Helices and Isolates in output of find_pair

[febos]

Hello, my name is Eugene. I'm using the X3DNA v 1.5 "find_pair" feature in my research (example of using: "find_pair -t xxxx.pdb xxxx.out"). So, i don't understand how the program marks helices and isolates. As I know "+" is for isolated bps and "|" or "x" are for helices. So could You pleace explain to me what helices and isolates marked by this program exactly mean? I'm sorry if this question has already been discussed. And also excuse me for my english. Thank you.

[xiangjun]

Thanks for using 3DNA. In 'find_pair' output, '+' means isolated base-pair (bp), i.e., a bp not in a helical context. '|' means the bp is part of a helix, and 'x' means helix breaks at the bp.

It would help if you provide an example -- then our discussion would be more specific.

Xiang-Jun

[febos]

Thank you for so quick answer. I think i didn't posed my question correctly. I understand what letters "+ | x" mean, but i'd like to know why the program says so. For example i attached a pdb file 1AJU.out5. This is the output of find_pair to model 5 of 1aju.pdb structure. As you can see the helix is made up of bps from 1-30 to 13-20. and pairs 15-18 and 16-17 are isolated. But all these bps don't conflict with each other and don't have any other problems so why the last ones aren't in helix? Is it because they consist of non-WC bonds?
While I was writing this text I remembered another issue. When bp is represented with bigger number first (like 20-9) does it mean anything?

[xiangjun]

For model #5 of PDB entry 1aju, let's store its coordinates in file 1aju-m5.pdb. Run

Code: [Select]

find_pair 1aju-m5.pdb 1aju-m5.bpsyou get 1aju-m5.bps, with the following content:

1aju-m5.pdb
1aju-m5.out
    2         # duplex
   13         # number of base-pairs
    1    1    # explicit bp numbering/hetero atoms
    1   30  0 #    1 | ...5>A:..16_:[..G]G-----C[..C]:..46_:A<...5  1.26  0.86 43.33  8.60  0.14
    2   29  0 #    2 | ...5>A:..17_:[..G]G-----C[..C]:..45_:A<...5  1.05  0.14 21.15  8.79 -2.62
    3   28  0 #    3 | ...5>A:..18_:[..C]C-----G[..G]:..44_:A<...5  0.47  0.27 13.69  9.09 -3.30
    4   27  0 #    4 | ...5>A:..19_:[..C]C-----G[..G]:..43_:A<...5  0.55  0.43 20.29  9.06 -2.56
    5   26  0 #    5 | ...5>A:..20_:[..A]A-----U[..U]:..42_:A<...5  1.04  1.00 16.36  8.68 -1.15
    6   25  0 #    6 | ...5>A:..21_:[..G]G-----C[..C]:..41_:A<...5  1.01  0.44  9.82  8.78 -2.61
    7   24  0 #    7 | ...5>A:..22_:[..A]A-----U[..U]:..40_:A<...5  0.88  0.75 23.30  8.87 -1.45
   10   23  0 #    8 | ...5>A:..26_:[..G]G-----C[..C]:..39_:A<...5  1.16  0.44 20.37  8.79 -1.94
   11   22  0 #    9 | ...5>A:..27_:[..A]A-----U[..U]:..38_:A<...5  1.09  1.03 16.74  8.87 -1.00
   12   21  0 #   10 | ...5>A:..28_:[..G]G-----C[..C]:..37_:A<...5  0.94  0.83 22.27  8.99 -1.29
   13   20  9 #   11 x ...5>A:..29_:[..C]C-----G[..G]:..36_:A<...5  1.14  0.55 24.72  8.76 -1.53
   15   18  1 #   12 + ...5>A:..31_:[..U]U-**--G[..G]:..34_:A<...5  4.82  2.03 40.01  7.97  7.88
   16   17  1 #   13 + ...5>A:..32_:[..G]G-**+-G[..G]:..33_:A<...5  6.66  0.32 62.30  6.72  9.42
##### Base-pair criteria used:     4.00     0.00    15.00     2.50    65.00     4.50     7.50 [ O N]
##### 2 non-Watson-Crick base-pairs, and 3 helices (2 isolated bps)
##### Helix #1 (11): 1 - 11  ***broken O3'(i) to P(i+1) linkage***
##### Helix #2 (1): 12
##### Helix #3 (1): 13

The helix continues up to base pair (bp) "A:..29_:[..C]C-----G[..G]:..36_:A" (#11). The next two bps are isolated, i.e., not part of a continuous helix formed by bps from 1 to 11. Please see the attached blocview-image showing nucleotides 28 to 37, with green for G, cyan for U, red for A, and yellow for C.

Regarding your question,

When bp is represented with bigger number first (like 20-9) does it mean anything?

As shown above, the numerical values for bps (the left two columns) from find_pair are nucleotide sequential numbers as they appear in the input PDB file. What do you mean "does it mean anything?". As always, please be specific, using an example to illustrate your point.

HTH,

Xiang-Jun

[febos]

Thank you again for your detailed answer. I attached file 1Z58.out1. In this output bps with numbers 148  (pdb numbers of nucleotides 337-347) and 149 (338-346) are in one helix. But there is another bp with number 130 (348-336) and this bp is a part of another helix. So i thought pairs 336-348, 337-347 and 338-346 must compose a helix, why it isn't?. I hope this time I was enough specific.

[xiangjun]

Thanks for providing detailed info about a mis-assigned helix by find_pair. As shown in the attached image, in PDB entry 1z58, nucleotides 336-338 and 346-348 should indeed be assigned into a helix. While the helix assignment algorithm of find_pair works elegantly for the majority of cases, it is clearly not sophisticated enough to properly handle complicated structures such as 1z58 (the large ribosomal subunit from the eubacterium Deinococcus radiodurans): if you pay close attention to the output from find_pair, you will see warning messages in such cases.

I'm interested in refining 3DNA on those complicated structures, and your reported example is a concrete case to start with. Do you have more examples? The more varied and detailed cases I have, the easier to test find_pair against, and the more 3DNA can work for you in the end.

Xiang-Jun

[febos]

Thank you for the detailed explanation, it was very useful. I attached the list of pdb files with similar cases. I'm not sure about all of them, but at least the most part of these contain the same problem as 1Z58.pdb. All of these files contain ribosomal rna.

[xiangjun]

Thanks for providing a PDB list where find_pair cannot properly assign certain helices. It'd be more helpful if you could provide specific problematic helices, for at least some PDB entries, as you did for 1z58.

Best regards,

Xiang-Jun