Getting Unremediated PDB Files: Difference between revisions

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7-zip as a possible uncompressor
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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.<br>
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.
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The March 16, 2009 unremediated versions are available [ftp://snapshots.wwpdb.org/ via ftp at the RCSB Protein Data Bank] in the directory 20090316.<br>
The March 16, 2009 unremediated versions are available [ftp://snapshots.wwpdb.org/ via ftp at the RCSB Protein Data Bank] in the  
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directory 20090316.
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These files come back in a compressed form. The 2007 files are .Z compressed, while the 2009 files are .gz compressed.<br>
These files come back in a compressed form. The 2007 files are .Z compressed, while the 2009 files are .gz compressed.
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Thus to get the two forms of 1d66:
Thus to get the two forms of 1d66:<br>
* For prior to 2007 remediation: <nowiki>ftp://snapshots.wwpdb.org/20070731/pub/pdb/data/structures/all/pdb/pdb1d66.ent.Z</nowiki>
* For prior to 2009 remediation: <nowiki>ftp://snapshots.wwpdb.org/20090316/pub/pdb/data/structures/all/pdb/pdb1d66.ent.gz</nowiki>
 
To uncompress the downloaded files:
* 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.
** Eric Martz's site lists WinZip as an alternative for PC but this program is not free once a trial period expires;
** Stuffit Expander failed to uncompress such a file on a PC although Eric lists it as useful on Macs.
** I found to uncompress them, I could upload them to the Web hosting server I have access to and use 'zcat -d <nowiki>[FILE NAME]</nowiki>' to have it show an uncompressed form in my Secure Shell client using logging enabled to save a file of the output locally on my own drive.
** Others have mentioned using a DOS version of uncompress on a PC, called uncomp.exe.
* For uncompressing the 2009 files that are in .gz format:
** Stuffit Expander works to uncompress such a file on a PC and most likely Macs.
** Both .Z and .gz files can be uncompressed in Windows using [http://www.7-zip.org/ 7-Zip], which is freeware and open source.
 
''Please, note that .gz files can be displayed in Proteopedia without being uncompressed, since Jmol can read gzipped files directly.''
 


For prior to 2007 remediation: <nowiki>ftp://snapshots.wwpdb.org/20070731/pub/pdb/data/structures/all/pdb/pdb1d66.ent.Z</nowiki><br>
For prior to 2009 remediation: <nowiki>ftp://snapshots.wwpdb.org/20090316/pub/pdb/data/structures/all/pdb/pdb1d66.ent.gz</nowiki>
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For uncrompressing the 2007 files that are in .Z format:<br>
Eric Martz's site lists Winzip as an alternative for PC but this program is not free once a trial period expires; Stuffit expander failed to uncompress such a file on a PC although Eric lists it as useful on Macs. I found to uncompress them, I could upload them to the Web hosting server I have access to and use 'zcat -d <nowiki>[FILE NAME]</nowiki>' to have it show an uncompressed form in my Secure Shell client using logging enabled to save a file of the output locally on my own drive. Others have mentioned using a DOS version of uncompress on a PC, called uncomp.exe.
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<p>
For uncrompressing the 2009 files that are in .gz format:<br>
Stuffit expander works to uncompress such a file on a PC and most likely Macs.
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See also [[Standard Residues]] and [[Non-Standard Residues]]
See also [[Standard Residues]] and [[Non-Standard Residues]]
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