Hi LISA, if you send me more details I might be able to address your questions (as Phenix developer). Though a better place to post your Phenix related questions is a Phenix mailing list, not CCP4bb.
P.S.> Ugh, I find Ed's reply totally.. how to say it softer using my non-native-English... embarrassing. All the best, Pavel On Fri, May 25, 2012 at 4:01 AM, LISA <[email protected]> wrote: > 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 >
