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