4.6.1. Nucleic acid analysis — MDAnalysis.analysis.nuclinfo

Author:

Elizabeth Denning

Year:

2011

Copyright:

Lesser GNU Public License v2.1+

The module provides functions to analyze nucleic 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 [1][2].

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

[1]

Elizabeth J. Denning, U. Deva Priyakumar, Lennart Nilsson, and Alexander 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. Journal of Computational Chemistry, 32(9):1929–1943, 2011. doi:https://doi.org/10.1002/jcc.21777.

[2]

Elizabeth J. Denning and Alexander D. MacKerell. Intrinsic contribution of the 2'-hydroxyl to rna conformational heterogeneity. Journal of the American Chemical Society, 134(5):2800–2806, 2012. PMID: 22242623. doi:10.1021/ja211328g.

4.6.1.1. Distances

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

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

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

Parameters:

• universe (Universe) – Universe containing the trajectory

• i (int) – resid of the first base

• bp (int) – resid of the second base

• seg1 (str (optional)) – segment id for first base [“SYSTEM”]

• seg2 (str (optional)) – segment id for second base [“SYSTEM”]

Returns:

Watson-Crick base pair distance

Return type:

float

Notes

If failure occurs be sure to check the segment identification.

Added in version 0.7.6.

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

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.

Parameters:

• universe (Universe) – Universe containing the trajectory

• i (int) – resid of the first base

• bp (int) – resid of the second base

• seg1 (str (optional)) – segment id for first base [“SYSTEM”]

• seg2 (str (optional)) – segment id for second base [“SYSTEM”]

Returns:

Minor groove base pair distance

Return type:

float

Notes

If failure occurs be sure to check the segment identification.

Added in version 0.7.6.

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

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.

Parameters:

• universe (Universe) – Universe containing the trajectory

• i (int) – resid of the first base

• bp (int) – resid of the second base

• seg1 (str (optional)) – segment id for first base [“SYSTEM”]

• seg2 (str (optional)) – segment id for second base [“SYSTEM”]

Returns:

Major groove base pair distance

Return type:

float

Notes

If failure occurs be sure to check the segment identification.

Added in version 0.7.6.

4.6.1.2. 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.

Parameters:

• universe (Universe) – Universe containing the trajectory

• seg (str) – segment id for base

• i (int) – resid of the first base

Returns:

phase angle in degrees

Return type:

float

Added 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.

Parameters:

• universe (Universe) – Universe containing the trajectory

• seg (str) – segment id for base

• i (int) – resid of the first base

Returns:

phase angle in degrees

Return type:

float

Added in version 0.7.6.

4.6.1.3. Dihedral angles

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

Calculation of nucleic backbone dihedral angles.

The dihedral angles are alpha, beta, gamma, delta, epsilon, zeta, chi.

The dihedral is computed based on position of atoms for resid i.

Parameters:

• universe (Universe) – Universe containing the trajectory

• seg (str) – segment id for base

• i (int) – resid of the first base

Returns:

[alpha, beta, gamma, delta, epsilon, zeta, chi] – torsion angles in degrees

Return type:

list of floats

Notes

If failure occurs be sure to check the segment identification.

Added 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.

Parameters:

• universe (Universe) – Universe containing the trajectory

• seg (str) – segment id for base

• i (int) – resid of the first base

Returns:

alpha – torsion angle in degrees

Return type:

float

Added 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.

Parameters:

• universe (Universe) – Universe containing the trajectory

• seg (str) – segment id for base

• i (int) – resid of the first base

Returns:

beta – torsion angle in degrees

Return type:

float

Added 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.

Parameters:

• universe (Universe) – Universe containing the trajectory

• seg (str) – segment id for base

• i (int) – resid of the first base

Returns:

gamma – torsion angle in degrees

Return type:

float

Added 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.

Parameters:

• universe (Universe) – Universe containing the trajectory

• seg (str) – segment id for base

• i (int) – resid of the first base

Returns:

delta – torsion angle in degrees

Return type:

float

Added 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.

Parameters:

• universe (Universe) – Universe containing the trajectory

• seg (str) – segment id for base

• i (int) – resid of the first base

Returns:

epsilon – torsion angle in degrees

Return type:

float

Added 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.

Parameters:

• universe (Universe) – Universe containing the trajectory

• seg (str) – segment id for base

• i (int) – resid of the first base

Returns:

zeta – torsion angle in degrees

Return type:

float

Added 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.

Parameters:

• universe (Universe) – Universe containing the trajectory

• seg (str) – segment id for base

• i (int) – resid of the first base

Returns:

chi – torsion angle in degrees

Return type:

float

Added in version 0.7.6.

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

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, namely “C1’, C2’, O2’, H2’”.

Parameters:

• universe (Universe) – Universe containing the trajectory

• seg (str) – segment id for base

• i (int) – resid of the first base

Returns:

hydroxyl_angle – torsion angle in degrees

Return type:

float

Added in version 0.7.6.

MDAnalysis.analysis.nuclinfo.pseudo_dihe_baseflip(universe, bp1, bp2, i, seg1='SYSTEM', seg2='SYSTEM', seg3='SYSTEM')

pseudo dihedral for flipped bases. Useful only for nucleic acid base flipping

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.

Parameters:

• universe (Universe) – Universe containing the trajectory

• bp1 (int) – resid that base pairs with bp2

• bp2 (int) – resid below the base that flips

• i (int) – resid of the base that flips

• segid1 (str (optional)) – segid of resid base pairing with bp2

• segid2 (str (optional)) – segid, same as that of segid of flipping resid i

• segid3 (str (optional)) – segid of resid i that flips

Returns:

pseudo dihedral angle in degrees

Return type:

float

Added in version 0.8.0.