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General discussions (Q&As) / dimer step parameters calculation for a DNA with flipped bases
« on: June 13, 2017, 12:44:11 pm »
Dear Dr. Xian-Jun Lu,
I'm using 3DNA to calculate the dimer step parameters from a protein-DNA structure. The DNA has a slightly bent conformation with two bases at the central region that are completelly flipped in a hextrahelical conformation.
While running your software, the program do not calculate the dimer step parameters where the flipped bases are allocated. See attached the table with a gap in the middle section. Moreover, you can see the plot with the roll and twist parameters. Below the plot, there is the DNA sequence. Asterisks indicated the flipped bases.
Have you ever seen something like that? Is it because the presence of a flipped base makes impossible to calculate the dimer step parameters? Should I omit thie data points at the central region?
Thanks a lot,
Anna
I'm using 3DNA to calculate the dimer step parameters from a protein-DNA structure. The DNA has a slightly bent conformation with two bases at the central region that are completelly flipped in a hextrahelical conformation.
While running your software, the program do not calculate the dimer step parameters where the flipped bases are allocated. See attached the table with a gap in the middle section. Moreover, you can see the plot with the roll and twist parameters. Below the plot, there is the DNA sequence. Asterisks indicated the flipped bases.
Have you ever seen something like that? Is it because the presence of a flipped base makes impossible to calculate the dimer step parameters? Should I omit thie data points at the central region?
Thanks a lot,
Anna