The protassign Utility

The protassign script optimizes the hydrogen-bonding network, rotating hydroxyl and thiol hydrogens (including waters), generating appropriate protonation and tautomerization states of His, and performing chi flips in Asn, Gln, and His residues. For details of the methods used, see H-Bond Optimization Technical Notes. The syntax of the command is as follows:

protassign [options] input-file output-file

For information on the options, see protassign Command Help or use the command protassign -h. The input and output files must be Maestro files (.mae, .maegz, .mae.gz).

The log file reports an overall score for the structure, which you can use to compare different assignments.