Messages

1

General discussions (Q&As) / Re: Finding base pair having a overlap

« on: December 03, 2013, 02:21:24 am »

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

2

General discussions (Q&As) / Re: Finding base pair having a overlap

« on: December 02, 2013, 10:13:04 pm »

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

3

General discussions (Q&As) / Finding base pair having a overlap

« on: December 02, 2013, 04:16:14 am »

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

4

General discussions (Q&As) / Re: Problem of finding all base pairs in distorted DNA structure using 3DNA

« on: November 28, 2013, 09:46:10 pm »

Hello Xiang-Jun and Difei,
    I have the same problem with Difei and I tried to look for solutions in Simulation part of 3DNA Forum according to Xiang-Jun's suggestion, but I didn't find the exact steps to solve the problem.
    Could you please give me a hyperlink? Many thanks!

Chan Gu