[phenixbb] building dna in coot

Paul Emsley paul.emsley at bioch.ox.ac.uk
Tue May 19 15:41:24 PDT 2009

Raja Dey wrote:
> Dear Friends,

> Does anyone have experience of building dna in coot? I can see the clear density, but I need to move some 
 > nucleotides. Any suggestion/direction is welcome.

Dear Raja,

(Not that I've done a lot of this you understand) but what you need to 
do depends on how bad your model is (and how good your map is).  If it's 
close you can simply click and drag around a residue range (more than 3 
residues takes some experience to handle correctly (generally I don't do 

If the model is a long way off, I'd delete the bits that don't fit to 
density - and build off a well-fitting stump using add terminal residue 
and simple mutate (and then refine).  And repeat.

You might find the Watson-Crick Base Pair tool useful.



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