Table 2. Programs in the PDB_REDO pipeline.

Program	Software suite	Application in PDB_REDO
Stripper	PDB_REDO	Removes unwanted atoms and edits LINK records in PDB files
Cif2cif	PDB_REDO	Checks and standardizes reflection data in mmCIF files
Extractor	PDB_REDO	Extracts the description of the structure model and refinement from a PDB file
Fitr	PDB_REDO	Compares R factors
Chiron	PDB_REDO	Fixes chirality errors
Bselect	PDB_REDO	Selects B-factor model complexity
Picker	PDB_REDO	Selects the best refinement from a set
Centrifuge	PDB_REDO	Removes waters
SideAide	PDB_REDO	Real-space rebuilds side chains and add missing ones
pepflip	PDB_REDO	Flips peptide planes
What_todo	PDB_REDO	Parses WHAT_CHECK reports for SideAide
REFMAC	CCP4	Performs reciprocal-space refinement
TLSANL	CCP4	Checks TLS-group definitions and converts total B factors to residuals
CIF2MTZ	CCP4	Converts reflection data from mmCIF to MTZ format
MTZ2VARIOUS	CCP4	Converts reflection data from MTZ to mmCIF format
CTRUNCATE	CCP4	Converts reflection intensities to amplitudes
MTZUTILS	CCP4	Manipulates MTZ files
CAD	CCP4	Merges MTZ files
UNIQUE	CCP4	Creates all possible reflections given unit-cell parameters and resolution
FREERFLAG	CCP4	Creates and completes Rfree set
SFCHECK	CCP4	Calculates completeness, twinning fraction and BWilson
DSSP	—	Assigns secondary structure
Umfconverter	PDB-care	Validates carbohydrates in structure model
WHAT_CHECK	WHAT IF	Validates the structure model
Pdbout2html	WHAT IF	Converts WHAT_CHECK validation reports to html
YASARA Structure	YASARA	Creates scenes for result visualization