[phenixbb] How to include restraints when refining DNA?

Nathaniel Echols nechols at lbl.gov
Tue Jan 31 12:12:43 PST 2012

On Tue, Jan 31, 2012 at 12:04 PM, Xun Lu <xluncsu at gmail.com> wrote:
> 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?

I don't know why the secondary structure restraints wouldn't work -
could you please send me the PDB file off-list so I can see what's
going wrong?  (No data necessary.)

By the way, which version of Phenix are you using?

> 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?

Yes, see here:


But hopefully the secondary structure restraints can be made to work.


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