phenix.reduce: tool for adding hydrogens to a PDB model


phenix.reduce is a command line tool for adding hydrogens to a PDB structure file. Hydrogens are added in standardized geometry with optimization of the orientations of OH, SH, NH3+, Met methyls, Asn and Gln sidechain amides, and His rings. Both proteins and nucleic acids can be processed. HET groups can also be processed as long as the atom connectivity is provided. The program is described in Word, et al.(1999). J. Mol. Biol. 285, 1733-1745. For more information visit:

How to run

phenix.reduce is run from the command line:

% phenix.reduce [pdb_file] [options]

To get information about command line options type:

% phenix.reduce

or for a longer list:

% phenix.reduce -h

Hydrogens in refinement

Please refer to phenix.refine documentation to see how hydrogen atoms are used in structure refinement.