Getting Unremediated PDB Files
From Proteopedia
| Line 4: | Line 4: | ||
If a PDB file was published after August 1, 2007, it will not be available in unremediated form. | If a PDB file was published after August 1, 2007, it will not be available in unremediated form. | ||
| + | |||
===Why would you need an unremediated version of a pdb file?=== | ===Why would you need an unremediated version of a pdb file?=== | ||
| - | A large change made in the course of remediation was the distinction between ribonucleotides (A, C, G, I, T, U) and deoxyribonucleotides (DA, DC, DG, DI, DT, DU). The main reason for getting unremediated PDB files is that when the remediated PDB files contain DNA, Protein Explorer (and perhaps some other software) does not display the DNA properly. If the PDB file does not contain DNA (protein, RNA, solvent and ligands are OK), you probably don't need the unremediated file. | + | A large change made in the course of remediation was the distinction between ribonucleotides (A, C, G, I, T, U) and deoxyribonucleotides (DA, DC, DG, DI, DT, DU). The main reason for getting unremediated PDB files is that when the remediated PDB files contain DNA, Protein Explorer (and perhaps some other software) does not display the DNA properly. If the PDB file does not contain DNA (protein, RNA, solvent and ligands are OK), you probably don't need the unremediated file. If a PDB file was published after August 1, 2007, it will not be available in unremediated form. |
| + | |||
===How to get the unremediated version?=== | ===How to get the unremediated version?=== | ||
| - | Use the interface at [http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/unremed.htm Eric Martz's UMASS site] to get unremediated pdb files from the RCSB Protein Data Bank via FTP. | + | As detailed [http://www.rcsb.org/pdb/static.do?p=general_information/news_publications/news/news_2007.html#20070904 here], the unremediated PDB archive from before August 1, 2007 remains available at [ftp://ftp.rcsb.org via ftp at the RCSB Protein Data Bank].<br> |
| + | Use the interface at [http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/unremed.htm Eric Martz's UMASS site] to easily get unremediated pdb files from the RCSB Protein Data Bank via FTP.<br> | ||
| + | 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. | ||
Revision as of 02:42, 30 December 2008
All files obtained from the World Wide Protein Data Bank since August 1, 2007, are remediated. Information about the remediation project can be found at the Worldwide Protein Data Bank's Documentation page.
The unremediated PDB archive from before August 1, 2007 is available, as detailed here.
If a PDB file was published after August 1, 2007, it will not be available in unremediated form.
Why would you need an unremediated version of a pdb file?
A large change made in the course of remediation was the distinction between ribonucleotides (A, C, G, I, T, U) and deoxyribonucleotides (DA, DC, DG, DI, DT, DU). The main reason for getting unremediated PDB files is that when the remediated PDB files contain DNA, Protein Explorer (and perhaps some other software) does not display the DNA properly. If the PDB file does not contain DNA (protein, RNA, solvent and ligands are OK), you probably don't need the unremediated file. If a PDB file was published after August 1, 2007, it will not be available in unremediated form.
How to get the unremediated version?
As detailed here, the unremediated PDB archive from before August 1, 2007 remains available at via ftp at the RCSB Protein Data Bank.
Use the interface at Eric Martz's UMASS site to easily get unremediated pdb files from the RCSB Protein Data Bank via FTP.
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.
