About the contents of the PDBj data site
This page lists the files within the PDBj data archive. Information regarding data retrieval is written on the PDBj download page.
Files within the data site
efsite/data-web/${entryId}.mpbf.gz | |
pdb_versioned | Shared between all wwPDB members |
data | |
entries | |
${id23}/pdb0000${pdbid}/ | |
pdb_0000${pdbid}_xyz-ext-atom_v${version}.xml.gz | |
pdb_0000${pdbid}_xyz-no-atom_v${version}.xml.gz | |
pdb_0000${pdbid}_xyz_v${version}.cif.gz | |
pdb_0000${pdbid}_xyz_v${version}.xml.gz | |
removed | |
${id23}/pdb0000${pdbid}/ | |
pdb_0000${pdbid}_xyz-ext-atom_v${version}.xml.gz | |
pdb_0000${pdbid}_xyz-no-atom_v${version}.xml.gz | |
pdb_0000${pdbid}_xyz_v${version}.cif.gz | |
pdb_0000${pdbid}_xyz_v${version}.xml.gz | |
views | |
all | |
coordinates | |
mmcif | |
${id23}/pdb0000${pdbid}/ | |
pdb_0000${pdbid}_xyz_v${version}.cif.gz | |
pdbml | |
${id23}/pdb0000${pdbid}/ | |
pdb_0000${pdbid}_xyz_v${version}.xml.gz | |
latest | |
coordinates | |
mmcif | |
${id23}/pdb0000${pdbid}/ | |
pdb_0000${pdbid}_xyz.cif.gz | |
pdbml | |
${id23}/pdb0000${pdbid}/ | |
pdb_0000${pdbid}_xyz.xml.gz | |
pdbjplus | Data generated by PDBj for wwPDB data |
data | |
cc | chem_comp data (Chemie) |
mdl | |
${comp_id}.mdl.gz | |
mmcif | |
${comp_id}.cif.gz | |
mmjson | |
${comp_id}.json.gz | |
mmjson-plus | |
${comp_id}-plus.json.gz | |
rdf | |
${comp_id}.rdf.gz | |
svg | |
${comp_id}.svg.gz | |
xml | |
${comp_id}.xml.gz | |
ccmodel | |
mmcif | |
${model_id}.cif.gz | |
mmjson | |
${model_id}.json.gz | |
pdb | PDB data |
mmjson | |
${pdbid}.json.gz | |
mmjson-chain | |
${pdbid}_${asym_id}-chain.json.gz | |
mmjson-noatom | |
${pdbid}-noatom.json.gz | |
mmjson-plus | |
${pdbid}-plus.json.gz | |
rdf | |
${pdbid}.rdf.gz | |
prd | BIRD data |
mmcif | |
${prd_id}.cif.gz | |
mmcif-cc | |
${prd_id}-cc.cif.gz | |
mmjson | |
${prd_id}.json.gz | |
svg | |
${prd_id}.svg.gz | |
sifts | SIFTS data |
rdf | |
pdb_chain_cath_uniprot.ttl.gz | |
pdb_chain_enzyme.ttl.gz | |
pdb_chain_go.ttl.gz | |
pdb_chain_interpro.ttl.gz | |
pdb_chain_pfam.ttl.gz | |
pdb_chain_scop_uniprot.ttl.gz | |
pdb_chain_taxonomy.ttl.gz | |
pdb_chain_uniprot.ttl.gz | |
pdb_chain_uniprot_short.ttl.gz | |
pdb_pubmed.ttl.gz | |
uniprot_pdb.ttl.gz | |
dictionaries | Various dictionaries in various formats |
edmap2 | EDMap map data |
ccp4 | |
${pdbid}_validation_${type}_map_coef.ccp4 | |
mtz | |
${pdbid}_validation_${type}_map_coef.mtz | |
edmap.list | |
mine2 | |
dump | PostgreSQL RDB dump files |
rdb_docs | RDB documentation files in json format |
schema | RDB schema definitions in YAML format (used by mine2updater) |
statistics | RDB statistics; lists per column the number of non-null elements |
promode/data_web/${entryId}/ | The web-data for the secondary database Promode Elastic |
pub | Shared between all wwPDB members |
emdb | |
doc | |
obsoleted/${emdb_id}/header | Obsolete entries header files |
${emdb_id}-v19.xml | |
${emdb_id}-v30.xml | |
${emdb_id}.xml | |
status | |
archive | Weekly update history |
latest | Latest update history |
structures/${emdb_id}/ | Current entries data files |
header | |
${emdb_id}-v19.xml | |
${emdb_id}-v30.xml | |
${emdb_id}.xml | |
images/${emdb_id}.png | |
map/${emdb_id}.map.gz | |
${emdb_id}-v19.xml | |
validation_reports/${emdb_id}/ | |
${emdb_id}_full_validation.pdf.gz | |
${emdb_id}_validation.pdf.gz | |
${emdb_id}_validation.xml.gz | |
pdb | |
compatible/pdb_bundle/${id23}/${pdbid}/${pdbid}-pdb-bundle.tar.gz | |
data | |
biounit | |
PDB | |
all/${pdbid}.pdb${buid}.gz | |
divided/${id23}/${pdbid}/${pdbid}.pdb${buid}.gz | |
coordinates | |
all/${pdbid}.pdb${buid}.gz | |
divided/${id23}/${pdbid}/${pdbid}.pdb${buid}.gz | |
mmCIF | |
all/${pdbid}-assembly${buid}.gz | |
divided/${id23}/${pdbid}/${pdbid}-assembly${buid}.gz | |
bird | |
family | |
prd | |
component-models/complete/ | |
monomers/${comp_id} | |
status | List of weekly modified entries |
structures | |
all | |
XML/${pdbid}.xml.gz | |
XML-extatom/${pdbid}-extatom.xml.gz | |
XML-noatom/${pdbid}-noatom.xml.gz | |
mmCIF/${pdbid}.cif.gz | |
nmr_chemical_shifts/${pdbid}_cs.str.gz | |
nmr_data | |
${pdbid}_nmr-data.nef.gz | |
${pdbid}_nmr-data.str.gz | |
nmr_restraints/${pdbid}.mr.gz | |
nmr_restraints_v2/${pdbid}_mr.str.gz | |
pdb/pdb${pdbid}.ent.gz | PDB flatfile format |
structure_factors/r${pdbid}.ent.gz | mmCIF format |
divided | |
XML/${id23}/${pdbid}.xml.gz | |
XML-extatom/${id23}/${pdbid}-extatom.xml.gz | |
XML-noatom/${id23}/${pdbid}-noatom.xml.gz | |
mmCIF/${id23}/${pdbid}.cif.gz | |
nmr_chemical_shifts/${id23}/${pdbid}_cs.str.gz | |
nmr_data | |
${id23}/${pdbid}_nmr-data.nef.gz | |
${id23}/${pdbid}_nmr-data.str.gz | |
nmr_restraints/${id23}/${pdbid}.mr.gz | |
nmr_restraints_v2/${id23}/${pdbid}_mr.str.gz | |
pdb/${id23}/pdb${pdbid}.ent.gz | PDB flatfile format |
structure_factors/${id23}/r${pdbid}.ent.gz | mmCIF format |
models | |
current/pdb/${id23}/pdb${pdbid}.ent.gz | |
index | |
obsolete/pdb/${id23}/pdb${pdbid}.ent.gz | |
obsolete | |
XML/${id23}/${pdbid}.xml.gz | |
mmCIF/${id23}/${pdbid}.cif.gz | |
nmr_chemical_shifts/${id23}/${pdbid}_cs.str.gz | |
nmr_data | |
${id23}/${pdbid}_nmr-data.nef.gz | |
${id23}/${pdbid}_nmr-data.str.gz | |
nmr_restraints/${id23}/${pdbid}.mr.gz | |
nmr_restraints_v2/${id23}/${pdbid}_mr.str.gz | |
pdb/${id23}/pdb${pdbid}.ent.gz | PDB flatfile format |
structure_factors/${id23}/r${pdbid}.ent.gz | mmCIF format |
derived_data | |
doc | |
software | |
validation_reports${id23}/${pdbid} | |
${pdbid}_full_validation.pdf.gz | |
${pdbid}_multipercentile_validation.png.gz | |
${pdbid}_multipercentile_validation.svg.gz | |
${pdbid}_validation.pdf.gz | |
${pdbid}_validation.xml.gz | |
${pdbid}_validation_2fo-fc_map_coef.cif.gz | |
${pdbid}_validation_fo-fc_map_coef.cif.gz |
Explanation of the variables used in the above table:
${pdbid} | PDBID of the entry |
${comp_id} | comp_id (cc) of the entry |
${model_id} | Model ID (ccmodel) of the entry |
${prd_id} | PRD ID of the entry |
${emdb_id} | EMDB ID of the entry |
${id23} | 2nd and 3rd character of the PDBID |
${buid} | BU assembly ID |
${entryId} | Entry ID of the entry (efsite, promode) |
${version} | Version of the file |
Created: 2019-12-25 (last edited: more than 1 year ago)