[phenixbb] How to include restraints when refining DNA?

[Pavel Afonine]

Hi,

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..

Pavel

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.
>
> Cheers,
> Morten
>
> 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:
>
>     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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