[phenixbb] Refining partially occupied DNA on top of itself

Pavel Afonine PAfonine at lbl.gov
Thu May 7 08:33:30 PDT 2009

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.


On 5/7/09 8:25 AM, bschmidt at berkeley.edu 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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