Getting Unremediated PDB Files: Difference between revisions
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All files obtained from the World Wide Protein Data Bank since August 1, 2007, are remediated. Information about | 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 [http://www.wwpdb.org/docs.html the Worldwide Protein Data Bank's Documentation page]. | ||
The | The unremediated PDB archive from before August 1, 2007 is available, as detailed [http://www.rcsb.org/pdb/static.do?p=general_information/news_publications/news/news_2007.html#20070904 here]. | ||
If | 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. | ||
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. | 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. | ||
