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# 3.10. Nucleic acid analysis — `MDAnalysis.analysis.nuclinfo`

Author: | Elizabeth Denning
Year: | 2011
Copyright: | GNU Public License v3

The module provides functions to analyze nuclic acid structures, in particular

- backbone dihedrals,
- chi dihedrals,
- AS or CP phase angles,
- Watson-Crick N1-N3 distances, C2-O2 distances, N6-O4 distances, O6-N4 distances.

For applications of this kind of analysis see [Denning2011] and [Denning2012].

All functions take a `Universe` as an argument together with further parameters that specify the base or bases in question. Angles are in degrees. The functions use standard CHARMM names for nucleic acids and atom names.

References

[Denning2011] | E.J. Denning, U.D. Priyakumar, L. Nilsson, and A.D. Mackerell, Jr. Impact of 2’-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA. J. Comput. Chem. 32 (2011), 1929–1943. doi: 10.1002/jcc.21777

[Denning2012] | E.J. Denning and A.D. MacKerell, Jr. Intrinsic Contribution of the 2’-Hydroxyl to RNA Conformational Heterogeneity. J. Am. Chem. Soc. 134 (2012), 2800–2806. doi: 10.1021/ja211328g

## 3.10.1. Distances

`MDAnalysis.analysis.nuclinfo.``wc_pair`(universe, i, bp)

  Watson-Crick basepair distance for residue i with residue bp.

  The distance of the nitrogen atoms in a Watson-Crick hydrogen bond is computed.

  Arguments : | universe `Universe` containing the trajectory i resid of the first base bp resid of the second base

  New in version 0.7.6.

`MDAnalysis.analysis.nuclinfo.``minor_pair`(universe, i, bp)

  Minor-Groove basepair distance for residue i with residue bp.

  The distance of the nitrogen and oxygen atoms in a Minor-groove hydrogen bond is computed.

  Arguments : | universe `Universe` containing the trajectory i resid of the first base bp resid of the second base

  New in version 0.7.6.

`MDAnalysis.analysis.nuclinfo.``major_pair`(universe, i, bp)

  Major-Groove basepair distance for residue i with residue bp.

  The distance of the nitrogen and oxygen atoms in a Major-groove hydrogen bond is computed.

  Arguments : | universe `Universe` containing the trajectory i resid of the first base bp resid of the second base

  New in version 0.7.6.

## 3.10.2. Phases

`MDAnalysis.analysis.nuclinfo.``phase_cp`(universe, seg, i)

  Pseudo-angle describing the phase of the ribose pucker for residue i using the CP method

  The angle is computed by the positions of atoms in the ribose ring

  Arguments : | universe `Universe` containing the trajectory segid segment identity of resid i resid of the base

  New in version 0.7.6.

`MDAnalysis.analysis.nuclinfo.``phase_as`(universe, seg, i)

  Pseudo-angle describing the phase of the ribose pucker for residue i using the AS method

  The angle is computed by the position vector of atoms in the ribose ring

  Arguments : | universe `Universe` containing the trajectory segid segment identity of resid i resid of the base

  New in version 0.7.6.

## 3.10.3. Dihedral angles

`MDAnalysis.analysis.nuclinfo.``tors`(universe, seg, i)

  Backbone dihedrals includes alpha, beta, gamma, delta, epsilon, zeta, chi

  The dihedral is computed based on position atoms for resid i

  Arguments : | universe `Universe` containing the trajectory segid segid of resid i resid of the base

  New in version 0.7.6.

`MDAnalysis.analysis.nuclinfo.``tors_alpha`(universe, seg, i)

  alpha backbone dihedral

  The dihedral is computed based on position atoms for resid i

  Arguments : | universe `Universe` containing the trajectory segid segid of resid i resid of the base

  New in version 0.7.6.

`MDAnalysis.analysis.nuclinfo.``tors_beta`(universe, seg, i)

  beta backbone dihedral

  The dihedral is computed based on position atoms for resid i

  Arguments : | universe `Universe` containing the trajectory segid segid of resid i resid of the base

  New in version 0.7.6.

`MDAnalysis.analysis.nuclinfo.``tors_gamma`(universe, seg, i)

  Gamma backbone dihedral

  > The dihedral is computed based on position atoms for resid i

  Arguments : | universe `Universe` containing the trajectory segid segid of resid i resid of the base

  New in version 0.7.6.

`MDAnalysis.analysis.nuclinfo.``tors_delta`(universe, seg, i)

  delta backbone dihedral

  The dihedral is computed based on position atoms for resid i

  Arguments : | universe `Universe` containing the trajectory segid segid of resid i resid of the base

  New in version 0.7.6.

`MDAnalysis.analysis.nuclinfo.``tors_eps`(universe, seg, i)

  Epsilon backbone dihedral

  The dihedral is computed based on position atoms for resid i

  Arguments : | universe `Universe` containing the trajectory segid segid of resid i resid of the base

  New in version 0.7.6.

`MDAnalysis.analysis.nuclinfo.``tors_zeta`(universe, seg, i)

  Zeta backbone dihedral

  The dihedral is computed based on position atoms for resid i

  Arguments : | universe `Universe` containing the trajectory segid segid of resid i resid of the base

  New in version 0.7.6.

`MDAnalysis.analysis.nuclinfo.``tors_chi`(universe, seg, i)

  chi nucleic acid dihedral

  The dihedral is computed based on position atoms for resid i

  Arguments : | universe `Universe` containing the trajectory segid segid of resid i resid of the base

  New in version 0.7.6.

`MDAnalysis.analysis.nuclinfo.``hydroxyl`(universe, seg, i)

  2-hydroxyl dihedral. Useful only for RNA calculations.

  The dihedral is computed based on position atoms for resid i

  Note : | This dihedral calculation will only work if using atom names as documented by charmm force field parameters.
  Arguments : | universe `Universe` containing the trajectory segid segid of resid i resid of the base

  New in version 0.7.6.

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