[phenixbb] How to include restraints when refining DNA?
pafonine at lbl.gov
Wed May 2 23:08:24 PDT 2012
I would check phenixbb archives: I vaguely recall someone reported a
similar problem in the past, and I guess what's Morten suggested was the
solution. Though I might be confusing it with something else..
On 5/2/12 8:20 AM, Morten Groftehauge wrote:
> 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
> <mailto:nechols at lbl.gov>> wrote:
> On Tue, Jan 31, 2012 at 12:04 PM, Xun Lu <xluncsu at gmail.com
> <mailto: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.
> phenixbb mailing list
> phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
> Morten K Grøftehauge, PhD
> Pohl Group
> Durham University
> phenixbb mailing list
> phenixbb at phenix-online.org
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