OCA and get a list of PDB ids entries related to sclerosis with Zn as Associated group |
use /oca-bin/ocaids?di=SCLEROSIS&ht=ZN
| (see at the bottom the list of valid query tags) |
To retrieve a list of ON-HOLD structures related to tuberculosis |
use /oca-bin/ocaids?hl=TUBERCULOSIS |
|
To retrieve a list of structures that contain ligand BTN |
use /oca-bin/ocaids?m=du;ht=BTN |
(mode du; hetero BTN) |
To retrieve a list of structures that contain ligand BTN and that belong to Author Freitag |
use /oca-bin/ocaids?m=du;ht=BTN;au=Freitag |
(mode du; hetero BTN; author Freitag) |
To retrieve a list of PDB IDs for structures associated with Protein Ontology ID PRO:000000090 |
use /oca-bin/ocaids?m=id;idns=pro;id=90 |
(mode id; namespace PRO; PROid 90) |
To retrieve a list of PDB structures by Resolution |
use /oca-bin/ocaids?m=id;rs=2.17-2.20
use /oca-bin/ocaids?m=du;rs=<0.6 |
(resolution between 2.17-2.20, only ids)
(resolution smaller than 0.6, short line) |
To retrieve a list of PDB structures released between 01-Jan-2009 and 01-Jan-2010 |
use /oca-bin/ocaids?m=du;lower=01-01-2009;upper=01-Jan-2010 |
(mode du; lower and upper dates) |