I need to get helical parameters from a trajectory file. Though "do_x3DNA" software does the same job it excludes damaged section of base pairs by default. How can I calculate parameters for full sequence without excluding base pairs which are far off.
There is a bend in the DNA due to which base pairs are moved far off
Try modifying the output of "find_pair" program. See this forum thread:
http://forum.x3dna.org/general-discussions/problem-of-finding-all-base-pairs-in-distorted-dna-structure-using-3dna/
Initially I was using x3DNA only, if we are dealing with few files this software is appropriate to use. It does the job in two steps, in step 1 it generate input files using "find_pair" command. In case of far off bases we mention exclusively to consider them as a pair. In second step this modified input is supplied through "analyze" command in order to obtain all the parameters. However editing the files for more than 5000 pdb files is time consuming. So Do_x3DNA dna does the same job for trajectory, but there is only one step to execute and it generates all the files in one go.
The "find_pair" program needs to be executed only once for each trajectory/system. One can generate multi-model PDB file ("ensemble.pdb") from the trajectory (with some little scripting) and then use "x3dna_ensemble" program to process the ensemble (using the output of "find_pair" program executed on the same PDB file):
find_pair ensemble.pdb -o x3dna.in
x3dna_ensemble analyze -b x3dna.in -e ensemble.pdb -o ensemble.x3dna
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Note: If the base pair is very distorted from the standard DNA helical conformations, some of the 66 DNA geometry parameters calculated by X3DNA have no meaning for that base pair . . .
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