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General discussions (Q&As) / large deviations in output values
« on: March 27, 2013, 09:36:21 am »
Below is a part of the 3DNA analysis with 3SJ2.
There are large deviations from average values in some of the parameters. Are the values real? What is the best way to view them in structures if so ? Thank you.
****************************************************************************
Local base-pair parameters
bp Shear Stretch Stagger Buckle Propeller Opening
1 G-C -0.34 -0.09 -0.07 -10.44 -5.94 -1.70
2 G-C -0.14 -0.02 0.12 -0.70 -9.80 0.43
3 G-U -2.33 -0.47 0.13 2.30 -12.27 1.61
4 C-G 0.22 -0.06 -0.00 3.70 -18.31 2.91
5 C-G 0.22 -0.10 0.10 0.15 -4.59 -0.12
6 G+G -1.48 -3.61 -0.15 11.94 4.31 87.72
7 G-C -0.10 -0.07 0.07 -5.76 -5.64 -0.74
8 C-G 0.16 -0.07 0.12 2.42 -3.10 -1.07
9 G+G -1.38 -3.56 -0.12 13.17 -2.07 89.05
10 G-C -0.12 -0.10 0.07 -1.15 -6.71 -1.03
11 C-G 0.06 -0.08 0.02 0.46 -7.58 -1.22
12 G+G 1.34 3.61 0.06 -12.38 3.07 -90.48
13 G-C -0.17 -0.07 0.10 -3.49 -1.85 -1.08
14 G-C -0.32 -0.10 -0.11 -0.11 -12.53 0.12
15 U-G 2.39 -0.57 -0.03 2.97 -16.49 -0.59
16 C-G 0.36 -0.10 -0.05 1.84 -7.91 0.41
17 C-G 0.24 -0.05 -0.16 7.91 1.98 -0.94
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -0.08 -0.32 0.00 0.76 -6.20 4.90
s.d. 1.05 1.53 0.10 6.69 6.42 38.26
****************************************************************************
Local base-pair step parameters
step Shift Slide Rise Tilt Roll Twist
1 GG/CC 0.64 -1.40 3.07 -0.19 8.24 27.95
2 GG/UC 1.08 -2.61 3.00 -0.59 8.45 19.57
3 GC/GU -0.27 -1.52 3.22 0.01 1.61 42.87
4 CC/GG -0.61 -1.97 3.29 -1.87 9.30 30.50
5 CG/GG 0.04 -3.25 -1.34 -170.79 31.71 160.42
6 GG/CG -0.47 -3.69 -3.19 128.85 -110.61 97.02
7 GC/GC -0.14 -1.57 3.19 -0.08 4.46 31.15
8 CG/GG 0.44 -3.37 -1.24 -173.11 29.11 140.36
9 GG/CG -1.16 -3.03 -3.68 130.70 -108.41 64.11
10 GC/GC -0.17 -1.96 3.23 0.06 2.30 33.86
11 CG/GG 1.27 -3.43 3.14 7.99 5.06 81.71
12 GG/CG -1.38 0.36 3.26 -1.43 3.54 -20.48
13 GG/CC 0.29 -1.83 3.28 1.40 7.23 28.66
14 GU/GC -0.13 -1.43 3.18 -0.68 6.40 41.94
15 UC/GG -0.04 -1.99 3.12 2.74 7.83 26.52
16 CC/GG 0.12 -2.06 3.23 0.34 3.18 25.15
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -0.03 -2.17 1.80 -4.79 -5.66 51.96
s.d. 0.71 1.03 2.54 78.54 41.46 46.78
****************************************************************************
Local base-pair helical parameters
step X-disp Y-disp h-Rise Incl. Tip h-Twist
1 GG/CC -4.37 -1.31 2.55 16.60 0.39 29.12
2 GG/UC -9.65 -3.11 1.71 23.49 1.63 21.31
3 GC/GU -2.24 0.37 3.16 2.20 -0.01 42.90
4 CC/GG -5.15 0.80 2.63 17.16 3.46 31.91
5 CG/GG -1.60 0.09 -1.43 15.86 85.44 178.93
6 GG/CG -2.37 -0.37 -1.04 -56.14 -65.39 173.26
7 GC/GC -3.68 0.24 2.94 8.25 0.16 31.46
8 CG/GG -1.65 0.02 -1.50 14.58 86.68 178.49
9 GG/CG -2.36 -0.43 -1.07 -55.73 -67.19 171.37
10 GC/GC -3.71 0.30 3.09 3.95 -0.10 33.94
11 CG/GG -2.73 -0.78 3.06 3.86 -6.09 82.16
12 GG/CG -2.48 -4.42 3.05 -9.84 -3.98 -20.83
13 GG/CC -5.03 -0.30 2.75 14.31 -2.77 29.58
14 GU/GC -2.59 0.12 2.94 8.88 0.94 42.41
15 UC/GG -5.79 0.66 2.42 16.55 -5.80 27.77
16 CC/GG -5.58 -0.19 2.96 7.27 -0.77 25.35
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -3.81 -0.52 1.76 1.95 1.66 67.44
s.d. 2.09 1.39 1.84 23.93 39.72 67.36
****************************************************************************
There are large deviations from average values in some of the parameters. Are the values real? What is the best way to view them in structures if so ? Thank you.
****************************************************************************
Local base-pair parameters
bp Shear Stretch Stagger Buckle Propeller Opening
1 G-C -0.34 -0.09 -0.07 -10.44 -5.94 -1.70
2 G-C -0.14 -0.02 0.12 -0.70 -9.80 0.43
3 G-U -2.33 -0.47 0.13 2.30 -12.27 1.61
4 C-G 0.22 -0.06 -0.00 3.70 -18.31 2.91
5 C-G 0.22 -0.10 0.10 0.15 -4.59 -0.12
6 G+G -1.48 -3.61 -0.15 11.94 4.31 87.72
7 G-C -0.10 -0.07 0.07 -5.76 -5.64 -0.74
8 C-G 0.16 -0.07 0.12 2.42 -3.10 -1.07
9 G+G -1.38 -3.56 -0.12 13.17 -2.07 89.05
10 G-C -0.12 -0.10 0.07 -1.15 -6.71 -1.03
11 C-G 0.06 -0.08 0.02 0.46 -7.58 -1.22
12 G+G 1.34 3.61 0.06 -12.38 3.07 -90.48
13 G-C -0.17 -0.07 0.10 -3.49 -1.85 -1.08
14 G-C -0.32 -0.10 -0.11 -0.11 -12.53 0.12
15 U-G 2.39 -0.57 -0.03 2.97 -16.49 -0.59
16 C-G 0.36 -0.10 -0.05 1.84 -7.91 0.41
17 C-G 0.24 -0.05 -0.16 7.91 1.98 -0.94
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -0.08 -0.32 0.00 0.76 -6.20 4.90
s.d. 1.05 1.53 0.10 6.69 6.42 38.26
****************************************************************************
Local base-pair step parameters
step Shift Slide Rise Tilt Roll Twist
1 GG/CC 0.64 -1.40 3.07 -0.19 8.24 27.95
2 GG/UC 1.08 -2.61 3.00 -0.59 8.45 19.57
3 GC/GU -0.27 -1.52 3.22 0.01 1.61 42.87
4 CC/GG -0.61 -1.97 3.29 -1.87 9.30 30.50
5 CG/GG 0.04 -3.25 -1.34 -170.79 31.71 160.42
6 GG/CG -0.47 -3.69 -3.19 128.85 -110.61 97.02
7 GC/GC -0.14 -1.57 3.19 -0.08 4.46 31.15
8 CG/GG 0.44 -3.37 -1.24 -173.11 29.11 140.36
9 GG/CG -1.16 -3.03 -3.68 130.70 -108.41 64.11
10 GC/GC -0.17 -1.96 3.23 0.06 2.30 33.86
11 CG/GG 1.27 -3.43 3.14 7.99 5.06 81.71
12 GG/CG -1.38 0.36 3.26 -1.43 3.54 -20.48
13 GG/CC 0.29 -1.83 3.28 1.40 7.23 28.66
14 GU/GC -0.13 -1.43 3.18 -0.68 6.40 41.94
15 UC/GG -0.04 -1.99 3.12 2.74 7.83 26.52
16 CC/GG 0.12 -2.06 3.23 0.34 3.18 25.15
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -0.03 -2.17 1.80 -4.79 -5.66 51.96
s.d. 0.71 1.03 2.54 78.54 41.46 46.78
****************************************************************************
Local base-pair helical parameters
step X-disp Y-disp h-Rise Incl. Tip h-Twist
1 GG/CC -4.37 -1.31 2.55 16.60 0.39 29.12
2 GG/UC -9.65 -3.11 1.71 23.49 1.63 21.31
3 GC/GU -2.24 0.37 3.16 2.20 -0.01 42.90
4 CC/GG -5.15 0.80 2.63 17.16 3.46 31.91
5 CG/GG -1.60 0.09 -1.43 15.86 85.44 178.93
6 GG/CG -2.37 -0.37 -1.04 -56.14 -65.39 173.26
7 GC/GC -3.68 0.24 2.94 8.25 0.16 31.46
8 CG/GG -1.65 0.02 -1.50 14.58 86.68 178.49
9 GG/CG -2.36 -0.43 -1.07 -55.73 -67.19 171.37
10 GC/GC -3.71 0.30 3.09 3.95 -0.10 33.94
11 CG/GG -2.73 -0.78 3.06 3.86 -6.09 82.16
12 GG/CG -2.48 -4.42 3.05 -9.84 -3.98 -20.83
13 GG/CC -5.03 -0.30 2.75 14.31 -2.77 29.58
14 GU/GC -2.59 0.12 2.94 8.88 0.94 42.41
15 UC/GG -5.79 0.66 2.42 16.55 -5.80 27.77
16 CC/GG -5.58 -0.19 2.96 7.27 -0.77 25.35
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -3.81 -0.52 1.76 1.95 1.66 67.44
s.d. 2.09 1.39 1.84 23.93 39.72 67.36
****************************************************************************