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:


File Name Last Modified ^ File Size
[DIR] all_pdb_files_20050106 2004-12-20 16:34 -
[DIR] all_mmcif_files_20050106 2004-12-20 19:27 -
[DIR] all_pdb_files_20060103 2005-11-14 18:23 -
[DIR] all_pdb_files_20070102 2005-11-14 18:23 -
[DIR] all_pdb_files_20070731 2005-11-14 18:23 -
[DIR] all_mmcif_files_20060103 2005-11-14 20:56 -
[DIR] all_mmcif_files_20070102 2005-11-14 20:56 -
[DIR] all_mmcif_files_20070731 2005-11-14 20:56 -
[DIR] all_xml_files_20060103 2005-11-14 21:08 -
[DIR] all_xml_files_20070102 2005-11-14 21:08 -
[DIR] all_xml_files_20070731 2005-11-14 21:08 -
[DIR] 20070102 2006-04-20 03:39 -
[DIR] all_mmcif_files_20080107 2007-04-25 11:39 -
[DIR] all_mmcif_files_20090105 2007-04-25 11:39 -
[DIR] all_mmcif_files_20090316 2007-04-25 11:39 -
[DIR] all_mmcif_files_20100104 2007-04-25 11:39 -
[DIR] all_mmcif_files_20110103 2007-04-25 11:39 -
[DIR] all_mmcif_files_20110707 2007-04-25 11:39 -
[DIR] all_pdb_files_20080107 2007-04-25 11:39 -
[DIR] all_pdb_files_20090105 2007-04-25 11:39 -
[DIR] all_pdb_files_20090316 2007-04-25 11:39 -
[DIR] all_pdb_files_20100104 2007-04-25 11:39 -
[DIR] all_pdb_files_20110103 2007-04-25 11:39 -
[DIR] all_pdb_files_20110707 2007-04-25 11:39 -
[DIR] all_pdb_files_20120102 2007-04-25 11:39 -
[DIR] all_pdb_files_20130101 2007-04-25 11:39 -
[DIR] all_pdb_files_20140102 2007-04-25 11:39 -
[DIR] all_pdb_files_20141203 2007-04-25 11:39 -
[DIR] all_pdb_files_20150102 2007-04-25 11:39 -
[DIR] all_pdb_files_20160101 2007-04-25 11:39 -
[DIR] all_pdb_files_20170101 2007-04-25 11:39 -
[DIR] all_pdb_files_20170710 2007-04-25 11:39 -
[DIR] all_pdb_files_20180101 2007-04-25 11:39 -
[DIR] all_pdb_files_20190101 2007-04-25 11:39 -
[DIR] all_pdb_files_20200101 2007-04-25 11:39 -
[DIR] all_pdb_files_20200722 2007-04-25 11:39 -
[DIR] all_xml_files_20080107 2007-04-25 11:39 -
[DIR] all_xml_files_20090105 2007-04-25 11:39 -
[DIR] all_xml_files_20090316 2007-04-25 11:39 -
[DIR] all_xml_files_20100104 2007-04-25 11:39 -
[DIR] all_xml_files_20110103 2007-04-25 11:39 -
[DIR] all_xml_files_20110707 2007-04-25 11:39 -
[DIR] 20070731 2007-07-31 21:59 -
[DIR] 20080107 2008-01-08 22:26 -
[DIR] 20090105 2009-01-07 00:34 -
[DIR] 20090316 2009-03-16 20:27 -
[DIR] 20100104 2010-01-05 17:20 -
[DIR] 20110103 2011-01-04 17:44 -
[DIR] all_xml_files_20120102 2011-07-06 19:07 -
[DIR] 20110707 2011-07-07 21:55 -
[DIR] all_mmcif_files_20120102 2011-11-22 14:23 -
[DIR] all_mmcif_files_20130101 2011-11-22 14:23 -
[DIR] all_mmcif_files_20141203 2011-11-22 14:23 -
[DIR] all_mmcif_files_20150102 2011-11-22 14:23 -
[DIR] all_mmcif_files_20160101 2011-11-22 14:23 -
[DIR] all_mmcif_files_20170101 2011-11-22 14:23 -
[DIR] all_mmcif_files_20170710 2011-11-22 14:23 -
[DIR] all_mmcif_files_20180101 2011-11-22 14:23 -
[DIR] all_mmcif_files_20200101 2011-11-22 14:23 -
[DIR] all_mmcif_files_20200722 2011-11-22 14:23 -
[DIR] 20120102 2012-01-02 09:33 -
[DIR] all_xml_files_20130101 2012-01-03 11:26 -
[DIR] all_xml_files_20141203 2012-01-03 11:26 -
[DIR] all_xml_files_20150102 2012-01-03 11:26 -
[DIR] all_xml_files_20160101 2012-01-03 11:26 -
[DIR] all_xml_files_20170101 2012-01-03 11:26 -
[DIR] all_xml_files_20170710 2012-01-03 11:26 -
[DIR] all_xml_files_20180101 2012-01-03 11:26 -
[DIR] all_xml_files_20190101 2012-01-03 11:26 -
[DIR] all_xml_files_20200101 2012-01-03 11:26 -
[DIR] all_xml_files_20200722 2012-01-03 11:26 -
[DIR] 20140102 2012-08-22 18:08 -
[DIR] 20141203 2012-08-22 18:08 -
[DIR] 20150102 2012-08-22 18:08 -
[DIR] 20160101 2012-08-22 18:08 -
[DIR] 20170101 2012-08-22 18:08 -
[DIR] 20130101 2012-08-22 18:08 -
[DIR] all_mmcif_files_20140102 2014-01-08 08:30 -
[DIR] all_xml_files_20140102 2014-01-08 08:31 -
[DIR] 20160302 2016-03-02 15:02 -
[DIR] 20170308 2017-03-08 17:09 -
[DIR] 20170710 2017-07-13 07:12 -
[DIR] 20180101 2017-12-15 01:48 -
[DIR] 20050106 2018-02-18 23:55 -
[DIR] 20060103 2018-02-18 23:56 -
[DIR] 20180321 2018-03-22 01:25 -
[DIR] 20190101 2018-12-18 03:04 -
[DIR] all_mmcif_files_20190101 2019-01-02 00:34 -
[DIR] 20200101 2019-12-20 05:48 -
[DIR] 20200610 2020-06-08 04:42 -
[DIR] all_mmcif_files_20210105 2020-07-04 12:41 -
[DIR] all_mmcif_files_20220103 2020-07-04 12:41 -
[DIR] all_mmcif_files_20230102 2020-07-04 12:41 -
[DIR] all_pdb_files_20210105 2020-07-04 12:41 -
[DIR] all_pdb_files_20220103 2020-07-04 12:41 -
[DIR] all_pdb_files_20230102 2020-07-04 12:41 -
[DIR] all_xml_files_20220103 2020-07-04 12:41 -
[DIR] all_xml_files_20230102 2020-07-04 12:41 -
[DIR] all_pdb_files_20240101 2020-07-04 12:41 -
[DIR] all_mmcif_files_20240101 2020-07-04 12:41 -
[DIR] all_xml_files_20240101 2020-07-04 12:41 -
[DIR] 20200722 2020-07-22 23:26 -
[DIR] 20200916 2020-09-16 11:46 -
[DIR] 20210105 2020-12-15 02:08 -
[DIR] all_xml_files_20210105 2021-01-06 00:11 -
[DIR] 20220103 2021-12-10 06:55 -
[DIR] 20230102 2022-11-29 05:50 -
[DIR] 20240101 2023-11-24 07:49 -
[TXT] README 2024-01-01 14:00 8.1K
[SCRIPT] rsyncSnapshots.sh 2024-01-01 14:00 7.6K

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 .