PDB Snapshot Archive

PDBj Snapshot Archive is the snapshots of PDB Archive. Typically we create it yearly at the head of year. But we also make it when we make major updates.

We provides snapshots of PDB Archive only with ftp and rsync. Some examples of usage are shown below:

Usage examples

ftp

Get all PDBx/mmCIF files for entries whose middle two digits of PDBID are "00".

$ ftp snapshots.pdbj.org
Connected to snapshots.pdbj.org.
220 Welcome to PDB Snapshot Archive FTP service.
Name (snapshots.pdbj.org:user): ftp
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> cd 20220103/pub/pdb/data/structures/divided/mmCIF/00
250 Directory successfully changed.
ftp> !mkdir 00
ftp> lcd 00
Local directory now: /home/user/00
ftp> mget *
mget 100d.cif.gz [anpqy?]? a
Prompting off for duration of mget.
229 Entering Extended Passive Mode (|||17423|)
150 Opening BINARY mode data connection for 100d.cif.gz (20910 bytes).
100% |*******************************************************| 20910       61.54 MiB/s    00:00 ETA
226 Transfer complete.
20910 bytes received in 00:00 (34.50 MiB/s)
229 Entering Extended Passive Mode (|||44627|)
150 Opening BINARY mode data connection for 200d.cif.gz (14772 bytes).
100% |*******************************************************| 14772      148.29 MiB/s    00:00 ETA
226 Transfer complete.
14772 bytes received in 00:00 (51.41 MiB/s)
229 Entering Extended Passive Mode (|||31259|)
150 Opening BINARY mode data connection for 200l.cif.gz (44370 bytes).
100% |*******************************************************| 44370       66.11 MiB/s    00:00 ETA
226 Transfer complete.
44370 bytes received in 00:00 (50.67 MiB/s)
229 Entering Extended Passive Mode (|||57306|)
150 Opening BINARY mode data connection for 300d.cif.gz (30277 bytes).
100% |*******************************************************| 30277       47.88 MiB/s    00:00 ETA
226 Transfer complete.
30277 bytes received in 00:00 (24.76 MiB/s)
229 Entering Extended Passive Mode (|||50634|)
150 Opening BINARY mode data connection for 400d.cif.gz (13492 bytes).
100% |*******************************************************| 13492       84.65 MiB/s    00:00 ETA
226 Transfer complete.
13492 bytes received in 00:00 (38.63 MiB/s)
ftp> bye
221 Goodbye.
$ ls -l 00
total 264
-rw-r--r--  1 user user  20910  4 21  2017 100d.cif.gz
-rw-r--r--  1 user user  14772  4 21  2017 200d.cif.gz
-rw-r--r--  1 user user  44370 11 25  2017 200l.cif.gz
-rw-r--r--  1 user user  30277  4 21  2017 300d.cif.gz
-rw-r--r--  1 user user  13492  3  3  2018 400d.cif.gz

rsync

Get the entry point list.

$ rsync -az snapshots.pdbj.org::
all             Entire Snapshots archive
20050106        January 6, 2005 snapshot
20060103        January 3, 2006 snapshot
20070102        January 2, 2007 snapshot
...

Get all the files in the entry point "20050106" to the local current directory.

$ rsync -az snapshots.pdbj.org::20050106 .

Get the README file in the entry point "20050106" to the local current directory.

$ rsync -az snapshots.pdbj.org::20050106/README .