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3.3.1. 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

3.3.1.1. Distances

MDAnalysis.analysis.nuclinfo.wc_pair(universe, i, bp, seg1='SYSTEM', seg2='SYSTEM')[source]

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

seg1

segment id for first base

i

resid of the first base

seg2

segment id for second base

bp

resid of the second base

NOTE: if failure occurs be sure to check the segment identification

New in version 0.7.6.

MDAnalysis.analysis.nuclinfo.minor_pair(universe, i, bp, seg1='SYSTEM', seg2='SYSTEM')[source]

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

seg1

segment id for first base

i

resid of the first base

seg2

segment id for second base

bp

resid of the second base

NOTE: if failure occurs be sure to check the segment identification

New in version 0.7.6.

MDAnalysis.analysis.nuclinfo.major_pair(universe, i, bp, seg1='SYSTEM', seg2='SYSTEM')[source]

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

seg1

segment id for first base

i

resid of the first base

seg2

segment id for second base

bp

resid of the second base

NOTE: if failure occurs be sure to check the segment identification

New in version 0.7.6.

3.3.1.2. Phases

MDAnalysis.analysis.nuclinfo.phase_cp(universe, seg, i)[source]

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)[source]

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.

3.3.1.3. Dihedral angles

MDAnalysis.analysis.nuclinfo.tors(universe, seg, i)[source]

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

NOTE: if failure occurs be sure to check the segment identification

MDAnalysis.analysis.nuclinfo.tors_alpha(universe, seg, i)[source]

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)[source]

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)[source]

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)[source]

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)[source]

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)[source]

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)[source]
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)[source]
2-hydroxyl dihedral. Useful only for RNA calculations.
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.