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Hello Xiang-jun:
I'am using 3DNA and meet a problem that there is a "missing pair". According to the definition of a "base pair" in 3DNA, the two bases in one pair should not have a overlap, which is not documented in misc_3dna.par.
If I want to force the overlapped bases to a "pair", what should I do? (Your suggestion in a topic is making manual changes of the .inp file and the steps can be found in Simulation part. But I didn't find the steps, could you please give me a hyperlink?)
Thank you very much!
Chan Gu
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Could you please post a specific example? The defaults in 3DNA/DSSR have been set the way they are for solid reasons, and work well for the vast majority of cases.
Xiang-Jun
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Hi Xiang-jun,
Thanks for your reply. My system should have 30 base pairs:
200_f1.pdb
200_f1.out
2 # duplex
30 # number of base-pairs
1 1 # explicit bp numbering/hetero atoms
1 60 0 # 1 | ....>-:...1_:[DA5]a-**--t[DT3]:..60_:-<.... 8.75 4.01 60.74 12.24 19.80
2 59 0 # 2 | ....>-:...2_:[.RU]U-----A[.DA]:..59_:-<.... 0.43 0.13 29.17 9.18 -2.86
3 58 0 # 3 | ....>-:...3_:[.DA]A-----U[.RU]:..58_:-<.... 0.86 0.78 14.86 9.15 -1.84
4 57 0 # 4 | ....>-:...4_:[.RU]U-----A[.DA]:..57_:-<.... 0.53 0.08 22.83 9.11 -1.18
5 56 0 # 5 | ....>-:...5_:[.DA]A-----U[.RU]:..56_:-<.... 1.00 0.71 17.87 9.37 -1.68
6 55 0 # 6 | ....>-:...6_:[.RU]U-----A[.DA]:..55_:-<.... 1.15 0.03 21.96 9.32 -2.68
7 54 0 # 7 | ....>-:...7_:[.DA]A-----U[.RU]:..54_:-<.... 0.88 0.35 24.57 9.55 -2.20
8 53 0 # 8 | ....>-:...8_:[.RU]U-----A[.DA]:..53_:-<.... 0.61 0.28 18.93 9.14 -2.87
9 52 0 # 9 | ....>-:...9_:[.DA]A-----U[.RU]:..52_:-<.... 0.82 0.37 26.23 9.46 -2.14
10 51 0 # 10 | ....>-:..10_:[.RU]U-----A[.DA]:..51_:-<.... 0.95 0.91 22.73 9.20 -1.10
11 50 0 # 11 | ....>-:..11_:[.DA]A-----U[.RU]:..50_:-<.... 0.90 0.11 19.12 9.17 -2.93
12 49 0 # 12 | ....>-:..12_:[.RU]U-----A[.DA]:..49_:-<.... 0.43 0.10 11.85 9.30 -1.77
13 48 0 # 13 | ....>-:..13_:[.DA]A-----U[.RU]:..48_:-<.... 0.37 0.36 26.80 9.17 -2.57
14 47 0 # 14 | ....>-:..14_:[.RU]U-----A[.DA]:..47_:-<.... 0.64 0.15 27.80 9.22 -2.66
15 46 0 # 15 | ....>-:..15_:[.DA]A-----U[.RU]:..46_:-<.... 0.68 0.20 2.20 9.31 -3.81
16 45 0 # 16 | ....>-:..16_:[.RU]U-----A[.DA]:..45_:-<.... 1.35 0.97 10.04 9.51 -1.20
17 44 0 # 17 | ....>-:..17_:[.DA]A-----U[.RU]:..44_:-<.... 0.86 0.83 27.72 9.06 -1.08
18 43 0 # 18 | ....>-:..18_:[.RU]U-----A[.DA]:..43_:-<.... 0.11 0.05 24.73 9.23 -3.55
19 42 0 # 19 | ....>-:..19_:[.DA]A-----U[.RU]:..42_:-<.... 0.86 0.69 19.68 9.13 0.22
20 41 0 # 20 | ....>-:..20_:[.RU]U-----A[.DA]:..41_:-<.... 0.86 0.56 25.33 9.45 -1.76
21 40 0 # 21 | ....>-:..21_:[.DA]A-----U[.RU]:..40_:-<.... 0.41 0.07 11.48 9.44 -3.87
22 39 0 # 22 | ....>-:..22_:[.RU]U-----A[.DA]:..39_:-<.... 0.54 0.52 16.31 9.45 -2.60
23 38 0 # 23 | ....>-:..23_:[.DA]A-----U[.RU]:..38_:-<.... 0.46 0.02 22.40 9.16 -3.38
24 37 0 # 24 | ....>-:..24_:[.RU]U-----A[.DA]:..37_:-<.... 0.49 0.36 20.01 9.14 -2.79
25 36 0 # 25 | ....>-:..25_:[.DA]A-----U[.RU]:..36_:-<.... 1.09 0.84 6.19 9.45 -1.93
26 35 0 # 26 | ....>-:..26_:[.RU]U-----A[.DA]:..35_:-<.... 0.41 0.07 18.96 9.28 -3.51
27 34 0 # 27 | ....>-:..27_:[.DA]A-----U[.RU]:..34_:-<.... 0.81 0.57 17.84 9.08 -2.16
28 33 0 # 28 | ....>-:..28_:[.RU]U-----A[.DA]:..33_:-<.... 0.83 0.27 11.33 9.65 -3.07
29 32 0 # 29 | ....>-:..29_:[.DA]A-**+-U[.RU]:..32_:-<.... 3.04 1.58 16.90 11.00 7.05
30 31 0 # 30 | ....>-:..30_:[DT3]t-**--a[DA5]:..31_:-<.... 12.19 1.99 34.61 9.46 16.89
##### Base-pair criteria used: 30.00 0.00 20.00 30.00 90.00 0.00 20.00 [ O N]
##### 3 non-Watson-Crick base-pairs, and 1 helix (0 isolated bps)
##### Helix #1 (30): 1 - 30
However, due to the overlap, the first pair sometime missed:
11_f1.pdb
11_f1.out
2 # duplex
29 # number of base-pairs
1 1 # explicit bp numbering/hetero atoms
2 59 0 # 1 | ....>-:...2_:[.RU]U-----A[.DA]:..59_:-<.... 1.88 1.82 46.49 8.64 2.83
3 58 0 # 2 | ....>-:...3_:[.DA]A-----U[.RU]:..58_:-<.... 0.95 0.91 23.98 9.27 -1.02
4 57 0 # 3 | ....>-:...4_:[.RU]U-----A[.DA]:..57_:-<.... 0.64 0.00 20.86 9.50 -3.31
5 56 0 # 4 | ....>-:...5_:[.DA]A-----U[.RU]:..56_:-<.... 0.65 0.32 14.91 9.56 -2.97
6 55 0 # 5 | ....>-:...6_:[.RU]U-----A[.DA]:..55_:-<.... 0.25 0.19 11.95 9.40 -3.78
7 54 0 # 6 | ....>-:...7_:[.DA]A-----U[.RU]:..54_:-<.... 0.40 0.21 16.46 9.53 -3.36
8 53 0 # 7 | ....>-:...8_:[.RU]U-----A[.DA]:..53_:-<.... 0.20 0.16 14.72 9.14 -3.74
9 52 0 # 8 | ....>-:...9_:[.DA]A-----U[.RU]:..52_:-<.... 0.13 0.05 24.32 9.25 -3.56
10 51 0 # 9 | ....>-:..10_:[.RU]U-----A[.DA]:..51_:-<.... 0.66 0.21 31.04 9.52 -2.37
11 50 0 # 10 | ....>-:..11_:[.DA]A-----U[.RU]:..50_:-<.... 0.34 0.15 24.63 9.36 -3.13
12 49 0 # 11 | ....>-:..12_:[.RU]U-----A[.DA]:..49_:-<.... 0.45 0.06 34.52 9.16 -0.70
13 48 0 # 12 | ....>-:..13_:[.DA]A-----U[.RU]:..48_:-<.... 0.52 0.21 27.79 9.35 -2.67
14 47 0 # 13 | ....>-:..14_:[.RU]U-----A[.DA]:..47_:-<.... 0.28 0.05 27.74 9.29 -3.23
15 46 0 # 14 | ....>-:..15_:[.DA]A-----U[.RU]:..46_:-<.... 0.26 0.21 21.63 9.17 -3.23
16 45 0 # 15 | ....>-:..16_:[.RU]U-----A[.DA]:..45_:-<.... 0.84 0.37 9.27 9.61 -2.96
17 44 0 # 16 | ....>-:..17_:[.DA]A-----U[.RU]:..44_:-<.... 0.80 0.63 28.07 9.40 -1.55
18 43 0 # 17 | ....>-:..18_:[.RU]U-----A[.DA]:..43_:-<.... 0.66 0.61 28.18 9.33 -1.72
19 42 0 # 18 | ....>-:..19_:[.DA]A-----U[.RU]:..42_:-<.... 0.69 0.07 9.82 9.36 -3.68
20 41 0 # 19 | ....>-:..20_:[.RU]U-----A[.DA]:..41_:-<.... 0.73 0.73 7.95 9.50 -2.40
21 40 0 # 20 | ....>-:..21_:[.DA]A-----U[.RU]:..40_:-<.... 0.67 0.14 29.09 9.59 -2.60
22 39 0 # 21 | ....>-:..22_:[.RU]U-----A[.DA]:..39_:-<.... 0.29 0.18 23.75 9.01 -3.17
23 38 0 # 22 | ....>-:..23_:[.DA]A-----U[.RU]:..38_:-<.... 0.42 0.04 19.41 9.46 -3.53
24 37 0 # 23 | ....>-:..24_:[.RU]U-----A[.DA]:..37_:-<.... 0.86 0.18 11.37 9.66 -3.21
25 36 0 # 24 | ....>-:..25_:[.DA]A-----U[.RU]:..36_:-<.... 0.47 0.14 11.46 9.31 -3.69
26 35 0 # 25 | ....>-:..26_:[.RU]U-----A[.DA]:..35_:-<.... 0.19 0.15 15.49 9.06 -3.75
27 34 0 # 26 | ....>-:..27_:[.DA]A-----U[.RU]:..34_:-<.... 0.32 0.17 25.31 9.56 -3.08
28 33 0 # 27 | ....>-:..28_:[.RU]U-----A[.DA]:..33_:-<.... 0.81 0.62 18.75 9.34 -2.01
29 32 0 # 28 | ....>-:..29_:[.DA]A-----U[.RU]:..32_:-<.... 0.64 0.36 24.17 9.25 -0.43
30 31 0 # 29 | ....>-:..30_:[DT3]t-----a[DA5]:..31_:-<.... 1.12 0.99 41.81 9.43 0.19
##### Base-pair criteria used: 30.00 0.00 20.00 30.00 90.00 0.00 20.00 [ O N]
##### 0 non-Watson-Crick base-pairs, and 1 helix (0 isolated bps)
##### Helix #1 (29): 1 - 29
So the question is how to force the first overlaped pair to a "pair"?
The attachments include : two pdb files that in normal situation(normal.pdb) and having a overlap(overlap.pdb), respectively, and a picture showing the overlap.
Many thanks!
Chan Gu
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Hi Chan Gu,
Thanks for posting two PDB files and an image, which help clarify the issues. Firstly, I'd say that you are certainly on the extreme side for some bp-defining parameters (e.g., H-bond distance cutoff of 20 Å). I am glad to see that 'find_pair' is still working properly, without giving many extraneous bps. Secondly, to force a pair between DA5/1 and DT3/60, you could simply edit the default output file as below:
From:
2 # duplex
29 # number of base-pairs
1 1 # explicit bp numbering/hetero atoms
2 59 0 # 1 | ....>-:...2_:[.RU]U-----A[.DA]:..59_:-<.... 1.88 1.82 46.49 8.64 2.83
****************************************************************************
To:
2 # duplex
30 # number of base-pairs
1 1 # explicit bp numbering/hetero atoms
1 60
2 59 0 # 1 | ....>-:...2_:[.RU]U-----A[.DA]:..59_:-<.... 1.88 1.82 46.49 8.64 2.83
As shown clearly in your attach image, DA5/1 and DT3/60 are stacking instead of pairing. In such extreme cases, 'find_pair' does not work as you'd expect, for solid reasons. Here certain manual editing is required, as illustrated above. I take this 'extra work' as an advantage since it reminds users to pay attentions to the abnormality.
If you are analyzing MD trajectories for an ensemble of similar structures, you do not need to run 'find_pair' for each model. See x3dna_ensemble analyze -h for further info.
HTH,
Xiang-Jun
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Hi xiang-jun,
Thank you very much! I've tried your suggestion and it works. I did not use x3dna_ensemble for some reasons, but I' ll certainly try it latter.
Thanks again!
Chan Gu
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