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Author Topic: How to fix missing (superfluous) base pairs identified by find_pair?  (Read 3302 times)

Offline xiangjun

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Structural analysis of nucleic acid used to be a rather tedious process, especially for irregular, complicated RNA structures and nucleic acid-protein complexes (e.g., the large ribosomal subunit 1jj2/rr0033). Without valid base-pairing information as input, the various analysis software will produce meaningless results. The program find_pair was originally created to solve this specific problem, by generating input file to 3DNA analysis routines (analyze/cehs) directly from a PDB file.

In its core, find_pair uses a pure geometric approach to identify all possible pairs (Watson-Cricks or non-canonical pairs actually exist in a structure), their H-bonding patterns and helix context. Specifically, the major criteria used are as follows:
  • The distance between the origins of the two bases (as defined by their standard reference frames) must be less than certain limit (15.0 Å by default) - otherwise, they would be too far away to be called a pair.
  • The vertical separation (i.e., stagger) between the two base planes must be less than certain limit (2.5 Å by default) - otherwise, they would be stacking instead of pairing.
  • The angle between the two base z-axes (i.e., their normal vectors) is less than a cut-off (65.0° by default).
  • There is at least one pair of nitrogen/oxygen base atoms that are within a H-bonding cut off distance (4.0 Å by default).
If two bases fulfill these geometric requirements, they are defined to be a pair, without taking consideration of their chemical constituents. Thus our method allows for identification of unconventional pairs as easily as the canonical ones. The program then checks for possible H-bonding patterns, whether the normal donor-acceptor (noted by '-' as in O6 - N4 for a G·C pair) or the unusual donor-donor, acceptor-acceptor (noted by '*' as in O2 * N3 for a C·C pair in urx057). The non-canonical pairs, especially those with unusual H-bonding patterns, should be checked more carefully - they could be due to errors in structure determination, or they could have some special meaning/significance unnoticed previously.

The default criteria mentioned above are based on a survey of the NDB structures. Generally speaking, they are pretty generous and work quite well in the most common cases we've encountered. However, we are aware of the possibilities of special cases where some of them might be too restrict or too generous, thus leading to find_pair to miss or produce superfluous base pairs. The default settings are stored in a text file named misc_3dna.par under the directory $X3DNA/config/ where users can modify as they see fit. Changes in that directory will have a global effect - wherever you run find_pair on your system, the modified values will be used. Alternately, users could make a copy of misc_3dna.par to their current working directory and change it over there for local effect. Note that the local setting has precedence over the global one.

As an example, find_pair will miss the 127th base-pair I:..53_:[.DT]T-----A[.DA]:.-53_:J in structure 1kx5/pd0287 in its default settings. This is because the H-bonding distance between T:N3 - A:N1 is 4.20 Å and that for T:O4 - A:N6 is 4.85 Å; both of them are larger than the default 4.0 Å cut off. Increasing the H-bonding criterion in file misc_3dna.par from 4.0 Å to 5.0 Å will solve this problem. Please note that in 3DNA, users can start directly from an uncompressed PDB file, without having to extract the DNA fragment first:
  • find_pair 1kx5.pdb 1kx5.inp to get input file for analyze
  • analyze 1kx5.inp to get detailed structural parameters in file 1kx5.out
  • The above two steps can be combined into one: find_pair 1kx5.pdb stdout | analyze stdin
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.

Also worth noting is the -p option of find_pair: without this option, find_pair locates base pairs in double-helical regions; thus the Watson-Crick pairs take precedence over the Wobble and other non-canonical pairs. With the -p, then all pairs and higher order base associations (i.e., triplets and above) are detected.

 
« Last Edit: June 21, 2017, 04:09:37 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline sli

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some questions about find_pair?
« Reply #1 on: January 02, 2018, 02:01:25 am »
Dear Dr. Lu
        I want to get DNA structure's information  from a pdb file of DNA-protein complex.when I use 'find_pair' program , the mismatched base pairs which one base is completely flipping are default deleted.  My object is collect the size of the roll angle of the mismatched base pair. Due to my.bps file is lack of the mismatched base pair,when I use 'analyze my.bps' to generate 'bp_step.par', there are not  the mismatched base pairs information. I referenced the method of ' How to fix missing (superfluous) base pairs identified by find_pair?'  .But I still  not solve my problem. Could you give me some suggestions? Thank you!
« Last Edit: January 02, 2018, 02:04:27 am by sli »

Offline xiangjun

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Re: How to fix missing (superfluous) base pairs identified by find_pair?
« Reply #2 on: January 02, 2018, 10:33:09 am »
In your my.pdb structure, the DNA nucleotide D.UF2/17 is flipped out of the duplex, instead of forming a pair with C.DG12. In such cases, you could proceed as noted in the FAQ:

Quote
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.

So you could manually edit the find_pair output: changing 27 to 28, and add an extra line "209 242" as highlighted in red below. Note that in such cases, the step parameters (such as slide/roll etc) may not make intuitive sense (the numbers look weird). Nevertheless, they can be used to rigorously "rebuild" the original base geometry. See the 2008 3DNA Nature Protocols paper for more info.

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
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline sli

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Re: How to fix missing (superfluous) base pairs identified by find_pair?
« Reply #3 on: January 03, 2018, 02:29:58 am »
Thank you very much! I add a line as following:
    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   9 #   11 x ....>C:..11_:[.DC]C-----G[.DG]:..18_:D<....   0.35   0.30  19.14   8.92  -3.08
  209   242   0 #   12 | ....>C:..12_:[.DG]G-----UF2[.DUF2]:..17_:D<....
  210   241   0 #   13 | ....>C:..13_:[.DT]T-----A[.DA]:..16_:D<....   0.29   0.11  18.66   8.94  -3.55
  211   240   0 #   14 | ....>C:..14_:[.DG]G-----C[.DC]:..15_:D<....   0.18   0.13  10.54   9.00  -4.03
  212   239   0 #   15 | ....>C:..15_:[.DA]A-----T[.DT]:..14_:D<....   0.48   0.02   7.98   8.84  -4.09
  213   238   0 #   16 | ....>C:..16_:[.DG]G-----C[.DC]:..13_:D<....   0.29   0.21   8.86   9.02  -3.85
  214   237   0 #   17 | ....>C:..17_:[.DC]C-----G[.DG]:..12_:D<....   0.39   0.09  11.91   8.95  -3.84
  215   236   0 #   18 | ....>C:..18_:[.DG]G-----C[.DC]:..11_:D<....   0.46   0.11  16.51   8.89  -3.50
  216   235   0 #   19 | ....>C:..19_:[.DA]A-----T[.DT]:..10_:D<....   0.23   0.20  15.04   8.89  -3.62
  217   234   0 #   20 | ....>C:..20_:[.DT]T-----A[.DA]:...9_:D<....   0.12   0.02  13.95   8.86  -4.15
  218   233   0 #   21 | ....>C:..21_:[.DG]G-----C[.DC]:...8_:D<....   0.27   0.03   4.95   8.88  -4.43
  219   232   0 #   22 | ....>C:..22_:[.DG]G-----C[.DC]:...7_:D<....   0.36   0.19  14.07   8.97  -3.55
  220   231   0 #   23 | ....>C:..23_:[.DA]A-----T[.DT]:...6_:D<....   0.11   0.03  11.03   9.00  -4.27
  221   230   0 #   24 | ....>C:..24_:[.DC]C-----G[.DG]:...5_:D<....   0.26   0.01   5.16   9.01  -4.46
  222   229   0 #   25 | ....>C:..25_:[.DA]A-----T[.DT]:...4_:D<....   0.12   0.08  11.88   8.99  -4.13
  223   228   0 #   26 | ....>C:..26_:[.DG]G-----C[.DC]:...3_:D<....   0.19   0.10  12.55   9.07  -3.98
  224   227   0 #   27 | ....>C:..27_:[.DC]C-----G[.DG]:...2_:D<....   0.70   0.08  13.79   8.87  -3.45
  225   226   0 #   28 | ....>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

I found that on the line I added, the result of the output file(be_step.par) was the same whether I add the number(like as 0.30   0.35  18.14   9.92  -3.33 ) or not. and then I use the modified file(my.bps) to "analyze" and finally "rebuild" DNA structure.In addition, I align the original DNA structure and the rebuild DNA structure by Pymol(pair_fit) ,they are not completely same. So I am not sure that my rebuild structure is right. Because I can not well understand means of your words:"Nevertheless, they can be used to rigorously "rebuild" the original base geometry". Is it said that the rebuild structure should completely as the original one? The aligned result is shown in the attachment.

Best wishes!


 
« Last Edit: January 03, 2018, 02:49:39 am by sli »

Offline xiangjun

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Re: How to fix missing (superfluous) base pairs identified by find_pair?
« Reply #4 on: January 03, 2018, 10:59:04 am »
Hi,

Thanks for your followup. I sort of understand your confusions in general. Your case could serve as an excellent example to clarify some subtle points in 3DNA. To proceed, could you please provide details what you did, especially how you generate the attached image?

Best regards,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline sli

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Re: How to fix missing (superfluous) base pairs identified by find_pair?
« Reply #5 on: January 07, 2018, 07:37:30 am »
Dear Dr. Lu,

         I am sorry I have not reply you on time. The above image generation process can be obtained from my attached file.

Best wishes!

Offline xiangjun

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Re: How to fix missing (superfluous) base pairs identified by find_pair?
« Reply #6 on: January 07, 2018, 11:11:01 am »
Hi,

Thanks for providing an attachment detailing the procedures you used to generate the above image. Discussions based on concrete examples are (far) more likely to achieve meaning results (in my experience, at least).

As a side note (for you and other viewers of the thread), it would have be more convenient for reference and discussion if the step-by-step procedures were directly listed (in plain text where possible) within your post. Images etc. can be attached separately, and referenced in the post. If one composite attachment is needed, PDF format is preferred.


Now let's return to the main topic on the rigor of the 3DNA analyze/rebuild cycle. You used PyMOL "pair_fit" to compare your original vs 3DNA-generated coordinates and noticed differences. The result is expected since your PyMOL selections used sugar atoms, but not I intended in the original response.

As noted in the two major 3DNA publications (2003 NAR, and 2008 Nature Protocols), the 3DNA analyze/rebuild routines are rigorously reversible for base (pair) geometries only. The sugar and phosphate backbone have many more conformational flexibility than can be captured by the base-pair parameters (e.g., in file bp_step.par you referred to in your attachment).

The intended procedure is described below, using your original my.pdb as an example.

Code: Bash
  1. # create a new directory, here I call it 'check-3dna'
  2. mkdir check-3dna
  3. cd check-3dna
  4.  
  5. # copy your original coordinate 'my.pdb' into it
  6. cp ~/Downloads/my.pdb .
  7.  
  8. # The following step creates file 'bp_step.par' with 27 base pairs
  9. #   which does not include the flipped out 'base pair'
  10. find_pair my.pdb | analyze
  11.  
  12. # Copy 'bp_step.par' to a different name for later reference and
  13. #   to avoid being over-written
  14. cp bp_step.par bp_step-01.par
  15.  
  16. # Rebuild the structure with base atoms, using 'bp_step.par'
  17. rebuild -atomic bp_step-01.par my-3DNA-noFlippedBP.pdb
  18.  
  19. # The 3DNA-rebuilt structure 'my-3DNA-noFlippedBP.pdb' has virtually
  20. #   the same base geometry as that in your original 'my.pdb'
  21. # You could perform a least-square fit between them, and the RMSD
  22. #   should be ~0.05 A, as reported in Table 3 of the 2003 NAR paper
  23.  
  24. # Another way, which is more convenient, is to re-analyze the generated structure
  25. #   and you should get virtually the same base-pair parameters.
  26. #   Compare files: bp_step-01.par and bp_step-02.par
  27. find_pair my-3DNA-noFlippedBP.pdb | analyze
  28. cp bp_step.par bp_step-02.par

Content of bp_step-01.par derived by 3DNA from my.pdb:
Code: [Select]
  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

Content of bp_step-02.par derived by 3DNA from my-3DNA-noFlippedBP.pdb:
Code: [Select]
  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

For your verification, I've attached the following four files:

  • my.pdb -- your original coordinate file
  • bp_step-01.par -- base-pair parameters used for rebuilding
  • my-3DNA-noFlippedBP.pdb -- 3DNA-generated structure based on bp_step-01.par
  • bp_step-02.par -- base-pair parameters from 3DNA-generated structure

Please repeat the above procedure with the flipped base-pair included, and report back your findings. I'll be happy to help if necessary.

Best regards,

Xiang-Jun
« Last Edit: January 07, 2018, 01:31:42 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline sli

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Re: How to fix missing (superfluous) base pairs identified by find_pair?
« Reply #7 on: January 14, 2018, 07:40:37 am »
Thanks for your help and your suggestions!

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.