Hi Chan Gu,
Thanks for posting two PDB files and an image, which help clarify the issues. Firstly, I'd say that you are certainly on the extreme side for some bp-defining parameters (e.g., H-bond distance cutoff of 20 Å). I am glad to see that '
find_pair' is still working properly, without giving many extraneous bps. Secondly, to force a pair between DA5/1 and DT3/60, you could simply edit the default output file as below:
From:
2 # duplex
29 # number of base-pairs
1 1 # explicit bp numbering/hetero atoms
2 59 0 # 1 | ....>-:...2_:[.RU]U-----A[.DA]:..59_:-<.... 1.88 1.82 46.49 8.64 2.83
****************************************************************************
To:
2 # duplex
30 # number of base-pairs
1 1 # explicit bp numbering/hetero atoms
1 60
2 59 0 # 1 | ....>-:...2_:[.RU]U-----A[.DA]:..59_:-<.... 1.88 1.82 46.49 8.64 2.83
As shown clearly in your attach image, DA5/1 and DT3/60 are stacking instead of pairing. In such extreme cases, '
find_pair' does not work as you'd expect, for solid reasons. Here certain manual editing is required, as illustrated above. I take this 'extra work' as an advantage since it reminds users to pay attentions to the abnormality.
If you are analyzing MD trajectories for an ensemble of similar structures, you do not need to run '
find_pair' for each model. See
x3dna_ensemble analyze -h for further info.
HTH,
Xiang-Jun
Topic: Finding base pair having a overlap (Read 16391 times)