[phenixbb] Refining partially occupied DNA on top of itself

[bschmidt at berkeley.edu]

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