[phenixbb] How to include restraints when refining DNA?

Morten Groftehauge mortengroftehauge.work at gmail.com
Wed May 2 08:20:44 PDT 2012

Hi Xun Lu,

Sounds like inverted oxygens on the phosphate backbone.
Go into Coot and find your DNA. Go 'Calculate' > 'Other Modelling Tools...'
> 'Base Pair'. Now click one of your bases and go to the new base generated
and compare the stereochemistry of OP1 and OP2 of your DNA and the one
you've just made. I'll bet you anything that a few of them have been
reversed and if you fix the naming you will get much better refinement.


On 31 January 2012 20:12, Nathaniel Echols <nechols at lbl.gov> wrote:

> 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
> > 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:
> https://www.phenix-online.org/version_docs/dev-973/refinement.htm#anch341
> But hopefully the secondary structure restraints can be made to work.
> -Nat
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Morten K Grøftehauge, PhD
Pohl Group
Durham University
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