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find_pair sel.pdb stdout
sel.pdb
sel.out
2 # duplex
23 # number of base-pairs
1 1 # explicit bp numbering/hetero atoms
2 47 0 # 1 | ....>A:...2_:[..G]G-----C[..C]:..48_:B<.... 0.77 0.76 28.01 8.85 -1.31
3 46 0 # 2 | ....>A:...3_:[..T]T-----A[..A]:..47_:B<.... 0.32 0.02 11.50 9.26 -4.07
4 45 0 # 3 | ....>A:...4_:[..G]G-----C[..C]:..46_:B<.... 0.83 0.64 4.42 9.11 -2.68
5 44 0 # 4 | ....>A:...5_:[..T]T-----A[..A]:..45_:B<.... 0.54 0.32 21.12 8.91 -2.76
6 43 0 # 5 | ....>A:...6_:[..G]G-----C[..C]:..44_:B<.... 0.45 0.27 27.61 8.88 -2.64
7 42 0 # 6 | ....>A:...7_:[..A]A-**+-T[..T]:..43_:B<.... 3.71 0.96 28.75 7.04 4.07
8 41 0 # 7 | ....>A:...8_:[..G]G-----C[..C]:..42_:B<.... 0.45 0.32 3.39 8.97 -3.75
9 40 0 # 8 | ....>A:...9_:[..C]C-----G[..G]:..41_:B<.... 1.05 0.47 8.17 8.82 -2.61
10 39 0 # 9 | ....>A:..10_:[..G]G-----C[..C]:..40_:B<.... 0.76 0.50 21.19 8.86 -2.17
11 38 0 # 10 | ....>A:..11_:[..T]T-----A[..A]:..39_:B<.... 0.34 0.27 5.44 9.01 -3.84
12 37 0 # 11 | ....>A:..12_:[..G]G-----C[..C]:..38_:B<.... 0.58 0.48 12.17 9.02 -2.85
13 36 0 # 12 | ....>A:..13_:[..G]G-----C[..C]:..37_:B<.... 0.24 0.03 16.54 9.08 -3.88
14 35 0 # 13 | ....>A:..14_:[..G]G-----C[..C]:..36_:B<.... 0.69 0.69 14.12 9.14 -2.22
15 34 0 # 14 | ....>A:..15_:[..C]C-----G[..G]:..35_:B<.... 0.41 0.09 14.35 9.02 -3.70
16 33 0 # 15 | ....>A:..16_:[..G]G-----C[..C]:..34_:B<.... 0.40 0.39 26.56 9.03 -2.49
17 32 0 # 16 | ....>A:..17_:[..T]T-----A[..A]:..33_:B<.... 0.70 0.62 8.01 9.49 -2.65
18 31 0 # 17 | ....>A:..18_:[..A]A-----T[..T]:..32_:B<.... 0.26 0.21 18.44 8.96 -3.41
19 30 0 # 18 | ....>A:..19_:[..C]C-----G[..G]:..31_:B<.... 0.26 0.09 25.81 9.27 -3.27
20 29 0 # 19 | ....>A:..20_:[..A]A-----T[..T]:..30_:B<.... 0.63 0.21 19.54 8.96 -2.98
21 28 0 # 20 | ....>A:..21_:[..C]C-----G[..G]:..29_:B<.... 0.57 0.33 6.64 9.06 -3.43
22 27 0 # 21 | ....>A:..22_:[..A]A-----T[..T]:..28_:B<.... 1.09 1.01 10.89 8.63 -1.34
23 26 0 # 22 | ....>A:..23_:[..C]C-----G[..G]:..27_:B<.... 0.66 0.37 28.93 9.04 -2.16
24 25 0 # 23 | ....>A:..24_:[..A]A-----T[..T]:..26_:B<.... 2.72 2.29 25.44 7.75 5.57
##### Base-pair criteria used: 4.00 0.00 15.00 2.50 65.00 4.50 7.50 [ O N]
##### 1 non-Watson-Crick base-pair, and 1 helix (0 isolated bps)
##### Helix #1 (23): 1 - 23
I am not sure if this is too much to ask you.No, it's not; I always welcome user questions such as this one, and I strive to be as helpful as I could.
&inp file=sel.pdb,
lis=sel,
fit=.t.,
lib=./standard,
isym=1,
&end
2 1 -1 0 0
2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24
47 46 45 44 43 42 41 40 39 38 37 36 35 34 33 32 31 30 29 28 27 26 25
Combined strands have 15 levels ...
Strand 1 has 15 bases (5'-3'): GTGTGAGCGTGGGCG
Strand 2 has 15 bases (3'-5'): CACACTCGCACCCGC
2 3 4 5 6 7 8 9 10 11Run Curves+ on it again, do you get what you expect?
47 46 45 44 43 42 41 40 39 38
2:24Run Curves+, what do you get?
47:25
Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.