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
Topic: This structure has broken O3' to P[i+1] linkages (Read 13689 times)