[phenixbb] How to include restraints when refining DNA?

Xun Lu xluncsu at gmail.com
Tue Jan 31 12:04:06 PST 2012

Dear all,

I am refining a protein-DNA complex structure at 2.9A resolution. The
R/Rfree is 0.2181/0.2501, which is pretty good, but I can tell that the DNA
is not well refined. Some sugar puckers are not right. The distances
between some base-paired bases are kind of short (~2.5A). I've tried
including a reference model for the DNA, or including a cif file, and I've
also tried to turn on the secondary_structure_restraints.... nothing
worked. I must have not done it in a correct way. But how to do it? And how
to deal with sugar puckers?
In refmac, I can set the distances between bases during the refinement, so
there must be a way to do it in phenix as well?

Any advice is welcome.


Department of Molecular and Structural Biochemistry
North Carolina State University
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20120131/f406cd78/attachment.htm>

More information about the phenixbb mailing list