Hi Wei,
If you have an interpretable density, the efficientest way in my
opinion, is to construct manually (only 6bp).
You can use coot and the button "add residue". Coot can add nucleotide
directly at the extremity of your existing nucleic acid model.
Hope to help you.
Nicolas
Le 18/03/13 03:43, Wei Shi a écrit :
Hi all,
I am refining a structure of protein-DNA complex with coot. The DNA in
my search model is shorter than the DNA in the crystal, and now I
could see the density for extra DNA(6 base pairs) on either end of the
search model DNA. But, I don't know how to build the extra DNA back to
fit the density or whether I should build the whole DNA manually to
fit the density.
I used calculate-> other model tools-> ideal DNA/RNA to generate a 6
base pairs (B form) and then, I use calculate->
model/fit/refine->rotate/Translate molecule to move the 6 bp long
stretch of double strand DNA to fit the density, but it's hard for me
to fit the DNA into the density and it seems that the B form DNA I
generate doesn't
fit the density well. I am wondering how to fit the DNA into the
density and whether we could fit the DNA into density like we add
amino acid to fit the density.
Thank you so much!
Best,
Wei
