Dear Smith, You can use the mutate function in either Coot or pymol. I am not aware of how or if this can be done in Phenix Hope this helps Joel From: phenixbb-bounces@phenix-online.org [mailto:phenixbb-bounces@phenix-online.org] On Behalf Of Smith Liu Sent: Sunday, 8 March 2015 11:11 p.m. To: phenixbb@phenix-online.org Subject: [phenixbb] how to correct residuess with missing atoms Dear All, Is any function of Phenix or some other software which can be used to correct residuess with missing atoms in the PDB file? I am looking forward to getting your reply. Smith