[Xplor-nih] RNA-DNA Hybrid

[John Kuszewski]

On Jul 5, 2007, at 4:28 PM, <brinson at umbi.umd.edu> wrote:

>  I am unable to get the NCS restraints to work. My problem seems to  
> be this: in all the examples I have looked up, the degree of  
> symmetry seems to be higher (e.g. near or perfect palindromes, for  
> instance). In my case, the RNA is mostly purines, and the DNA is  
> mostly pyrimidines.

In that case, you shouldn't apply the NCS term at all.  Sorry for the  
misunderstanding.

You didn't mention any restraints across base pairs aside from Hbond  
NOEs.  You could add planarity restraints across
your basepairs, or if there's a significant propeller twist, a  
torsion angle restraint across the basepair.

--JK