Getting Unremediated PDB Files: Difference between revisions

Two rounds of remediation have now taken place between 2007 and 2009 to better standardize and enhance the PDB files deposited before December 2, 2008. The details of the two rounds can be found at [http://www.wwpdb.org/docs.html the Worldwide Protein Data Bank's Documentation page]. The most recent version was released March 17th, 2009 as described on the [http://www.pdb.org/pdb/static.do?p=general_information/news_publications/news/news_2009.html#20090317a news page at the Protein Data Bank].

 

The unremediated PDB archive from before March 17, 2008 is available, as detailed [http://www.pdb.org/pdb/static.do?p=general_information/news_publications/news/news_2009.html#20090317a here] because a time-stamped snapshot of the PDB archive before the March 17th release exists [ftp://snapshots.wwpdb.org/ here] in the directory 20090316.  

===Why would you need an unremediated version of a pdb file?===

A significant change made in the course of the first round (2007) 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 from before the 2007 remediation is that when the remediated PDB files contain DNA, CHIME-based 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 released after August 1, 2007, it will not be available in unremediated form that suits CHIME-based (and perhaps other) software. The second round of remediation (2008 round; released March 17th 2000) also mainly affected nucleic acid residues and atoms.<br>

Proteopedia also needs the unremediated files (pre-March 17th 2009). Proteopedia actually premiered between the two rounds of remediation and relied on the atom serial numbers for saving the scenes, yet contacts the PDB to get the current PDB file. Thus when the March 17th remediated version of the database was released with differing atom serial numbers, scenes involving nucleic acid using the newer files often no longer looked correct because some atom serial numbers now do not match. A global fix for this is currently being worked on according to Eran Hodis and Jaime Prilusky (see the gray banner at the top of the page for updates).

===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.

The March 16, 2009 unremediated versions are available [ftp://snapshots.wwpdb.org/ via ftp at the RCSB Protein Data Bank] in the  

 

See also [[Standard Residues]] and [[Non-Standard Residues]]