Hi all, I am refining a DNA-protein complex structure by phenix. My protein is a nuclease and the DNA bound to protein is a mixture of the substrate and product. Partial DNA was cleavaged by the protein and others is keep a un-cleavaged strand. I am trying to rerine this mixture with phenix. My DNA sequence is NNNN*AG*NNNNNN. Half of DNA was cleavaged between AG and half DNA keep a uncleavaged strand as my sequence. Nucleic acid AG have two conformations in this structure and a water molecule located close to the phosphate group when it uncleavaged. I defined AADE and BADE, AGUA and BGUA with 0.5 occupancy. I also give the water mentioned above 0.5 occupancy. I try to refine this structure by phenix but failed. Please give me some suggestion about this DNA alternative confromation refinement? How should I define the occ.params file? Thank you in advance.
Lisa
