Getting Unremediated PDB Files: Difference between revisions
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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 unremediated pdb files [ftp://snapshots.wwpdb.org/ via ftp at the RCSB Protein Data Bank].<br> | >OK, both the pre-remediation snapshots are working. The trick is | ||
>that the 2007 files are .Z compressed, while the 2009 files are .gz | |||
>compressed. (True, this is stated in the ftp help files!) Thus to get 1lbg: | |||
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]. 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]. | |||
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. 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]] | ||
