Getting Unremediated PDB Files: Difference between revisions
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Periodically, the [[Protein Data Bank]] remediates [[PDB files]] in the worldwide archive that it maintains. Two rounds of remediation took place between 2007 and 2009, in order to better standardize and enhance the PDB files deposited before December 2, 2008. The details of the two rounds can be found at [http://www.wwpdb.org/docs.html the Worldwide Protein Data Bank's Documentation page]. The most recent version was released March 17th, 2009 as described on the [http://www.pdb.org/pdb/static.do?p=general_information/news_publications/news/news_2009.html#20090317a news page at the Protein Data Bank]. | Periodically, the [[Protein Data Bank]] remediates [[PDB files]] in the worldwide archive that it maintains. Two rounds of [[PDB#Remediation|remediation]] took place between 2007 and 2009, in order to better standardize and enhance the PDB files deposited before December 2, 2008. The details of the two rounds can be found at [http://www.wwpdb.org/docs.html the Worldwide Protein Data Bank's Documentation page]. The most recent version was released March 17th, 2009 as described on the [http://www.pdb.org/pdb/static.do?p=general_information/news_publications/news/news_2009.html#20090317a news page at the Protein Data Bank]. | ||
The unremediated PDB archive from before March 17, 2009 is available, as detailed [http://www.pdb.org/pdb/static.do?p=general_information/news_publications/news/news_2009.html#20090317a here] because a time-stamped snapshot of the PDB archive before the March 17th release exists [ftp://snapshots.wwpdb.org/ here] in the directory 20090316. | The unremediated PDB archive from before March 17, 2009 is available, as detailed [http://www.pdb.org/pdb/static.do?p=general_information/news_publications/news/news_2009.html#20090317a here] because a time-stamped snapshot of the PDB archive before the March 17th release exists [ftp://snapshots.wwpdb.org/ here] in the directory 20090316. | ||
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==How to get the unremediated version?== | ==How to get the unremediated version?== | ||
Use the simple interface [http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/unremed.htm here at Eric Martz's UMASS site] to easily get July 31, 2007 unremediated pdb files [ftp://snapshots.wwpdb.org/ via ftp at the RCSB Protein Data Bank] in the directory 20070731. This is primarily for obtaining DNA before the residues were re-named DC, DG, DT, DA, for Protein Explorer/Chime. | <!--Use the simple interface [http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/unremed.htm here at Eric Martz's UMASS site] to easily get July 31, 2007 unremediated pdb files [ftp://snapshots.wwpdb.org/ via ftp at the RCSB Protein Data Bank] in the directory 20070731. This is primarily for obtaining DNA before the residues were re-named DC, DG, DT, DA, for Protein Explorer/Chime.--> | ||
The March 16, 2009 unremediated versions are available [ftp://snapshots.wwpdb.org/ via ftp at the | The March 16, 2009 unremediated versions are available [ftp://snapshots.wwpdb.org/ via ftp at the World Wide Protein Data Bank] in the | ||
directory 20090316. | directory 20090316. | ||
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To uncompress the downloaded files: | To uncompress the downloaded files: | ||
* First try simply double-clicking the compressed file. On Macs (in 2019) this decompresses them. | |||
* For uncompressing the 2007 files that are in .Z format: | * For uncompressing the 2007 files that are in .Z format: | ||
** Both .Z and .gz files can be uncompressed in Windows using [http://www.7-zip.org/ 7-Zip], which is freeware and open source. | ** Both .Z and .gz files can be uncompressed in Windows using [http://www.7-zip.org/ 7-Zip], which is freeware and open source. | ||
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''Please, note that .gz files can be displayed in Proteopedia without being uncompressed, since Jmol can read gzipped files directly.'' | ''Please, note that .gz files can be displayed in Proteopedia without being uncompressed, since Jmol can read gzipped files directly.'' | ||
==See Also== | |||
*[[Atomic coordinate files]] | |||
*[[PDB file format]] | |||
*[[PDB#Remediation|Remediation]] | |||
*[[Standard Residues]] | |||
*[[Non-Standard Residues]] | |||