Hi Bryan, when you place them one on another with the occupancy 0.5, you need to treat them as "alternative conformations", that is set altloc identifiers A and B. In this case they will not "see" each other through non-bonded interactions term and therefore will not be pushed apart. Their relative occupancies will also be refined. Please let me know if you have any difficulty with this. I do not understand why xyz refinement is off. If you send me the inputs (data+model+commands), I will be happy to have a closer look. Pavel. On 5/7/09 8:25 AM, [email protected] wrote:
Hello, I am having difficulty using Phenix to build and refine a DNA duplex. The issue is that my asymmetric unit consists of one protein monomer bound to DNA, but the protein is a dimer and the DNA is not palindromic, so each monomer is bound to a different sequence of DNA. As such, the density for the two different DNA half-sites is averaged out in the asymmetric unit. I have tried to place two duplexes directly on top of one another, each with 0.5 occupancy, and then refine. But I have noticed two problems. The first is that when xyz refinement is off, and I look at the output files, the density for DNA is awfully green, as if there were only *one* helix with 0.5 occupancy there. The other problem I noticed is that when I turn xyz refinement on, and look at the output files, one of the two half-sites gets moved several angtroms, so that it is in a region that generally has no density. I expect that, if done properly, the backbone of both half-site DNAs ought not to move. Any advice would be greatly appreciated. Thanks, Bryan Schmidt
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