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Questions and answers > MD simulations
local helical axis vector for strongly bent DNA
xiangjun:
Check the source code to get to the bottom of the technical details.
For the analysis of NMR ensembles or MD trajectories, however, manually editing 'find_pair'-generated base-pair file may be the preferred way to go, as documented for the 'x3dna_ensemble' script distributed with 3DNA.
Xiang-Jun
adihau:
Hi Xiang-Jun,
thank you for your answer. I still couldn't figure out a way, so that base-pairs are recognized, even if they are broken. Since I have a long trajectory, editing the 'find_pair'-generated base-pair file is maybe not the best option in this case.
I tried altering the criteria, but somehow there are still base-pairs not recognized, although I changed the criteria to quite high values. I will attach a few frames, with which I have problems. Do you know, what I did wrong? In those frames are broken base-pairs, but it should be possible to still match them, I think.
The criteria I changed were the following:
Section 3: for find_pair program
# maximum distance between base origins (was 15 originally)
<max_dorg>40.0</max_dorg>
# maximum vertical base separation, i.e., |stagger| (was 2.5 originally)
<max_dv>20</max_dv>
# maximum angle between base normals (in range 0..90) (was 65 originally)
<max_plane_angle>90.0</max_plane_angle>
# minimum distance between RN9/YN1 base atoms (was 4.5 originally)
<min_dNN>1</min_dNN>
# distance criterion for helix break (was 7.8 originally)
<helix_break>50</helix_break>
Thank you very much for your time and your help,
Adina
xiangjun:
Imagine if you do not have access to 'find_pair', how would manually provide the base-pairing information from a PDB file to the 3DNA 'analyze' program? No changes in the criteria can fit every possible cases, especially for extremely deformed 'base pairs'. In your F29.pdb and F30.pdb files, for example, the two terminal 'pairs' may not be called base pairs at all. That's why I suggested you using the result from 'find_pair' as a starting point, and make changes manually as needed, and then feed the revised pairing info to 'analyze'.
Two of your new attached files (Frame25574_13.pdb and Frame46393_9.pdb) are more common, where one base-pair is not detected by 'find_pair' in its default settings. Using Frame25574_13.pdb as an example,
find_pair Frame25574_13.pdb
will give the following result:
Frame25574_13.pdb
Frame25574_13.out
2 # duplex
17 # number of base-pairs
1 1 # explicit bp numbering/hetero atoms
1 36 0 # 1 | ....>X:...1_:[DG5]G-----C[DC3]:..36_:X<.... 1.11 0.58 20.02 8.77 -1.73
2 35 0 # 2 | ....>X:...2_:[.DC]C-----G[.DG]:..35_:X<.... 0.18 0.03 20.28 9.06 -3.74
3 34 0 # 3 | ....>X:...3_:[.DA]A-----T[.DT]:..34_:X<.... 0.34 0.29 13.33 9.12 -3.41
4 33 0 # 4 | ....>X:...4_:[.DC]C-----G[.DG]:..33_:X<.... 0.58 0.33 2.85 8.97 -3.62
5 32 0 # 5 | ....>X:...5_:[.DG]G-----C[.DC]:..32_:X<.... 0.43 0.15 11.47 9.00 -3.70
7 30 0 # 6 | ....>X:...7_:[.DA]A-----T[.DT]:..30_:X<.... 0.41 0.32 13.65 9.21 -3.26
8 29 0 # 7 | ....>X:...8_:[.DC]C-----G[.DG]:..29_:X<.... 0.55 0.48 8.48 8.98 -3.06
9 28 0 # 8 | ....>X:...9_:[.DG]G-----C[.DC]:..28_:X<.... 0.46 0.04 17.63 9.10 -3.58
10 27 0 # 9 | ....>X:..10_:[.DA]A-----T[.DT]:..27_:X<.... 0.39 0.04 10.30 9.03 -4.01
11 26 0 # 10 | ....>X:..11_:[.DA]A-----T[.DT]:..26_:X<.... 0.78 0.77 13.39 8.77 -2.02
12 25 0 # 11 | ....>X:..12_:[.DC]C-----G[.DG]:..25_:X<.... 0.81 0.80 12.58 9.12 -1.96
13 24 0 # 12 | ....>X:..13_:[.DG]G-----C[.DC]:..24_:X<.... 0.55 0.18 18.67 9.09 -3.15
14 23 0 # 13 | ....>X:..14_:[.DA]A-----T[.DT]:..23_:X<.... 0.52 0.28 17.64 8.98 -3.03
15 22 0 # 14 | ....>X:..15_:[.DA]A-----T[.DT]:..22_:X<.... 0.47 0.30 24.22 8.63 -2.72
16 21 0 # 15 | ....>X:..16_:[.DC]C-----G[.DG]:..21_:X<.... 0.52 0.27 10.14 9.00 -3.43
17 20 0 # 16 | ....>X:..17_:[.DG]G-----C[.DC]:..20_:X<.... 0.56 0.55 4.96 9.11 -3.09
18 19 0 # 17 | ....>X:..18_:[DC3]C-----G[DG5]:..19_:X<.... 0.33 0.19 16.06 9.22 -3.49
##### 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 1 helix (0 isolated bps)
##### Helix #1 (17): 1 - 17 ***broken O3' to P[i+1] linkage***
Note that the presumed base-pair between DA6 and DT31 is missed. See the the attached image for why it is not detected by 'find_pair'. If you want to have it the the output of 'analyze', simply add it in, as shown below. Note that the number of base-pairs has been increased from 17 to 18 to account for the additional pair.
Frame25574_13.pdb
Frame25574_13.out
2 # duplex
18 # number of base-pairs
1 1 # explicit bp numbering/hetero atoms
1 36 0 # 1 | ....>X:...1_:[DG5]G-----C[DC3]:..36_:X<.... 1.11 0.58 20.02 8.77 -1.73
2 35 0 # 2 | ....>X:...2_:[.DC]C-----G[.DG]:..35_:X<.... 0.18 0.03 20.28 9.06 -3.74
3 34 0 # 3 | ....>X:...3_:[.DA]A-----T[.DT]:..34_:X<.... 0.34 0.29 13.33 9.12 -3.41
4 33 0 # 4 | ....>X:...4_:[.DC]C-----G[.DG]:..33_:X<.... 0.58 0.33 2.85 8.97 -3.62
5 32 0 # 5 | ....>X:...5_:[.DG]G-----C[.DC]:..32_:X<.... 0.43 0.15 11.47 9.00 -3.70
6 31 0
7 30 0 # 6 | ....>X:...7_:[.DA]A-----T[.DT]:..30_:X<.... 0.41 0.32 13.65 9.21 -3.26
8 29 0 # 7 | ....>X:...8_:[.DC]C-----G[.DG]:..29_:X<.... 0.55 0.48 8.48 8.98 -3.06
9 28 0 # 8 | ....>X:...9_:[.DG]G-----C[.DC]:..28_:X<.... 0.46 0.04 17.63 9.10 -3.58
10 27 0 # 9 | ....>X:..10_:[.DA]A-----T[.DT]:..27_:X<.... 0.39 0.04 10.30 9.03 -4.01
11 26 0 # 10 | ....>X:..11_:[.DA]A-----T[.DT]:..26_:X<.... 0.78 0.77 13.39 8.77 -2.02
12 25 0 # 11 | ....>X:..12_:[.DC]C-----G[.DG]:..25_:X<.... 0.81 0.80 12.58 9.12 -1.96
13 24 0 # 12 | ....>X:..13_:[.DG]G-----C[.DC]:..24_:X<.... 0.55 0.18 18.67 9.09 -3.15
14 23 0 # 13 | ....>X:..14_:[.DA]A-----T[.DT]:..23_:X<.... 0.52 0.28 17.64 8.98 -3.03
15 22 0 # 14 | ....>X:..15_:[.DA]A-----T[.DT]:..22_:X<.... 0.47 0.30 24.22 8.63 -2.72
16 21 0 # 15 | ....>X:..16_:[.DC]C-----G[.DG]:..21_:X<.... 0.52 0.27 10.14 9.00 -3.43
17 20 0 # 16 | ....>X:..17_:[.DG]G-----C[.DC]:..20_:X<.... 0.56 0.55 4.96 9.11 -3.09
18 19 0 # 17 | ....>X:..18_:[DC3]C-----G[DG5]:..19_:X<.... 0.33 0.19 16.06 9.22 -3.49
##### 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 1 helix (0 isolated bps)
##### Helix #1 (17): 1 - 17 ***broken O3' to P[i+1] linkage***
Does this solve your problem? If so, please repeat the above procedures for the other two cases (Frame46393_9.pdb and Frame72614_2.pdb), showing clearly which pair is missing using a graphic image as I did for the DA6--DT31 pair. This would improve your understanding of the concept, and benefit other users.
Xiang-Jun
adihau:
Hello Xiang-Jun,
thank you very much for your detailed answer and your patience. This indeed helps me, and I understand that changing the criteria does not help in these cases.
So for everyone having the same problem, I used the following code:
--- Code: ---find_pair myframe.pdb myframe.inp
--- End code ---
this will create a file 'myframe.inp', which I modified in the way Xiang-Jun suggested in the answer above. Then
--- Code: ---analyze myframe.inp
--- End code ---
creates a file myframe.out with the results for all base-pairs including the broken one.
This worked in all cases so far, I will attach pictures of the problematic base-pairs of two more frames. I attached two pictures of the Frame72614_2 because it's not very clear to see, what is happening there in the first picture. The bases are not too far away from each other, but probably twisted too much.
Thank you again,
Adina
xiangjun:
Hi Adina,
Thanks for your followup. Note that for your 'Frame72614_2', the terminal G1 and C36 are stacking instead of pairing.
Presumably, the three structures (Frame25574_13.pdb, Frame46393_9.pdb, and Frame72614_2.pdb) are along the trajectory of an MD simulation of the same DNA molecule. The base-pair information would be the same: you do not need to run 'find_pair' repeatedly for each frame. Simply run 'find_pair' once for a selected frame (e.g., the first one), and edit the resulting pairing info as needed. Then that pairing info can be used for the analysis of each and every frame along the trajectory.
Best regards,
Xiang-Jun
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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.
