phenix.reduce: tool for adding hydrogens to a PDB model
Purpose
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: http://kinemage.biochem.duke.edu/software/reduce.php
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.
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