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Download Weekly Release of New Sequence and InChI

Every Saturday by 3:00 UTC, for every new entry, the wwPDB website provides: sequence(s) (amino acid or nucleotide) for each distinct polymer (new_release_structure_sequence.tsv) and, where appropriate, the InChI string(s) for each distinct ligand (new_release_structure_nonpolymer.tsv)

Download Archive - Data Download Instructions

The PDB FTP archive is quite large. As of May 14, 2014, the entire server contains more than 1,200,000 files requiring over 373 GBbytes of storage. It continues to grow with each weekly update.

A number of download locations and options are provided to make access as efficient as possible.

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Using rsync protocol:

rsync --port=33444 ftp.wwpdb.org::
ftp            	Top level of PDB ftp tree approximately 130 GB ( /pub/pdb )
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ftp_derived    	Derived data directory within PDB ftp archive Approximately 120 MB ( /pub/pdb/derived_data )
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Download coordinate files in PDB Exchange Format (mmCIF):

rsync -rlpt -v -z --delete --port=33444 \
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rsync -rlpt -v -z --delete --port=33444 \
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Download coordinate files in PDB Format:

rsync -rlpt -v -z --delete --port=33444 \
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rsync -rlpt -v -z --delete --port=33444 \
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Using ftp protocol:

ftp ftp.wwpdb.org

will connect to an anonymous ftp server containing the remediated wwPDB repository.

Download coordinate files in PDB Exchange Format (mmCIF):

ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/mmCIF

Download coordinate files in PDBML format:

ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/XML

Download coordinate files in PDB format:

ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb

Download EMDB data files:

ftp://ftp.wwpdb.org/pub/emdb/structures

Download the validation report files:

ftp://ftp.wwpdb.org/pub/pdb/validation_reports

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PDBe:

Using rsync protocol:

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Download coordinate files in PDB Exchange Format (mmCIF):

rsync -rlpt -v -z --delete \
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./mmCIF

Download coordinate files in PDBML Format (xml):

rsync -rlpt -v -z --delete \
rsync.ebi.ac.uk::pub/databases/rcsb/pdb-remediated/data/structures/divided/XML/ \
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Download coordinate files in PDB Format:

rsync -rlpt -v -z --delete \
rsync.ebi.ac.uk::pub/databases/rcsb/pdb-remediated/data/structures/divided/pdb/ \
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Download EMDB map metadata header files (xml):

rsync -rlpt -v -z --delete --include "emd-*.xml" \
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Download directories/files for EMDB entry EMD-1003:

rsync -rlpt -v -z --delete \
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Download the validation report files:

rsync -rlpt -v -z --delete \
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Using ftp protocol:

	
ftp ftp.ebi.ac.uk

will connect to an anonymous ftp server containing the remediated wwPDB repository.

Download coordinate files in PDB Exchange Format (mmCIF):


ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/data/structures/divided/mmCIF

Download coordinate files in PDBML format:


ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/data/structures/divided/XML

Download coordinate files in PDB format:


ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/data/structures/divided/pdb

Download the full PDB ftp tree:

ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/

Download EMDB data files:

ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures

Download the validation report files:


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Need further help with the EBI site: Please contact Gaurav Sahni (gaurav@ebi.ac.uk) if you have any problems connecting to ftp.ebi.ac.uk.

PDBj:

Using rsync protocol:

rsync ftp.pdbj.org::

ftp            	Top level of PDB ftp tree approximately 145 GB ( /pub/pdb )
ftp_data       	Data directory within PDB ftp archive Approximately 144 GB ( /pub/pdb/data )
ftp_derived    	Derived data directory within PDB ftp archive Approximately 130 MB ( /pub/pdb/derived_data )
ftp_doc        	Doc directory within PDB ftp archive Approximately 331 MB ( /pub/pdb/doc )
emdb		Top level of EMDB ftp tree Approximately 49 GB ( /pub/emdb )
rsync           Top level of PDBj FTP tree aproximately 423 GB ( / )

Download coordinate files in PDB Exchange Format (mmCIF):

rsync -rlpt -v -z --delete \
ftp.pdbj.org::ftp_data/structures/divided/mmCIF/ ./mmCIF

Download coordinate files in PDBML Format (xml):

rsync -rlpt -v -z --delete \
ftp.pdbj.org::ftp_data/structures/divided/XML/ ./XML

Download coordinate files in PDB Format:

rsync -rlpt -v -z --delete \
ftp.pdbj.org::ftp_data/structures/divided/pdb/ ./pdb

Download EMDB map metadata header files (xml):

rsync -rlpt -v -z --delete --include "emd-*.xml" \
"ftp.pdbj.org::emdb/structures/EMD-*/header/" ./header

Download directories/files for EMDB entry EMD-5001:

rsync -rlpt -v -z --delete \
ftp.pdbj.org::emdb/structures/EMD-5001/ ./EMD-5001

Download the validation report files:

rsync -rlpt -v -z --delete \
ftp.pdbj.org::ftp/validation_reports/ ./validation_reports

Using ftp protocol:

ftp ftp.pdbj.org

will connect to an anonymous ftp server at PDBj containing the remediated wwPDB repository.

Download coordinate files in PDB Exchange Format (mmCIF):

ftp://ftp.pdbj.org/pub/pdb/data/structures/divided/mmCIF/

Download coordinate files in PDBML format (all):

ftp://ftp.pdbj.org/pub/pdb/data/structures/divided/XML/

Download coordinate files in PDBML format (no-atom site information):

ftp://ftp.pdbj.org/pub/pdb/data/structures/divided/XML-noatom/

Download coordinate files in PDBML format (atom site information only):

ftp://ftp.pdbj.org/pub/pdb/data/structures/divided/XML-extatom/

Download coordinate files in PDB format:

ftp://ftp.pdbj.org/pub/pdb/data/structures/divided/pdb/

Download EMDB data files:

ftp://ftp.pdbj.org/pub/emdb/structures

Download the validation report files:

ftp://ftp.pdbj.org/pub/pdb/validation_reports/

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