Hi Josh, There's a short Python script at the end of this message that produces a fixed PDB file. If there is an 'H' in the problem column and the atom name is four characters long ending in a digit, it will switch the fourth character of the name around to the front. The scripts expects the problem file name as a command-line argument and prints the corrected file to standard output. Hope this helps... Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu --- script --- #!/bin/env python import sys pdbFile = file(sys.argv[1], "rU") for line in pdbFile: if (line.startswith("ATOM ") or line.startswith("HETATM")) and line[12] == "H" and line[15].isdigit(): print line[:12] + line[15] + line[12:15] + line[16:], else: print line, pdbFile.close()