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Hi,
I am using DSSR to find base pairs in a DNA duplex MD structure. It is a 12-mer DNA duplex which I expect there should be only 12 canonical base pairs. However, DSSR told me there are 13 base pairs which means it over counted one base pair. Is there any way to change the criteria to define a base pair (like hydrogen bond length) in DSSR?
I would really appreciate your reply.
Best,
Honglue
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Hi Honglue,
Thanks for using DSSR. Could you please provide an example to illustrate the case? Overall, the default base-pair criteria are well tested for the most common use cases and they are configurable from the command line.
Best regards,
Xiang-Jun
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Hi,
Thanks for your feedback. Here is the case. This structure is from MD simulation:
Command: x3dna-dssr -i=A2-dna-1-102-37034.pdb --more
Date and time: Wed Jul 27 19:34:34 2016
File name: A2-dna-1-102-37034.pdb
no. of DNA/RNA chains: 1 [X=24]
no. of nucleotides: 24
no. of atoms: 759
no. of waters: 0
no. of metals: 0
total number of base pairs: 13
total number of helices: 1
total number of stems: 1
****************************************************************************
So, the DNA is a 12-mer double helix but it said the total number of base pairs are 13.
I double checked the output information and it seems it counted a non-canonical base pair.
2 X.CYT2 X.THY22 C-T -- n/a cWW cW-W
[-156.0(anti) .... lambda=29.3] [-156.4(anti) .... lambda=37.6]
d(C1'-C1')=12.14 d(N1-N9)=9.71 d(C6-C8)=9.88 tor(C1'-N1-N9-C1')=7.5
H-bonds[1]: "N4(amino)-O4(carbonyl)[3.39]"
interBase-angle=8 Simple-bpParams: Shear=-0.74 Stretch=0.15 Buckle=-3.0 Propeller=-7.0
bp-pars: [-0.75 0.09 -1.80 -2.46 -7.18 -39.36]
Is there anyway to avoid this non-canonical base pair?
Also, if this overcounted base pair is A-T or G-C pair (maybe they are not base pair but just very close), is there anyway to avoid this?
Best,
Honglue
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Hi,
Thanks for providing a sample output from DSSR on your MD simulation. I understand your point, but in reality it is hard to decide if two bases close together should be taken as a (mostly non-canonical) 'pair'. From the text output, I see no reason why DSSR should exclude the extra 'C-T' pair from the its output. There are certainly similiar C-U pairs in RNA structures. For illustration purpose, it helps if you could attach this DSSR-(mis)identified 'pair' in PDB format. Or better off, also attach a molecular image of this pair (using Jmol or PyMOL).
The way to solve your problem is to use 'find_pair' to get a prelimary list of pairs, presumably 13 with the extra you want to get rid of. Then edit this file to remove the extra pair, and run 'analyze' to get the parameters. I am planning to add the 'find_pair/analyze' functionality to DSSR that allows users to add/remove base pairs for the analysis.
Xiang-Jun
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Hi,
Thank you so much for your feedback.
I totally understand your explanation. The reason why it is annoying is that we trying to analyze a lot of pdb files simultaneously from a big MD trajectories and sometimes the annoying extra base pairs will show up. Is there anyway to turn off the non-canonical base pair when we analyze them? Or is there anyway to change the criteria like decrease the H bond cutoff? I have a lot of trajectory pdb files and it will take me a long time to check them one by one and delete the extra base pair. I would really appreciate if you could provide a more efficient way to deal with this issue.
Thank you again.
Best,
Honglue
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Here is the C-T mispair pdb file:
ATOM 1 P CYT X 2 -4.828 -14.185 11.900 1.00 0.00 P
ATOM 2 C5' CYT X 2 -3.306 -15.035 10.007 1.00 0.00 C
ATOM 3 O5' CYT X 2 -3.975 -13.976 10.569 1.00 0.00 O
ATOM 4 C4' CYT X 2 -2.679 -15.009 8.557 1.00 0.00 C
ATOM 5 O4' CYT X 2 -3.655 -14.996 7.464 1.00 0.00 O
ATOM 6 C3' CYT X 2 -1.900 -13.688 8.251 1.00 0.00 C
ATOM 7 O3' CYT X 2 -0.605 -13.621 8.812 1.00 0.00 O
ATOM 8 C2' CYT X 2 -1.801 -13.797 6.740 1.00 0.00 C
ATOM 9 C1' CYT X 2 -2.880 -14.764 6.256 1.00 0.00 C
ATOM 10 N1 CYT X 2 -3.562 -14.188 5.167 1.00 0.00 N
ATOM 11 C2 CYT X 2 -3.112 -14.364 3.848 1.00 0.00 C
ATOM 12 O2 CYT X 2 -2.006 -14.948 3.627 1.00 0.00 O
ATOM 13 N3 CYT X 2 -3.853 -13.910 2.768 1.00 0.00 N
ATOM 14 C4 CYT X 2 -4.877 -13.125 3.056 1.00 0.00 C
ATOM 15 N4 CYT X 2 -5.718 -12.746 2.182 1.00 0.00 N
ATOM 16 C5 CYT X 2 -5.302 -12.812 4.399 1.00 0.00 C
ATOM 17 C6 CYT X 2 -4.588 -13.309 5.428 1.00 0.00 C
ATOM 18 OP1 CYT X 2 -3.980 -14.962 12.864 1.00 0.00 O
ATOM 19 OP2 CYT X 2 -5.426 -12.878 12.246 1.00 0.00 O
ATOM 20 H5 CYT X 2 -6.111 -12.133 4.626 1.00 0.00 H
ATOM 21 H6 CYT X 2 -4.706 -12.971 6.447 1.00 0.00 H
ATOM 22 H1' CYT X 2 -2.306 -15.648 5.979 1.00 0.00 H
ATOM 23 H2' CYT X 2 -1.915 -12.835 6.242 1.00 0.00 H
ATOM 24 H3' CYT X 2 -2.624 -12.890 8.412 1.00 0.00 H
ATOM 25 H4' CYT X 2 -1.967 -15.825 8.434 1.00 0.00 H
ATOM 26 H41 CYT X 2 -5.572 -12.927 1.199 1.00 0.00 H
ATOM 27 H5' CYT X 2 -3.923 -15.932 10.068 1.00 0.00 H
ATOM 28 H42 CYT X 2 -6.452 -12.121 2.483 1.00 0.00 H
ATOM 29 H2'' CYT X 2 -0.849 -14.165 6.357 1.00 0.00 H
ATOM 30 H5'' CYT X 2 -2.521 -15.314 10.710 1.00 0.00 H
ATOM 31 P THY X 22 -6.463 -9.660 -9.742 1.00 0.00 P
ATOM 32 C5' THY X 22 -4.221 -10.672 -8.863 1.00 0.00 C
ATOM 33 O5' THY X 22 -5.614 -10.548 -8.755 1.00 0.00 O
ATOM 34 C4' THY X 22 -3.634 -11.570 -7.724 1.00 0.00 C
ATOM 35 O4' THY X 22 -3.758 -10.896 -6.525 1.00 0.00 O
ATOM 36 C3' THY X 22 -4.179 -12.977 -7.575 1.00 0.00 C
ATOM 37 O3' THY X 22 -3.695 -13.924 -8.501 1.00 0.00 O
ATOM 38 C2' THY X 22 -3.741 -13.131 -6.143 1.00 0.00 C
ATOM 39 C1' THY X 22 -3.446 -11.753 -5.486 1.00 0.00 C
ATOM 40 N1 THY X 22 -4.184 -11.605 -4.172 1.00 0.00 N
ATOM 41 C2 THY X 22 -3.584 -12.077 -3.008 1.00 0.00 C
ATOM 42 O2 THY X 22 -2.595 -12.776 -3.092 1.00 0.00 O
ATOM 43 N3 THY X 22 -4.123 -11.676 -1.813 1.00 0.00 N
ATOM 44 C4 THY X 22 -5.294 -10.960 -1.674 1.00 0.00 C
ATOM 45 O4 THY X 22 -5.658 -10.677 -0.504 1.00 0.00 O
ATOM 46 C5 THY X 22 -6.019 -10.683 -2.925 1.00 0.00 C
ATOM 47 C6 THY X 22 -5.459 -11.019 -4.148 1.00 0.00 C
ATOM 48 C7 THY X 22 -7.457 -10.363 -2.839 1.00 0.00 C
ATOM 49 OP1 THY X 22 -6.052 -9.807 -11.195 1.00 0.00 O
ATOM 50 OP2 THY X 22 -7.882 -9.938 -9.400 1.00 0.00 O
ATOM 51 H3 THY X 22 -3.747 -12.012 -0.938 1.00 0.00 H
ATOM 52 H6 THY X 22 -5.992 -10.780 -5.057 1.00 0.00 H
ATOM 53 H1' THY X 22 -2.365 -11.803 -5.356 1.00 0.00 H
ATOM 54 H2' THY X 22 -4.589 -13.608 -5.652 1.00 0.00 H
ATOM 55 H3' THY X 22 -5.260 -12.920 -7.706 1.00 0.00 H
ATOM 56 H4' THY X 22 -2.570 -11.599 -7.960 1.00 0.00 H
ATOM 57 H5' THY X 22 -3.739 -9.695 -8.895 1.00 0.00 H
ATOM 58 H71 THY X 22 -7.996 -11.113 -2.260 1.00 0.00 H
ATOM 59 H72 THY X 22 -7.608 -9.383 -2.388 1.00 0.00 H
ATOM 60 H73 THY X 22 -7.994 -10.274 -3.784 1.00 0.00 H
ATOM 61 H2'' THY X 22 -2.874 -13.790 -6.092 1.00 0.00 H
ATOM 62 H5'' THY X 22 -3.986 -11.120 -9.829 1.00 0.00 H
END
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This is that mispair and its neighbors:
ATOM 1 P CYT X 2 -4.828 -14.185 11.900 1.00 0.00 P
ATOM 2 C5' CYT X 2 -3.306 -15.035 10.007 1.00 0.00 C
ATOM 3 O5' CYT X 2 -3.975 -13.976 10.569 1.00 0.00 O
ATOM 4 C4' CYT X 2 -2.679 -15.009 8.557 1.00 0.00 C
ATOM 5 O4' CYT X 2 -3.655 -14.996 7.464 1.00 0.00 O
ATOM 6 C3' CYT X 2 -1.900 -13.688 8.251 1.00 0.00 C
ATOM 7 O3' CYT X 2 -0.605 -13.621 8.812 1.00 0.00 O
ATOM 8 C2' CYT X 2 -1.801 -13.797 6.740 1.00 0.00 C
ATOM 9 C1' CYT X 2 -2.880 -14.764 6.256 1.00 0.00 C
ATOM 10 N1 CYT X 2 -3.562 -14.188 5.167 1.00 0.00 N
ATOM 11 C2 CYT X 2 -3.112 -14.364 3.848 1.00 0.00 C
ATOM 12 O2 CYT X 2 -2.006 -14.948 3.627 1.00 0.00 O
ATOM 13 N3 CYT X 2 -3.853 -13.910 2.768 1.00 0.00 N
ATOM 14 C4 CYT X 2 -4.877 -13.125 3.056 1.00 0.00 C
ATOM 15 N4 CYT X 2 -5.718 -12.746 2.182 1.00 0.00 N
ATOM 16 C5 CYT X 2 -5.302 -12.812 4.399 1.00 0.00 C
ATOM 17 C6 CYT X 2 -4.588 -13.309 5.428 1.00 0.00 C
ATOM 18 OP1 CYT X 2 -3.980 -14.962 12.864 1.00 0.00 O
ATOM 19 OP2 CYT X 2 -5.426 -12.878 12.246 1.00 0.00 O
ATOM 20 H5 CYT X 2 -6.111 -12.133 4.626 1.00 0.00 H
ATOM 21 H6 CYT X 2 -4.706 -12.971 6.447 1.00 0.00 H
ATOM 22 H1' CYT X 2 -2.306 -15.648 5.979 1.00 0.00 H
ATOM 23 H2' CYT X 2 -1.915 -12.835 6.242 1.00 0.00 H
ATOM 24 H3' CYT X 2 -2.624 -12.890 8.412 1.00 0.00 H
ATOM 25 H4' CYT X 2 -1.967 -15.825 8.434 1.00 0.00 H
ATOM 26 H41 CYT X 2 -5.572 -12.927 1.199 1.00 0.00 H
ATOM 27 H5' CYT X 2 -3.923 -15.932 10.068 1.00 0.00 H
ATOM 28 H42 CYT X 2 -6.452 -12.121 2.483 1.00 0.00 H
ATOM 29 H2'' CYT X 2 -0.849 -14.165 6.357 1.00 0.00 H
ATOM 30 H5'' CYT X 2 -2.521 -15.314 10.710 1.00 0.00 H
ATOM 31 P ADE X 3 0.355 -12.309 8.677 1.00 0.00 P
ATOM 32 C5' ADE X 3 2.068 -13.534 7.100 1.00 0.00 C
ATOM 33 O5' ADE X 3 1.168 -12.470 7.328 1.00 0.00 O
ATOM 34 C4' ADE X 3 2.477 -13.635 5.591 1.00 0.00 C
ATOM 35 O4' ADE X 3 1.233 -13.637 4.893 1.00 0.00 O
ATOM 36 C3' ADE X 3 3.323 -12.466 5.127 1.00 0.00 C
ATOM 37 O3' ADE X 3 4.429 -12.899 4.395 1.00 0.00 O
ATOM 38 C2' ADE X 3 2.302 -11.682 4.259 1.00 0.00 C
ATOM 39 C1' ADE X 3 1.291 -12.755 3.815 1.00 0.00 C
ATOM 40 N1 ADE X 3 -2.345 -11.476 0.422 1.00 0.00 N
ATOM 41 C2 ADE X 3 -1.286 -12.239 0.285 1.00 0.00 C
ATOM 42 N3 ADE X 3 -0.343 -12.471 1.201 1.00 0.00 N
ATOM 43 C4 ADE X 3 -0.686 -11.883 2.403 1.00 0.00 C
ATOM 44 C5 ADE X 3 -1.736 -11.117 2.707 1.00 0.00 C
ATOM 45 C6 ADE X 3 -2.603 -10.958 1.584 1.00 0.00 C
ATOM 46 N6 ADE X 3 -3.668 -10.176 1.637 1.00 0.00 N
ATOM 47 N7 ADE X 3 -1.714 -10.736 4.077 1.00 0.00 N
ATOM 48 C8 ADE X 3 -0.669 -11.318 4.535 1.00 0.00 C
ATOM 49 N9 ADE X 3 -0.005 -12.019 3.591 1.00 0.00 N
ATOM 50 OP1 ADE X 3 1.325 -12.362 9.734 1.00 0.00 O
ATOM 51 OP2 ADE X 3 -0.563 -11.125 8.609 1.00 0.00 O
ATOM 52 H2 ADE X 3 -1.092 -12.660 -0.690 1.00 0.00 H
ATOM 53 H8 ADE X 3 -0.337 -11.317 5.563 1.00 0.00 H
ATOM 54 H1' ADE X 3 1.509 -13.198 2.843 1.00 0.00 H
ATOM 55 H2' ADE X 3 1.806 -11.067 5.010 1.00 0.00 H
ATOM 56 H3' ADE X 3 3.583 -11.853 5.989 1.00 0.00 H
ATOM 57 H4' ADE X 3 2.950 -14.612 5.487 1.00 0.00 H
ATOM 58 H5' ADE X 3 1.617 -14.442 7.500 1.00 0.00 H
ATOM 59 H61 ADE X 3 -4.251 -10.028 0.825 1.00 0.00 H
ATOM 60 H62 ADE X 3 -3.955 -9.962 2.581 1.00 0.00 H
ATOM 61 H2'' ADE X 3 2.782 -11.201 3.407 1.00 0.00 H
ATOM 62 H5'' ADE X 3 3.037 -13.389 7.578 1.00 0.00 H
ATOM 63 P THY X 4 5.602 -11.838 4.004 1.00 0.00 P
ATOM 64 C5' THY X 4 4.943 -11.921 1.422 1.00 0.00 C
ATOM 65 O5' THY X 4 5.116 -11.173 2.689 1.00 0.00 O
ATOM 66 C4' THY X 4 4.168 -11.183 0.392 1.00 0.00 C
ATOM 67 O4' THY X 4 2.923 -10.912 1.019 1.00 0.00 O
ATOM 68 C3' THY X 4 4.744 -9.789 -0.005 1.00 0.00 C
ATOM 69 O3' THY X 4 5.281 -9.844 -1.404 1.00 0.00 O
ATOM 70 C2' THY X 4 3.496 -8.941 0.048 1.00 0.00 C
ATOM 71 C1' THY X 4 2.335 -9.950 0.222 1.00 0.00 C
ATOM 72 N1 THY X 4 1.146 -9.320 0.758 1.00 0.00 N
ATOM 73 C2 THY X 4 0.040 -9.071 -0.054 1.00 0.00 C
ATOM 74 O2 THY X 4 0.076 -9.359 -1.249 1.00 0.00 O
ATOM 75 N3 THY X 4 -1.050 -8.360 0.451 1.00 0.00 N
ATOM 76 C4 THY X 4 -1.039 -7.828 1.717 1.00 0.00 C
ATOM 77 O4 THY X 4 -1.973 -7.172 2.118 1.00 0.00 O
ATOM 78 C5 THY X 4 0.111 -8.179 2.597 1.00 0.00 C
ATOM 79 C6 THY X 4 1.106 -8.902 2.053 1.00 0.00 C
ATOM 80 C7 THY X 4 0.035 -7.663 4.010 1.00 0.00 C
ATOM 81 OP1 THY X 4 6.827 -12.537 3.617 1.00 0.00 O
ATOM 82 OP2 THY X 4 5.704 -10.708 4.916 1.00 0.00 O
ATOM 83 H3 THY X 4 -1.789 -8.233 -0.225 1.00 0.00 H
ATOM 84 H6 THY X 4 2.009 -9.051 2.626 1.00 0.00 H
ATOM 85 H1' THY X 4 2.215 -10.378 -0.773 1.00 0.00 H
ATOM 86 H2' THY X 4 3.458 -8.381 0.982 1.00 0.00 H
ATOM 87 H3' THY X 4 5.530 -9.421 0.655 1.00 0.00 H
ATOM 88 H4' THY X 4 4.252 -11.898 -0.427 1.00 0.00 H
ATOM 89 H5' THY X 4 4.376 -12.830 1.621 1.00 0.00 H
ATOM 90 H71 THY X 4 0.958 -8.085 4.409 1.00 0.00 H
ATOM 91 H72 THY X 4 0.013 -6.574 3.990 1.00 0.00 H
ATOM 92 H73 THY X 4 -0.809 -8.186 4.460 1.00 0.00 H
ATOM 93 H2'' THY X 4 3.482 -8.324 -0.850 1.00 0.00 H
ATOM 94 H5'' THY X 4 5.916 -12.339 1.165 1.00 0.00 H
TER 95 THY X 4
ATOM 96 P ADE X 21 -9.903 -4.235 -8.464 1.00 0.00 P
ATOM 97 C5' ADE X 21 -7.477 -5.260 -8.680 1.00 0.00 C
ATOM 98 O5' ADE X 21 -8.739 -5.329 -7.999 1.00 0.00 O
ATOM 99 C4' ADE X 21 -6.411 -6.192 -8.056 1.00 0.00 C
ATOM 100 O4' ADE X 21 -6.179 -5.914 -6.724 1.00 0.00 O
ATOM 101 C3' ADE X 21 -6.855 -7.638 -8.180 1.00 0.00 C
ATOM 102 O3' ADE X 21 -6.125 -8.210 -9.228 1.00 0.00 O
ATOM 103 C2' ADE X 21 -6.428 -8.148 -6.781 1.00 0.00 C
ATOM 104 C1' ADE X 21 -5.596 -7.065 -6.189 1.00 0.00 C
ATOM 105 N1 ADE X 21 -3.423 -8.024 -1.589 1.00 0.00 N
ATOM 106 C2 ADE X 21 -2.982 -8.348 -2.801 1.00 0.00 C
ATOM 107 N3 ADE X 21 -3.582 -8.145 -3.919 1.00 0.00 N
ATOM 108 C4 ADE X 21 -4.833 -7.499 -3.753 1.00 0.00 C
ATOM 109 C5 ADE X 21 -5.383 -7.160 -2.537 1.00 0.00 C
ATOM 110 C6 ADE X 21 -4.550 -7.411 -1.463 1.00 0.00 C
ATOM 111 N6 ADE X 21 -4.705 -7.007 -0.200 1.00 0.00 N
ATOM 112 N7 ADE X 21 -6.675 -6.610 -2.677 1.00 0.00 N
ATOM 113 C8 ADE X 21 -6.794 -6.527 -3.978 1.00 0.00 C
ATOM 114 N9 ADE X 21 -5.764 -7.113 -4.682 1.00 0.00 N
ATOM 115 OP1 ADE X 21 -10.031 -4.296 -9.924 1.00 0.00 O
ATOM 116 OP2 ADE X 21 -11.101 -4.421 -7.556 1.00 0.00 O
ATOM 117 H2 ADE X 21 -2.024 -8.845 -2.852 1.00 0.00 H
ATOM 118 H8 ADE X 21 -7.624 -6.059 -4.486 1.00 0.00 H
ATOM 119 H1' ADE X 21 -4.538 -7.208 -6.409 1.00 0.00 H
ATOM 120 H2' ADE X 21 -7.315 -8.216 -6.151 1.00 0.00 H
ATOM 121 H3' ADE X 21 -7.939 -7.725 -8.256 1.00 0.00 H
ATOM 122 H4' ADE X 21 -5.475 -6.107 -8.608 1.00 0.00 H
ATOM 123 H5' ADE X 21 -7.166 -4.215 -8.652 1.00 0.00 H
ATOM 124 H61 ADE X 21 -3.971 -7.212 0.462 1.00 0.00 H
ATOM 125 H62 ADE X 21 -5.511 -6.433 0.003 1.00 0.00 H
ATOM 126 H2'' ADE X 21 -5.862 -9.075 -6.874 1.00 0.00 H
ATOM 127 H5'' ADE X 21 -7.608 -5.512 -9.732 1.00 0.00 H
TER 128 ADE X 21
ATOM 129 P THY X 22 -6.463 -9.660 -9.742 1.00 0.00 P
ATOM 130 P THY X 22 -6.463 -9.660 -9.742 1.00 0.00 P
ATOM 131 C5' THY X 22 -4.221 -10.672 -8.863 1.00 0.00 C
ATOM 132 C5' THY X 22 -4.221 -10.672 -8.863 1.00 0.00 C
ATOM 133 O5' THY X 22 -5.614 -10.548 -8.755 1.00 0.00 O
ATOM 134 O5' THY X 22 -5.614 -10.548 -8.755 1.00 0.00 O
ATOM 135 C4' THY X 22 -3.634 -11.570 -7.724 1.00 0.00 C
ATOM 136 C4' THY X 22 -3.634 -11.570 -7.724 1.00 0.00 C
ATOM 137 O4' THY X 22 -3.758 -10.896 -6.525 1.00 0.00 O
ATOM 138 O4' THY X 22 -3.758 -10.896 -6.525 1.00 0.00 O
ATOM 139 C3' THY X 22 -4.179 -12.977 -7.575 1.00 0.00 C
ATOM 140 C3' THY X 22 -4.179 -12.977 -7.575 1.00 0.00 C
ATOM 141 O3' THY X 22 -3.695 -13.924 -8.501 1.00 0.00 O
ATOM 142 O3' THY X 22 -3.695 -13.924 -8.501 1.00 0.00 O
ATOM 143 C2' THY X 22 -3.741 -13.131 -6.143 1.00 0.00 C
ATOM 144 C2' THY X 22 -3.741 -13.131 -6.143 1.00 0.00 C
ATOM 145 C1' THY X 22 -3.446 -11.753 -5.486 1.00 0.00 C
ATOM 146 C1' THY X 22 -3.446 -11.753 -5.486 1.00 0.00 C
ATOM 147 N1 THY X 22 -4.184 -11.605 -4.172 1.00 0.00 N
ATOM 148 N1 THY X 22 -4.184 -11.605 -4.172 1.00 0.00 N
ATOM 149 C2 THY X 22 -3.584 -12.077 -3.008 1.00 0.00 C
ATOM 150 C2 THY X 22 -3.584 -12.077 -3.008 1.00 0.00 C
ATOM 151 O2 THY X 22 -2.595 -12.776 -3.092 1.00 0.00 O
ATOM 152 O2 THY X 22 -2.595 -12.776 -3.092 1.00 0.00 O
ATOM 153 N3 THY X 22 -4.123 -11.676 -1.813 1.00 0.00 N
ATOM 154 N3 THY X 22 -4.123 -11.676 -1.813 1.00 0.00 N
ATOM 155 C4 THY X 22 -5.294 -10.960 -1.674 1.00 0.00 C
ATOM 156 C4 THY X 22 -5.294 -10.960 -1.674 1.00 0.00 C
ATOM 157 O4 THY X 22 -5.658 -10.677 -0.504 1.00 0.00 O
ATOM 158 O4 THY X 22 -5.658 -10.677 -0.504 1.00 0.00 O
ATOM 159 C5 THY X 22 -6.019 -10.683 -2.925 1.00 0.00 C
ATOM 160 C5 THY X 22 -6.019 -10.683 -2.925 1.00 0.00 C
ATOM 161 C6 THY X 22 -5.459 -11.019 -4.148 1.00 0.00 C
ATOM 162 C6 THY X 22 -5.459 -11.019 -4.148 1.00 0.00 C
ATOM 163 C7 THY X 22 -7.457 -10.363 -2.839 1.00 0.00 C
ATOM 164 C7 THY X 22 -7.457 -10.363 -2.839 1.00 0.00 C
ATOM 165 OP1 THY X 22 -6.052 -9.807 -11.195 1.00 0.00 O
ATOM 166 OP1 THY X 22 -6.052 -9.807 -11.195 1.00 0.00 O
ATOM 167 OP2 THY X 22 -7.882 -9.938 -9.400 1.00 0.00 O
ATOM 168 OP2 THY X 22 -7.882 -9.938 -9.400 1.00 0.00 O
ATOM 169 H3 THY X 22 -3.747 -12.012 -0.938 1.00 0.00 H
ATOM 170 H3 THY X 22 -3.747 -12.012 -0.938 1.00 0.00 H
ATOM 171 H6 THY X 22 -5.992 -10.780 -5.057 1.00 0.00 H
ATOM 172 H6 THY X 22 -5.992 -10.780 -5.057 1.00 0.00 H
ATOM 173 H1' THY X 22 -2.365 -11.803 -5.356 1.00 0.00 H
ATOM 174 H1' THY X 22 -2.365 -11.803 -5.356 1.00 0.00 H
ATOM 175 H2' THY X 22 -4.589 -13.608 -5.652 1.00 0.00 H
ATOM 176 H2' THY X 22 -4.589 -13.608 -5.652 1.00 0.00 H
ATOM 177 H3' THY X 22 -5.260 -12.920 -7.706 1.00 0.00 H
ATOM 178 H3' THY X 22 -5.260 -12.920 -7.706 1.00 0.00 H
ATOM 179 H4' THY X 22 -2.570 -11.599 -7.960 1.00 0.00 H
ATOM 180 H4' THY X 22 -2.570 -11.599 -7.960 1.00 0.00 H
ATOM 181 H5' THY X 22 -3.739 -9.695 -8.895 1.00 0.00 H
ATOM 182 H5' THY X 22 -3.739 -9.695 -8.895 1.00 0.00 H
ATOM 183 H71 THY X 22 -7.996 -11.113 -2.260 1.00 0.00 H
ATOM 184 H71 THY X 22 -7.996 -11.113 -2.260 1.00 0.00 H
ATOM 185 H72 THY X 22 -7.608 -9.383 -2.388 1.00 0.00 H
ATOM 186 H72 THY X 22 -7.608 -9.383 -2.388 1.00 0.00 H
ATOM 187 H73 THY X 22 -7.994 -10.274 -3.784 1.00 0.00 H
ATOM 188 H73 THY X 22 -7.994 -10.274 -3.784 1.00 0.00 H
ATOM 189 H2'' THY X 22 -2.874 -13.790 -6.092 1.00 0.00 H
ATOM 190 H2'' THY X 22 -2.874 -13.790 -6.092 1.00 0.00 H
ATOM 191 H5'' THY X 22 -3.986 -11.120 -9.829 1.00 0.00 H
ATOM 192 H5'' THY X 22 -3.986 -11.120 -9.829 1.00 0.00 H
ATOM 193 P GUA X 23 -4.319 -15.414 -8.683 1.00 0.00 P
ATOM 194 C5' GUA X 23 -2.225 -16.576 -7.639 1.00 0.00 C
ATOM 195 O5' GUA X 23 -3.654 -16.281 -7.543 1.00 0.00 O
ATOM 196 C4' GUA X 23 -1.521 -16.982 -6.358 1.00 0.00 C
ATOM 197 O4' GUA X 23 -1.882 -16.094 -5.335 1.00 0.00 O
ATOM 198 C3' GUA X 23 -1.781 -18.434 -5.890 1.00 0.00 C
ATOM 199 O3' GUA X 23 -0.540 -18.845 -5.375 1.00 0.00 O
ATOM 200 C2' GUA X 23 -2.822 -18.264 -4.780 1.00 0.00 C
ATOM 201 C1' GUA X 23 -2.326 -16.890 -4.344 1.00 0.00 C
ATOM 202 N1 GUA X 23 -3.804 -14.997 0.129 1.00 0.00 N
ATOM 203 C2 GUA X 23 -2.836 -15.910 -0.108 1.00 0.00 C
ATOM 204 N2 GUA X 23 -1.945 -16.249 0.771 1.00 0.00 N
ATOM 205 N3 GUA X 23 -2.482 -16.314 -1.312 1.00 0.00 N
ATOM 206 C4 GUA X 23 -3.329 -15.904 -2.282 1.00 0.00 C
ATOM 207 C5 GUA X 23 -4.463 -15.115 -2.131 1.00 0.00 C
ATOM 208 C6 GUA X 23 -4.731 -14.651 -0.778 1.00 0.00 C
ATOM 209 O6 GUA X 23 -5.723 -14.008 -0.278 1.00 0.00 O
ATOM 210 N7 GUA X 23 -5.160 -14.916 -3.326 1.00 0.00 N
ATOM 211 C8 GUA X 23 -4.517 -15.726 -4.163 1.00 0.00 C
ATOM 212 N9 GUA X 23 -3.309 -16.175 -3.605 1.00 0.00 N
ATOM 213 OP1 GUA X 23 -3.872 -15.864 -10.013 1.00 0.00 O
ATOM 214 OP2 GUA X 23 -5.774 -15.251 -8.489 1.00 0.00 O
ATOM 215 H1 GUA X 23 -3.990 -14.674 1.067 1.00 0.00 H
ATOM 216 H8 GUA X 23 -4.840 -15.925 -5.174 1.00 0.00 H
ATOM 217 H1' GUA X 23 -1.454 -17.112 -3.728 1.00 0.00 H
ATOM 218 H2' GUA X 23 -3.834 -18.201 -5.179 1.00 0.00 H
ATOM 219 H21 GUA X 23 -2.158 -15.885 1.688 1.00 0.00 H
ATOM 220 H3' GUA X 23 -2.105 -19.115 -6.677 1.00 0.00 H
ATOM 221 H22 GUA X 23 -1.289 -17.002 0.623 1.00 0.00 H
ATOM 222 H4' GUA X 23 -0.438 -16.860 -6.360 1.00 0.00 H
ATOM 223 H5' GUA X 23 -1.712 -15.640 -7.860 1.00 0.00 H
ATOM 224 H2'' GUA X 23 -2.691 -19.004 -3.990 1.00 0.00 H
ATOM 225 H5'' GUA X 23 -1.968 -17.243 -8.462 1.00 0.00 H
END
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Hi,
Thanks for posting two PDB files associated with the 'extra' C-T pair. Instead of directly posting the content, did you know that you can attach files as you do for email, by clicking:
"Attachments and other options"?
Also, THY22 has duplicated atom records. See below for example:
ATOM 153 N3 THY X 22 -4.123 -11.676 -1.813 1.00 0.00 N
ATOM 154 N3 THY X 22 -4.123 -11.676 -1.813 1.00 0.00 N
The files clarify the issue. I agree that in your case, it'd be better if DSSR does not report the 'C-T' pair. Such cases may be removed in future releases of DSSR. However, for the analysis of MD simulation trajectories, one cannot count on DSSR or find_pair to automatically identify the same set of WC pairs. For example, changing criteria for H-bond cutoffs would help here since you may well lose some WC pairs (or H-bonds thereof) along the trajectories.
Please check "x3dna_ensemble analyze -h" or do_x3dna (http://rjdkmr.github.io/do_x3dna/). In either case, you need to prepare a file with base-pair information. The file itself can be first generated with 'find_pair' and edit as necessary.
HTH,
Xiang-Jun
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As a follow-up of our conversation along the thread, I've just added a new DSSR option, "--pair-list", to allow full flexibility on the base pairs to be analyzed. There are two ways to use the option, for both writing and reading of the list of base pairs. As always, the case can be best illustrated with an example. Here, I am using PDB entry 1msy (http://www.rcsb.org/pdb/explore/explore.do?structureId=1msy) to make it clear on how to use the --pair-list option.
- First, run DSSR with --pair-list specified,
x3dna-dssr -i=1msy.pdb --pair-list
In the list of additional files in the end of DSSR output, you will see the following line:
4 dssr-pairs.txt -- a list of base pairs (to be edited and input to DSSR)
With content as below:
12 # number of pairs
1 27 # 1 A.U2647 A.G2673
2 26 # 2 A.G2648 A.U2672
3 25 # 3 A.C2649 A.G2671
4 24 # 4 A.U2650 A.A2670
5 23 # 5 A.C2651 A.G2669
6 22 # 6 A.C2652 A.G2668
7 21 # 7 A.U2653 A.C2667
8 20 # 8 A.A2654 A.C2666
10 19 # 9 A.U2656 A.A2665
11 18 # 10 A.A2657 A.G2664
12 17 # 11 A.C2658 A.G2663
13 16 # 12 A.G2659 A.A2662
This is a plain text file, with the number of base pairs in the first line, and following lines each specifies a list of two bases to be paired. The # and following characters in a line are for comment only. Note that the number of pairs and the following list of pairs need to be consistent, for obvious reasons.
- Edit the file as you see fit, for example delete the first two pairs. Rename/save the file to a new name (other than "dssr-pairs.txt"), e.g., "my_pairs.txt".
10 # number of pairs
3 25 # 3 A.C2649 A.G2671
4 24 # 4 A.U2650 A.A2670
5 23 # 5 A.C2651 A.G2669
6 22 # 6 A.C2652 A.G2668
7 21 # 7 A.U2653 A.C2667
8 20 # 8 A.A2654 A.C2666
10 19 # 9 A.U2656 A.A2665
11 18 # 10 A.A2657 A.G2664
12 17 # 11 A.C2658 A.G2663
13 16 # 12 A.G2659 A.A2662
- Run DSSR again, with --pair-list=my-pairs.txt specified,
x3dna-dssr -i=1msy.pdb --pair-list=my-pairs.txt
Now, the DSSR output results would be only for the pairs specified in "my-pairs.txt".
This should solve your problem, and you can use the same pairs list for the whole MD simulation trajectories. Please download DSSR again, and report back how it goes.
Xiang-Jun
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Thank you so much for your help!
I have another question:
If I also want to output local helical parameters (roll, tilt, twist, slide), can I also input a file (like pair list) to tell dssr which steps do I want to analyze as we analyze the base pair parameters?
Best,
Honglue
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If I also want to output local helical parameters (roll, tilt, twist, slide), can I also input a file (like pair list) to tell dssr which steps do I want to analyze as we analyze the base pair parameters?
Not yet (if I understand you correctly). What're you missing? Do you have a specific use-case? Please provide concrete (even contrived) examples to make your point clear.
Xiang-Jun
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Hi,
Hoestly, I haven't tested it yet but I will need these local helical parameters (twist roll side propeller tilt ...) later.
The reason why I ask this question is that DSSR sometimes will overcount base pairs (like my example above) in a duplex DNA but we can fix this issue by inputing which base pair steps we want to analyze. I am not sure if local helical parameters also has this issue that it will mess up when it overcount some extra base pairs in a duplex DNA because these local helical parameters are dependent on base pairs, right?
I will try this later but if you have some advice about this please let me know.
Thanks a lot.
Best,
Honglue
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