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In addition to (or instead of) manipulating parameters in misc_3dna.par, oftentimes it may be preferable to manually edit find_pair-generated base-piar files before feeding them into analyze/cehs. This allows for maximum flexibility as to which pair to consider in calculating 3DNA structural parameters.
my.pdb
my.out
2 # duplex
28 # number of base-pairs
1 1 # explicit bp numbering/hetero atoms
198 253 0 # 1 | ....>C:...1_:[.DC]C-----G[.DG]:..28_:D<.... 0.09 0.00 12.58 9.13 -4.27
199 252 0 # 2 | ....>C:...2_:[.DA]A-----T[.DT]:..27_:D<.... 0.29 0.11 12.49 8.76 -3.87
200 251 0 # 3 | ....>C:...3_:[.DG]G-----C[.DC]:..26_:D<.... 0.38 0.17 11.55 8.98 -3.71
201 250 0 # 4 | ....>C:...4_:[.DC]C-----G[.DG]:..25_:D<.... 1.05 0.36 15.27 8.77 -2.47
202 249 0 # 5 | ....>C:...5_:[.DT]T-----A[.DA]:..24_:D<.... 0.18 0.01 12.00 8.93 -4.21
203 248 0 # 6 | ....>C:...6_:[.DC]C-----G[.DG]:..23_:D<.... 0.19 0.02 9.73 9.01 -4.29
204 247 0 # 7 | ....>C:...7_:[.DT]T-----A[.DA]:..22_:D<.... 0.28 0.04 8.95 9.03 -4.18
205 246 0 # 8 | ....>C:...8_:[.DG]G-----C[.DC]:..21_:D<.... 0.34 0.08 7.51 8.96 -4.12
206 245 0 # 9 | ....>C:...9_:[.DT]T-----A[.DA]:..20_:D<.... 0.20 0.12 8.73 8.88 -4.12
207 244 0 # 10 | ....>C:..10_:[.DA]A-----T[.DT]:..19_:D<.... 0.23 0.18 13.22 8.78 -3.75
208 243 0 # 11 x ....>C:..11_:[.DC]C-----G[.DG]:..18_:D<.... 0.35 0.30 19.14 8.92 -3.08
209 242 0
210 241 0 # 12 | ....>C:..13_:[.DT]T-----A[.DA]:..16_:D<.... 0.29 0.11 18.66 8.94 -3.55
211 240 0 # 13 | ....>C:..14_:[.DG]G-----C[.DC]:..15_:D<.... 0.18 0.13 10.54 9.00 -4.03
212 239 0 # 14 | ....>C:..15_:[.DA]A-----T[.DT]:..14_:D<.... 0.48 0.02 7.98 8.84 -4.09
213 238 0 # 15 | ....>C:..16_:[.DG]G-----C[.DC]:..13_:D<.... 0.29 0.21 8.86 9.02 -3.85
214 237 0 # 16 | ....>C:..17_:[.DC]C-----G[.DG]:..12_:D<.... 0.39 0.09 11.91 8.95 -3.84
215 236 0 # 17 | ....>C:..18_:[.DG]G-----C[.DC]:..11_:D<.... 0.46 0.11 16.51 8.89 -3.50
216 235 0 # 18 | ....>C:..19_:[.DA]A-----T[.DT]:..10_:D<.... 0.23 0.20 15.04 8.89 -3.62
217 234 0 # 19 | ....>C:..20_:[.DT]T-----A[.DA]:...9_:D<.... 0.12 0.02 13.95 8.86 -4.15
218 233 0 # 20 | ....>C:..21_:[.DG]G-----C[.DC]:...8_:D<.... 0.27 0.03 4.95 8.88 -4.43
219 232 0 # 21 | ....>C:..22_:[.DG]G-----C[.DC]:...7_:D<.... 0.36 0.19 14.07 8.97 -3.55
220 231 0 # 22 | ....>C:..23_:[.DA]A-----T[.DT]:...6_:D<.... 0.11 0.03 11.03 9.00 -4.27
221 230 0 # 23 | ....>C:..24_:[.DC]C-----G[.DG]:...5_:D<.... 0.26 0.01 5.16 9.01 -4.46
222 229 0 # 24 | ....>C:..25_:[.DA]A-----T[.DT]:...4_:D<.... 0.12 0.08 11.88 8.99 -4.13
223 228 0 # 25 | ....>C:..26_:[.DG]G-----C[.DC]:...3_:D<.... 0.19 0.10 12.55 9.07 -3.98
224 227 0 # 26 | ....>C:..27_:[.DC]C-----G[.DG]:...2_:D<.... 0.70 0.08 13.79 8.87 -3.45
225 226 0 # 27 | ....>C:..28_:[.DT]T-----A[.DA]:...1_:D<.... 0.32 0.23 16.73 8.85 -3.38
##### Base-pair criteria used: 4.00 0.00 15.00 2.50 65.00 4.50 7.80 [ O N]
##### 0 non-Watson-Crick base-pairs, and 2 helices (0 isolated bps)
##### Helix #1 (11): 1 - 11
##### Helix #2 (16): 12 - 27
27 # base-pairs
0 # ***local base-pair & step parameters***
# Shear Stretch Stagger Buckle Prop-Tw Opening Shift Slide Rise Tilt Roll Twist
C-G 0.024 -0.090 0.005 6.772 -10.617 -5.789 0.000 0.000 0.000 0.000 0.000 0.000
A-T -0.235 -0.122 0.109 7.664 -9.878 4.793 0.858 0.172 3.336 2.918 1.014 36.431
G-C -0.314 -0.136 0.169 6.500 -9.562 -0.082 -0.285 -0.085 3.345 -3.583 4.594 32.884
C-G 0.908 -0.373 0.361 -2.969 -14.984 0.844 -0.033 -0.543 3.503 -1.181 1.058 40.091
T-A 0.141 -0.106 -0.007 0.613 -11.986 -0.729 -0.262 -0.322 3.111 4.851 5.221 31.076
C-G -0.128 -0.143 -0.018 -6.366 -7.366 -1.917 0.166 -0.074 3.344 0.674 3.320 38.090
T-A -0.267 -0.086 -0.045 -2.563 -8.559 -4.240 -0.195 0.042 3.225 0.735 3.922 31.086
G-C -0.292 -0.166 0.077 -2.822 -6.954 -0.544 0.321 0.426 3.290 -1.721 6.687 39.395
T-A -0.116 -0.100 0.123 -0.937 -8.673 1.568 -0.192 -0.485 3.262 -0.351 3.766 27.420
A-T -0.001 -0.140 0.182 5.758 -11.903 3.559 -0.055 0.800 3.198 -1.188 3.163 38.313
C-G 0.116 -0.132 -0.304 10.768 -15.829 1.506 -0.045 0.140 3.165 4.626 -3.320 33.025
T-A -0.258 -0.054 0.114 -11.001 -15.078 -1.647 -2.308 1.316 8.892 -4.317 41.393 38.812
G-C -0.088 -0.073 -0.133 0.310 -10.536 1.897 0.382 1.086 3.191 -0.110 8.307 34.361
A-T 0.447 -0.165 0.016 -0.099 -7.962 0.665 -0.652 -0.040 3.312 -5.166 3.761 35.830
G-C -0.139 -0.145 0.207 6.023 -6.516 -2.554 -1.012 0.163 3.163 -3.561 3.126 34.190
C-G 0.295 -0.232 0.091 1.023 -11.858 -3.258 -0.124 -0.238 3.404 0.838 1.644 37.078
G-C -0.374 -0.240 -0.110 -2.127 -16.386 -0.188 0.321 0.355 3.350 1.347 12.377 33.332
A-T -0.017 -0.100 -0.202 -8.205 -12.579 0.613 -0.320 0.038 3.344 -2.364 3.451 38.627
T-A -0.045 -0.112 -0.018 -3.031 -13.642 2.107 -0.323 -0.547 3.153 -0.891 1.361 28.238
G-C -0.143 -0.224 -0.025 -0.009 -4.949 -0.572 0.835 1.066 3.262 2.167 4.308 36.515
G-C -0.264 -0.139 -0.194 -2.023 -13.899 0.810 -1.167 0.841 3.376 -1.701 4.690 34.890
A-T 0.040 -0.101 -0.032 -2.595 -10.719 -3.810 -0.326 0.031 3.276 -2.461 2.045 38.245
C-G 0.195 -0.173 -0.010 2.489 -4.509 -3.218 0.899 -0.332 3.198 -0.443 1.198 31.804
A-T -0.073 -0.062 -0.077 6.348 -10.043 -1.996 -0.323 0.717 3.324 2.003 5.002 35.639
G-C -0.138 -0.095 0.097 5.909 -11.083 -2.265 -0.457 -0.121 3.331 -4.406 6.090 32.917
C-G 0.665 -0.218 0.076 2.871 -13.498 1.620 0.153 -0.549 3.373 -0.247 1.964 34.405
T-A -0.224 -0.042 0.232 -0.691 -16.719 5.480 0.498 -0.227 3.326 3.538 6.708 26.031
27 # base-pairs
0 # ***local base-pair & step parameters***
# Shear Stretch Stagger Buckle Prop-Tw Opening Shift Slide Rise Tilt Roll Twist
C-G 0.024 -0.090 0.006 6.763 -10.628 -5.790 0.000 0.000 0.000 0.000 0.000 0.000
A-T -0.235 -0.122 0.109 7.661 -9.872 4.801 0.858 0.172 3.336 2.922 1.020 36.430
G-C -0.314 -0.136 0.169 6.511 -9.550 -0.079 -0.285 -0.085 3.345 -3.590 4.592 32.886
C-G 0.908 -0.373 0.361 -2.975 -14.974 0.851 -0.033 -0.543 3.503 -1.180 1.059 40.091
T-A 0.141 -0.106 -0.006 0.603 -11.983 -0.723 -0.262 -0.322 3.111 4.846 5.214 31.074
C-G -0.128 -0.143 -0.018 -6.369 -7.377 -1.911 0.166 -0.074 3.344 0.676 3.325 38.095
T-A -0.268 -0.086 -0.046 -2.559 -8.549 -4.249 -0.196 0.042 3.225 0.737 3.921 31.075
G-C -0.292 -0.166 0.076 -2.830 -6.962 -0.538 0.321 0.426 3.290 -1.721 6.686 39.402
T-A -0.116 -0.100 0.123 -0.939 -8.667 1.569 -0.192 -0.485 3.262 -0.357 3.767 27.419
A-T -0.001 -0.140 0.183 5.764 -11.901 3.557 -0.055 0.800 3.198 -1.187 3.155 38.314
C-G 0.116 -0.132 -0.304 10.769 -15.820 1.512 -0.045 0.140 3.165 4.632 -3.314 33.027
T-A -0.258 -0.054 0.114 -11.005 -15.065 -1.643 -2.308 1.316 8.892 -4.314 41.391 38.806
G-C -0.088 -0.073 -0.134 0.300 -10.540 1.897 0.382 1.086 3.191 -0.111 8.319 34.364
A-T 0.447 -0.165 0.015 -0.095 -7.959 0.665 -0.652 -0.040 3.312 -5.162 3.752 35.826
G-C -0.139 -0.145 0.206 6.020 -6.517 -2.559 -1.012 0.163 3.163 -3.560 3.139 34.196
C-G 0.295 -0.232 0.091 1.007 -11.864 -3.258 -0.124 -0.238 3.404 0.830 1.641 37.074
G-C -0.374 -0.240 -0.111 -2.125 -16.385 -0.191 0.321 0.355 3.350 1.349 12.387 33.330
A-T -0.017 -0.100 -0.202 -8.203 -12.574 0.613 -0.320 0.038 3.344 -2.371 3.443 38.630
T-A -0.045 -0.112 -0.018 -3.029 -13.634 2.111 -0.323 -0.547 3.153 -0.892 1.357 28.236
G-C -0.143 -0.224 -0.024 -0.001 -4.957 -0.560 0.835 1.066 3.262 2.168 4.306 36.516
G-C -0.264 -0.139 -0.193 -2.012 -13.908 0.815 -1.167 0.841 3.376 -1.700 4.690 34.890
A-T 0.040 -0.101 -0.033 -2.618 -10.725 -3.809 -0.326 0.031 3.277 -2.455 2.045 38.244
C-G 0.195 -0.173 -0.010 2.488 -4.495 -3.214 0.899 -0.332 3.197 -0.450 1.201 31.803
A-T -0.073 -0.062 -0.078 6.342 -10.052 -1.990 -0.323 0.717 3.324 2.009 4.999 35.641
G-C -0.138 -0.095 0.097 5.907 -11.081 -2.258 -0.457 -0.121 3.331 -4.412 6.094 32.917
C-G 0.665 -0.218 0.076 2.876 -13.506 1.621 0.153 -0.549 3.373 -0.252 1.962 34.406
T-A -0.224 -0.042 0.233 -0.695 -16.735 5.492 0.498 -0.227 3.326 3.539 6.702 26.033
Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids
Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University