Dear Nat, You are right. I added two metal ions Zn and Mg and after that I started getting this error. I did run phenix.metal_coordination to get elbow.edits and add this to refinement to to get same error. I am not running with water update option. I ran the pdb through readyset and added metal restraints, processed pdb file and ligand restraints to the refinement to get same error. The Zinc and Mg are not coordinated well. I have added because nothing fits in the density. I am not sure lack coordination is creating the problem. I will send ATOM records to Pavel. Thanks a lot for looking in to this one. SDY From: [email protected] Date: Tue, 4 Mar 2014 07:50:31 -0800 Subject: Re: [phenixbb] phenix error To: [email protected] CC: [email protected] You probably have metal coordination restraints that are no longer valid - each time you run phenix.refine with the solvent update enabled, the numbering of waters will change and the old restraints become invalid. áThe utilities menu in the phenix.refine GUI has an option to clear these out entirely; you can then run ReadySet again to generate new restraints. -Nat On Mon, Mar 3, 2014 at 10:31 PM, SD Y wrote: Hi, Could you please tell me why am I getting this error " No atom selected: "name O and chain W and resname HOH and resseq 69".á Log file ends as follows: ============================= Scattering factors ============================= á á á á á á á á ----------X-ray scattering dictionary---------- á á á á á á á á Number of scattering types: 7á Type áNumber á ásf(0) á Gaussiansá áZn2+ á á 1 á á 27.88 á á á 1á áS á á á 10 á á 15.96 á á á 2á áP á á á á2 á á 14.95 á á á 2 á áMg2+ á á 3 á á á9.96 á á á 1á áO á á á635 á á á7.97 á á á 2á áN á á á523 á á á6.97 á á á 2á áC á á 1983 á á á5.97 á á á 2á sf(0) = scattering factor at diffraction angle 0. ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ======================== Summary of geometry restraints ======================= á Number of disulfides: simple=0, symmetry=0á Custom bonds:Sorry------------------------------ Thanks a lotSDY _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb