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General discussions (Q&As) / Problem of finding all base pairs in distorted DNA structure using 3DNA
« on: January 05, 2012, 03:26:12 pm »
Hello Xiang-Jun,
In order to find all base pairs, I have changed the values in misc_3dna.par to calculate the non-WC b.p in much distorted structure. I artificially increased all the values based on my understanding of these parameters.
Still, sometimes, find_pair program in 3DNA can not find all the pairs even through they are structurally very similar. An example is shown below to demonstrate the problem. The two 12-mer structures (md5.1004.mod.pdb and md5.1016.mod.pdb) are obtained from a molecular dynamics simulation at 1004 and 1016 ps.
So the question is how to change the parameter file to analyze all base pairs in these structures?
Difei
================
Changes in Misc_3dna.par
100.0 0.0 ON A1 # upper H-bond length limits/atoms, alternative location
100.0 # max. distance between paired base origins (FIND_PAIR)
100.0 # max. vertical distance between paired base origins (FIND_PAIR)
90.0 # max. angle between paired bases [0-90] (FIND_PAIR)
2.5 # MIN. distance between RN9/YN1 atoms (FIND_PAIR)
100.0 # max. distance criterion for helix break (FIND_PAIR)
0.6 # r7 criterion to decide if a helix is curved
3.2 # r8 H-bond distance for water molecules with base N/O atoms
10.50 # r9 maximum O3'--P distance for linkage (REBUILD)
Output files from find_pair in 3DNA
md5.1004.mod.pdb
md5.1004.mod.out
2 # duplex
11 # number of base-pairs
1 1 # explicit bp numbering/hetero atoms
1 24 0 # 1 | A:...1_:[..C]C-----G[..G]:..24_:B 0.99 0.99 20.12 9.24 1.47
2 23 0 # 2 | A:...2_:[..G]G-----C[..C]:..23_:B 0.79 0.72 12.67 8.99 0.73
3 22 0 # 3 | A:...3_:[..C]C-----G[..G]:..22_:B 0.21 0.16 4.17 9.00 -0.97
4 21 0 # 4 | A:...4_:[..G]G-----C[..C]:..21_:B 0.36 0.09 16.09 9.09 -0.97
5 20 0 # 5 | A:...5_:[..C]C-----G[..G]:..20_:B 0.61 0.33 6.50 9.12 -0.22
6 19 0 # 6 | A:...6_:[..C]C-----G[..G]:..19_:B 0.25 0.05 14.46 9.00 -1.15
7 18 0 # 7 | A:...7_:[..A]A-----T[..T]:..18_:B 1.00 0.96 38.08 8.78 1.41
8 17 0 # 8 | A:...8_:[..A]A-----T[..T]:..17_:B 0.43 0.24 17.20 8.74 -0.58
9 16 0 # 9 | A:...9_:[..C]C-----G[..G]:..16_:B 0.26 0.25 14.19 9.27 -0.73
10 15 0 # 10 | A:..10_:[..G]G-----C[..C]:..15_:B 0.63 0.28 21.27 9.16 -0.31
11 14 0 # 11 | A:..11_:[..C]C-----G[..G]:..14_:B 0.41 0.01 23.73 8.95 -1.07
##### Base-pair criteria used: 100.00100.00100.00 90.00 2.50100.00
##### 0 non-Watson-Crick base-pairs, and 1 helix (0 isolated bps)
##### Helix #1 (11): 1 - 11
md5.1016.mod.pdb
md5.1016.mod.out
2 # duplex
12 # number of base-pairs
1 1 # explicit bp numbering/hetero atoms
1 24 0 # 1 | A:...1_:[..C]C-----G[..G]:..24_:B 0.36 0.06 20.92 9.18 -1.01
2 23 0 # 2 | A:...2_:[..G]G-----C[..C]:..23_:B 0.44 0.42 18.28 9.14 -0.22
3 22 0 # 3 | A:...3_:[..C]C-----G[..G]:..22_:B 0.77 0.31 20.29 9.10 -0.11
4 21 0 # 4 | A:...4_:[..G]G-----C[..C]:..21_:B 0.34 0.01 2.58 8.97 -1.15
5 20 0 # 5 | A:...5_:[..C]C-----G[..G]:..20_:B 0.58 0.58 12.03 9.19 0.23
6 19 0 # 6 | A:...6_:[..C]C-----G[..G]:..19_:B 0.26 0.20 6.49 9.04 -0.85
7 18 0 # 7 | A:...7_:[..A]A-----T[..T]:..18_:B 0.94 0.91 22.58 8.69 1.26
8 17 0 # 8 | A:...8_:[..A]A-----T[..T]:..17_:B 0.71 0.70 22.61 8.72 0.61
9 16 0 # 9 | A:...9_:[..C]C-----G[..G]:..16_:B 0.59 0.54 3.06 9.03 0.17
10 15 0 # 10 | A:..10_:[..G]G-----C[..C]:..15_:B 0.56 0.42 7.20 9.02 -0.11
11 14 0 # 11 | A:..11_:[..C]C-----G[..G]:..14_:B 0.62 0.05 15.44 8.93 -0.79
12 13 0 # 12 | A:..12_:[..G]G-*---C[..C]:..13_:B 5.49 4.72 76.16 7.78 14.93
##### Base-pair criteria used: 100.00100.00100.00 90.00 2.50100.00
##### 1 non-Watson-Crick base-pair, and 1 helix (0 isolated bps)
##### Helix #1 (12): 1 - 12
In order to find all base pairs, I have changed the values in misc_3dna.par to calculate the non-WC b.p in much distorted structure. I artificially increased all the values based on my understanding of these parameters.
Still, sometimes, find_pair program in 3DNA can not find all the pairs even through they are structurally very similar. An example is shown below to demonstrate the problem. The two 12-mer structures (md5.1004.mod.pdb and md5.1016.mod.pdb) are obtained from a molecular dynamics simulation at 1004 and 1016 ps.
So the question is how to change the parameter file to analyze all base pairs in these structures?
Difei
================
Changes in Misc_3dna.par
100.0 0.0 ON A1 # upper H-bond length limits/atoms, alternative location
100.0 # max. distance between paired base origins (FIND_PAIR)
100.0 # max. vertical distance between paired base origins (FIND_PAIR)
90.0 # max. angle between paired bases [0-90] (FIND_PAIR)
2.5 # MIN. distance between RN9/YN1 atoms (FIND_PAIR)
100.0 # max. distance criterion for helix break (FIND_PAIR)
0.6 # r7 criterion to decide if a helix is curved
3.2 # r8 H-bond distance for water molecules with base N/O atoms
10.50 # r9 maximum O3'--P distance for linkage (REBUILD)
Output files from find_pair in 3DNA
md5.1004.mod.pdb
md5.1004.mod.out
2 # duplex
11 # number of base-pairs
1 1 # explicit bp numbering/hetero atoms
1 24 0 # 1 | A:...1_:[..C]C-----G[..G]:..24_:B 0.99 0.99 20.12 9.24 1.47
2 23 0 # 2 | A:...2_:[..G]G-----C[..C]:..23_:B 0.79 0.72 12.67 8.99 0.73
3 22 0 # 3 | A:...3_:[..C]C-----G[..G]:..22_:B 0.21 0.16 4.17 9.00 -0.97
4 21 0 # 4 | A:...4_:[..G]G-----C[..C]:..21_:B 0.36 0.09 16.09 9.09 -0.97
5 20 0 # 5 | A:...5_:[..C]C-----G[..G]:..20_:B 0.61 0.33 6.50 9.12 -0.22
6 19 0 # 6 | A:...6_:[..C]C-----G[..G]:..19_:B 0.25 0.05 14.46 9.00 -1.15
7 18 0 # 7 | A:...7_:[..A]A-----T[..T]:..18_:B 1.00 0.96 38.08 8.78 1.41
8 17 0 # 8 | A:...8_:[..A]A-----T[..T]:..17_:B 0.43 0.24 17.20 8.74 -0.58
9 16 0 # 9 | A:...9_:[..C]C-----G[..G]:..16_:B 0.26 0.25 14.19 9.27 -0.73
10 15 0 # 10 | A:..10_:[..G]G-----C[..C]:..15_:B 0.63 0.28 21.27 9.16 -0.31
11 14 0 # 11 | A:..11_:[..C]C-----G[..G]:..14_:B 0.41 0.01 23.73 8.95 -1.07
##### Base-pair criteria used: 100.00100.00100.00 90.00 2.50100.00
##### 0 non-Watson-Crick base-pairs, and 1 helix (0 isolated bps)
##### Helix #1 (11): 1 - 11
md5.1016.mod.pdb
md5.1016.mod.out
2 # duplex
12 # number of base-pairs
1 1 # explicit bp numbering/hetero atoms
1 24 0 # 1 | A:...1_:[..C]C-----G[..G]:..24_:B 0.36 0.06 20.92 9.18 -1.01
2 23 0 # 2 | A:...2_:[..G]G-----C[..C]:..23_:B 0.44 0.42 18.28 9.14 -0.22
3 22 0 # 3 | A:...3_:[..C]C-----G[..G]:..22_:B 0.77 0.31 20.29 9.10 -0.11
4 21 0 # 4 | A:...4_:[..G]G-----C[..C]:..21_:B 0.34 0.01 2.58 8.97 -1.15
5 20 0 # 5 | A:...5_:[..C]C-----G[..G]:..20_:B 0.58 0.58 12.03 9.19 0.23
6 19 0 # 6 | A:...6_:[..C]C-----G[..G]:..19_:B 0.26 0.20 6.49 9.04 -0.85
7 18 0 # 7 | A:...7_:[..A]A-----T[..T]:..18_:B 0.94 0.91 22.58 8.69 1.26
8 17 0 # 8 | A:...8_:[..A]A-----T[..T]:..17_:B 0.71 0.70 22.61 8.72 0.61
9 16 0 # 9 | A:...9_:[..C]C-----G[..G]:..16_:B 0.59 0.54 3.06 9.03 0.17
10 15 0 # 10 | A:..10_:[..G]G-----C[..C]:..15_:B 0.56 0.42 7.20 9.02 -0.11
11 14 0 # 11 | A:..11_:[..C]C-----G[..G]:..14_:B 0.62 0.05 15.44 8.93 -0.79
12 13 0 # 12 | A:..12_:[..G]G-*---C[..C]:..13_:B 5.49 4.72 76.16 7.78 14.93
##### Base-pair criteria used: 100.00100.00100.00 90.00 2.50100.00
##### 1 non-Watson-Crick base-pair, and 1 helix (0 isolated bps)
##### Helix #1 (12): 1 - 12