OCA© FAQ

FAQ, tips and suggestions to get more from OCA©.

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To link to the Atlas page	use /oca-bin/ocashort?id=1ACE	It will retrieve the newest available ID (1ACE is obsolete)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)

OCA query tags:
au: Author, Family name of depositor or author of associated publication 
kw: Keyword, Molecule name, class or family, or related term
tx: Text, Any word in the complete PDB text 
ex: Method of Structure Determination
    values xrd  X-Ray Diffraction
           nmr  NMR
           sxr  Synchrotron X-Ray Diffraction
           edi  Electron Diffraction
           emi  Electron Microscopy
           fdi  Fiber Diffraction
           ndi  Neutron Diffraction
           ftr  Fluorescence Transfer
           mod  Theoretical Model
gn: Gene designation
fu: Function
di: Disease           
ht: HET Group, Ligand, Associated group
hl: ON-HOLD structures (implies m=du)
lower: lower range date released structures
upper: upper range date released structures
fa: Query sequence in FASTA format
idns: ID namespace
    values pdb   PDB
           GO    GO Gene Ontology
           PRO   PRO Protein Ontology
           pmed  PubMed
           inter Interpro
           cath  CATH
           pfam  PFam


OCA valid output data modes:
tag m
  ci PDB in mmCIF format
  xm PDB in XML(CML) format
  cc Crystal Cards
  sh PDB Header Only
  fu PDB w/Coordinates
  fa Sequences (FASTA format)
  su Summary
  du Plain text list of hits
  id Plain text list of PDB ID