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Remediator

Remediator converts PDB files between PDBv2.3 and PDBv3.2 formats. It can accurately and rapidly convert in either direction: old to new OR new to old. Atom records of type ATOM, HETATM, TER, ANISOU, SIGATM, SIGUIJ, and LINK are converted, as are DNA residue names (e.g., A, C, T, G of v2.3 cf. DA, DC, DT, DG of v3.2). Remediator is available as a Perl or Python script. The scripts should work on any type of computing platform, as long as your operating system has the appropriate framework. You may need to edit the first line, the shebang, of the script to point at your computer's Perl or Python location.

Remediator uses the remediated Chemical Component Dictionary as its "rosetta stone" for conversion. The necessary information is incorporated into a hash table - internally for the Perl script, as an external file for the Python script.

Addtionally, the Perl script has an option to convert atom labels and probe dot labels for kinemage (KIN) files.
Script usage help is available internally by usage of an "-h" flag or by viewing the script itself in a text editor.
If you intend to use the Python script, be sure to download the master_hash.txt file.


Type Version Release date Download size Program
(click to download)
perl 1.58 11-May-11 1290 (Kb) download arrow remediator.1.58.110511.pl.zip
python 1.60 20-Nov-08 3 (Kb) download arrow remediator_python.1.60.081120.py.zip
python 1.60 11-May-11 554 (Kb) download arrow master_hash.1.60.110511.txt.zip

If you encounter an error in downloading, try to get the file from our browsable download section.