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. 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 more and whether we could fit the DNA into density like we add amino acid to fit the density. Thank you so much!
Best, Wei
