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.
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