Hi Madhusudhan,
As already mentioned, coot is perfectly adapted. But if you have a pretty long DNA
strand, maybe you can design an "artificial" DNA strand with
http://structure.usc.edu/make-na/server.html
It generated different form of DNA (B, Z and A). You can use your known
sequence and create a pdb model. Once you have this, you can fit it with you
favorites program or manually. Depending of your strategy, you will need to
merge your current model with the DNA one and continue to refine.
HTH
Nicolas
Nicolas Foos
PhD
Structural Biology Group
European Synchrotron Radiation Facility (E.S.R.F)
71, avenue des Martyrs
CS 40220
38043 GRENOBLE Cedex 9
+33 (0)6 76 88 14 87
+33 (0)4 76 88 45 19
On 20/03/2018 19:28, Madhu Sudhan wrote:
Dear all,
I have an X-ray diffraction data of a protein-DNA complex at 2.3A
resolution. I refined the structure, modeled the protein and the
R-free reached to 0.35. I am observing extra density for the bound DNA
molecule. As I am solving a protein-DNA complex structure for the
first time,
1) Could anyone suggest me whether any automated program available to
fit the DNA molecule into the density.
2) Also suggest me the other easiest ways, if any, to fit a DNA
molecule into the electron density map.
Thanks and Regards,
Madhusudhan
