This structure has broken O3' to P[i+1] linkages

[Vandana]

Hello dr Lu and other users,
I am new to 3DNA. I ran a pdb file with find_pair followed by analyze. I got this msg "This structure has broken O3' to P[i+1] linkages.". could any one help me in understanding what this means?? Also i need to know the major groove and minor groove which application do i run for the same. I have attached the pdb file i have used.

Regards
Vandana.R

[xiangjun]

Thanks for using 3DNA. Regarding 1le5, if you display 1le5.pdb (downloaded from PDB) in Jmol/PyMOL/RasMol, you will immediately notice that the structure in its asymmetric unit contains two copies of DNA duplexes. The two 'fragments' are not covalently connected, thus the message "This structure has broken O3' to P[i+1] linkages." -- it is for information only, not an error.

For the benefit of other viewers, here is what it looks like:

find_pair 1le5.pdb 1le5.inp
File '1le5.inp' has the following content:
1le5.pdb
1le5.out
    2         # duplex
   22         # number of base-pairs
    1    1    # explicit bp numbering/hetero atoms
    2   24  0 #    1 | ....>C:...2_:[GUA]G-----C[CYT]:..24_:D<....  0.61  0.60 14.96  9.14 -2.43
    3   23  0 #    2 | ....>C:...3_:[GUA]G-----C[CYT]:..23_:D<....  1.51  1.46 20.49  8.77  0.45
    4   22  0 #    3 | ....>C:...4_:[GUA]G-----C[CYT]:..22_:D<....  0.22  0.16 15.16  9.16 -3.69
    5   21  0 #    4 | ....>C:...5_:[ADE]A-----T[THY]:..21_:D<....  0.62  0.47 31.07  9.04 -1.89
    6   20  0 #    5 | ....>C:...6_:[ADE]A-----T[THY]:..20_:D<....  0.29  0.26  5.82  8.99 -3.91
    7   19  0 #    6 | ....>C:...7_:[ADE]A-----T[THY]:..19_:D<....  0.33  0.28 13.21  8.86 -3.45
    8   18  0 #    7 | ....>C:...8_:[THY]T-----A[ADE]:..18_:D<....  0.38  0.31 21.55  8.63 -2.92
    9   17  0 #    8 | ....>C:...9_:[THY]T-----A[ADE]:..17_:D<....  1.06  1.02 10.85  8.99 -1.37
   10   16  0 #    9 | ....>C:..10_:[CYT]C-----G[GUA]:..16_:D<....  1.03  1.00  4.76  9.04 -1.73
   11   15  0 #   10 | ....>C:..11_:[CYT]C-----G[GUA]:..15_:D<....  0.56  0.51 11.05  9.05 -2.87
   12   14  9 #   11 x ....>C:..12_:[THY]T-----A[ADE]:..14_:D<....  0.55  0.50 30.25  8.91 -1.94
   26   48  0 #   12 | ....>G:...2_:[GUA]G-----C[CYT]:..24_:H<....  0.88  0.72  5.00  8.59 -2.43
   27   47  0 #   13 | ....>G:...3_:[GUA]G-----C[CYT]:..23_:H<....  1.08  0.96 14.49  8.78 -1.27
   28   46  0 #   14 | ....>G:...4_:[GUA]G-----C[CYT]:..22_:H<....  0.40  0.24 12.49  8.79 -3.50
   29   45  0 #   15 | ....>G:...5_:[ADE]A-----T[THY]:..21_:H<....  0.41  0.30 13.27  8.63 -3.33
   30   44  0 #   16 | ....>G:...6_:[ADE]A-----T[THY]:..20_:H<....  0.95  0.80 21.23  8.37 -1.38
   31   43  0 #   17 | ....>G:...7_:[ADE]A-----T[THY]:..19_:H<....  0.86  0.81 19.69  8.59  0.46
   32   42  0 #   18 | ....>G:...8_:[THY]T-----A[ADE]:..18_:H<....  0.88  0.80 21.14  8.77 -1.45
   33   41  0 #   19 | ....>G:...9_:[THY]T-----A[ADE]:..17_:H<....  0.88  0.29 20.88  8.50 -2.50
   34   40  0 #   20 | ....>G:..10_:[CYT]C-----G[GUA]:..16_:H<....  0.70  0.34 11.58  8.42 -0.03
   35   39  0 #   21 | ....>G:..11_:[CYT]C-----G[GUA]:..15_:H<....  0.82  0.56  5.73  8.42  0.22
   36   38  0 #   22 | ....>G:..12_:[THY]T-----A[ADE]:..14_:H<....  1.18  0.85  5.25  8.14  0.13
##### Base-pair criteria used:     4.00     0.00    15.00     2.50    65.00     4.50     7.50 [ O N]
##### 0 non-Watson-Crick base-pairs, and 2 helices (0 isolated bps)
##### Helix #1 (11): 1 - 11
##### Helix #2 (11): 12 - 22

[/color]
The output from running "analyze 1le5.inp" contains parameters in file '1le5.out'. For groove widths, you just need to consider one section:

                  Minor Groove        Major Groove
                 P-P     Refined     P-P     Refined
   1 GG/CC       ---       ---       ---       ---
   2 GG/CC       ---       ---       ---       ---
   3 GA/TC      10.2       ---      20.6       ---
   4 AA/TT       8.1       8.1      18.2      18.1
   5 AA/TT       9.2       9.2      16.6      16.1
   6 AT/AT      10.5      10.5      17.1      17.0
   7 TT/AA       9.6       9.5      18.9      18.8
   8 TC/GA      10.9       ---      22.6       ---
   9 CC/GG       ---       ---       ---       ---
  10 CT/AG       ---       ---       ---       ---
  11 TG/CA       ---       ---       ---       ---

Alternatively, you may manually extract only chains C and D, and repeat the above procedure.

HTH,

Xiang-Jun

[Vandana]

Thankyou, I shall try the same again.


Regards
Vandana.R