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Hi Stephen, We are addressing this problem for the next release. With the current release, the best approach is to blank out the segid columns, for example with the small script below. Ralf Usage: phenix.python blank_out_segid.py original.pdb > modified.pdb ---------------------------------- cut --------------------------------------- import sys def run(args): for file_name in args: for line in open(file_name).read().splitlines(): if ( line.startswith("ATOM") or line.startswith("HETATM")): line += " " * max(0, 80-len(line)) line = line[:72] + " " + line[76:] print line.rstrip() if (__name__ == "__main__"): run(sys.argv[1:]) ---------------------------------- cut ---------------------------------------