Getting Unremediated PDB Files: Difference between revisions
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Eric Martz (talk | contribs) linked first occurrence of 'remediation' |
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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]] | |||
