Hey Norm, What are your sugar atoms named in the pdb? Coot likes to explode them if they have primes (C5') instead of stars (C5*).
Tim On Mon, Feb 8, 2010 at 3:23 PM, Norman Zhu <[email protected]> wrote: > hello there > > This email is a continuation of an inquiry I post last week. The > problem I had and still is i can't use the <real space refine > zone> and <regularization zone> functions on a DNA structure. Whenever i > ask the computer to fit the bases into the electron density it would give > me > a solution that would only satisfies the needs of the purine and pyrimidine > bases > but at the expense of the sugar and phosphate back bone. The solution > would > stretch all the atoms on the back bone beyond their bond length and place > some other ones out side of the density map. To see if this would also > happen to a base that doesn't need to be refined I used the real space > refine function on a base that sits comfortably in batch of well defined > electron density. The same thing happened. I attached two before and > after > images to show you what i am talking about. I tries this function again a > well defined protein residue and it worked just fine. To fix this problem > i > tried all kinds of methods but nothing worked. I tried lower the matrix > refinement from 60 to 10 to 2, as some people have suggested. I tried > anchoring atoms at few key positions. I moved atoms one by one into the > density refine it afterward, but nothing worked. It seems as though the > program can't recognize the nucleotides as nucleotide. It maybe trying to > refine it as a protein and using all the wrong constrains. i don't know, I > am not programmer. Has anybody encounter this problem before? > Norm > P.S. i also included a image of the base i trying to fix. I wanted to show > you how a straight forward a problem it should have been. Also that the > density of my map is good and should not causing the problem. > -- Timothy Silverstein Mount Sinai School of Medicine Structural and Chemical Biology 1425 Madison Avenue Box 1677 New York, NY 10029 212.659.8639
