I'm running watertidy to move all waters to the (symmetry-related) position closest to my protein. One protein chain (A), 144 waters (chain W).
Trouble is, one round of watertidy doesn't move many of the waters (e.g., a water only 2.7 Ang. from a carbonyl oxygen of a symm-related protein was not moved). Those that were moved seem OK (checked first few). What's more, if I specify 3 rounds (default in CCP4i), then I end up with a final file that has only 21 waters. Has anyone had better luck with watertidy? Is there another program that can simply move the waters (e.g., as the PDB says they do when you deposit coords)? Thanks, Dave David Borhani, Ph.D. D. E. Shaw Research 120 West Forty-Fifth Street, 39th Floor New York, NY 10036 [email protected] 212-478-0698 http://www.deshawresearch.com
