[Xplor-nih] Calculation of palindromic DNA sequence

[Charles at Schwieters.org]

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Hello Silke--

> I want to calculate a DNA duplex structure with a palindromic sequence from 
> NMR data, means I have the NOE restraints only from half of the duplex. In 
> my case the center is not a normal Watson-Crick base pair but two modified 
> bases, which coordinate linear a metal ion. At first I just duplicated the 
> NOE restraints for the others, but the structures looked really bad. So the 
> idea was to calculate the upper half, copy it for the lower one and set it 
> in the right way together. Is there any possibility to do so with xplor NIH? 
> And can I optimize the whole structure afterwards?
> 

You should really use a completely symmetric potential if when you
include all atoms- all terms should have the proper symmetry. In
addition you should use the NCS potential as in the eginput/dna_refi
example scripts.

I hope this helps--
Charles
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