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General discussions (Q&As) /
« on: February 19, 2007, 11:24:57 pm »
Yes, there is a way in 3DNA to calculate all backbone torsion angles of any nucleic acid structure in PDB format. It is as follows:
where option "-s" (or equivalently "-1") is used to treat the whole structure as a continuous single helix, needed for getting all backbone torsion angles.
The "-t" option also takes consideration of HETATM records for modified bases. Note that in the coming new release of 3DNA v2.0, "-t" will be set by default, thus it will no longer be needed.
Of course, this method assumes that the nucleotides in the PDB structure are in proper order in the 5'-->3' direction. This should normally be the case. If need arises, I will consider add a new functionality in "find_pair" to make the nucleotides in order no matter whatever their original positionings in the PDB file are.
HTH,
Xiang-Jun
Code: [Select]
find_pair -s -t PDBFILE stdout | analyze
where option "-s" (or equivalently "-1") is used to treat the whole structure as a continuous single helix, needed for getting all backbone torsion angles.
The "-t" option also takes consideration of HETATM records for modified bases. Note that in the coming new release of 3DNA v2.0, "-t" will be set by default, thus it will no longer be needed.
Of course, this method assumes that the nucleotides in the PDB structure are in proper order in the 5'-->3' direction. This should normally be the case. If need arises, I will consider add a new functionality in "find_pair" to make the nucleotides in order no matter whatever their original positionings in the PDB file are.
HTH,
Xiang-Jun