Re: [ccp4bb] How to fit DNA in density map of protein-DNA complex

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 creat

Re: [ccp4bb] How to fit DNA in density map of protein-DNA complex

Madhu Sudhan Sent: 20 March 2018 18:28:36 To: ccp4bb Subject: [ccp4bb] How to fit DNA in density map of protein-DNA complex 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

Re: [ccp4bb] How to fit DNA in density map of protein-DNA complex

Dear Madhu, Just use Coot since it should works Best, -- Rafael Molina, Associate Professor University of Copenhagen The Novo Nordisk Foundation Center for Protein Research Faculty of Health and Medical Sciences Blegdamsvej 3B Denmark My Research Gate profile

[ccp4bb] How to fit DNA in density map of protein-DNA complex

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) Coul