Getting Unremediated PDB Files: Difference between revisions
From Proteopedia
Jump to navigationJump to search
| Line 20: | Line 20: | ||
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.<br> | ||
The March 16, 2009 unremediated versions are also available [ftp://snapshots.wwpdb.org/ via ftp at the RCSB Protein Data Bank] in the directory 20090316. | The March 16, 2009 unremediated versions are also available [ftp://snapshots.wwpdb.org/ via ftp at the RCSB Protein Data Bank] in the directory 20090316.<b> | ||
These files come back in a compressed form. 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. | These files come back in a compressed form. The 2007 files are .Z compressed, while the 2009 files are .gz compressed. Thus to get the two forms of 1d66:<br> | ||
For prior to 2007 remediation:<no wiki>ftp://snapshots.wwpdb.org/20070731/pub/pdb/data/structures/all/pdb/pdb1d66.ent.Z</no wiki> | |||
For prior to 2009 remediation:<no wiki>ftp://snapshots.wwpdb.org/20090316/pub/pdb/data/structures/all/pdb/pdb1d66.ent.gz</no wiki> | |||
<br> | |||
For uncrompressing the 2007 files that are in .Z format: | |||
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. | |||
See also [[Standard Residues]] and [[Non-Standard Residues]] | See also [[Standard Residues]] and [[Non-Standard Residues]] | ||
