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**w3DNA -- web interface to 3DNA / Re: DNA bend angle calculation**

« **on:**May 11, 2013, 06:26:17 am »

Hi,

Thank you for your reply.

the vectors we used were

HETATM 9998 XS X X 999 68.227 2.641 -26.513

HETATM 9999 XE X X 999 67.797 -2.012 34.748

and the output obtained from w3dna is followed

Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs

Deviation from regular linear helix: 3.42(0.40)

Helix: -0.007 -0.076 0.997

HETATM 9998 XS X X 999 68.227 2.641 -26.513

HETATM 9999 XE X X 999 67.797 -2.012 34.748

Average and standard deviation of helix radius:

P: 9.51(0.62), O4': 6.66(0.67), C1': 6.05(0.65)Helix: -0.007 -0.076 0.997

we have normalized the vectors and got the dot product of two vectors and applied acos on the result of dot product of two vectors and then multiplied with 180/Pi. Precisely the following equation we have used to calculate the bend angle

acos(dot(a, b)) * 180/pi

Thank you

Joseph Hussain

Thank you for your reply.

the vectors we used were

HETATM 9998 XS X X 999 68.227 2.641 -26.513

HETATM 9999 XE X X 999 67.797 -2.012 34.748

and the output obtained from w3dna is followed

Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs

Deviation from regular linear helix: 3.42(0.40)

Helix: -0.007 -0.076 0.997

HETATM 9998 XS X X 999 68.227 2.641 -26.513

HETATM 9999 XE X X 999 67.797 -2.012 34.748

Average and standard deviation of helix radius:

P: 9.51(0.62), O4': 6.66(0.67), C1': 6.05(0.65)Helix: -0.007 -0.076 0.997

we have normalized the vectors and got the dot product of two vectors and applied acos on the result of dot product of two vectors and then multiplied with 180/Pi. Precisely the following equation we have used to calculate the bend angle

acos(dot(a, b)) * 180/pi

Thank you

Joseph Hussain