Author: | Elizabeth Denning |
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Year: | 2011 |
Copyright: | GNU Public License v3 |
The module provides functions to analyze nuclic acid structures, in particular
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 |
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: |
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NOTE: if failure occurs be sure to check the segment identification
New in version 0.7.6.
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: |
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NOTE: if failure occurs be sure to check the segment identification
New in version 0.7.6.
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: |
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NOTE: if failure occurs be sure to check the segment identification
New in version 0.7.6.
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: |
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New in version 0.7.6.
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: |
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New in version 0.7.6.
Backbone dihedrals includes alpha, beta, gamma, delta, epsilon, zeta, chi
The dihedral is computed based on position atoms for resid i
Arguments: |
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NOTE: if failure occurs be sure to check the segment identification
alpha backbone dihedral
The dihedral is computed based on position atoms for resid i
Arguments: |
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New in version 0.7.6.
beta backbone dihedral
The dihedral is computed based on position atoms for resid i
Arguments: |
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New in version 0.7.6.
Gamma backbone dihedral
The dihedral is computed based on position atoms for resid i
Arguments: |
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New in version 0.7.6.
delta backbone dihedral
The dihedral is computed based on position atoms for resid i
Arguments: |
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New in version 0.7.6.
Epsilon backbone dihedral
The dihedral is computed based on position atoms for resid i
Arguments: |
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New in version 0.7.6.
Zeta backbone dihedral
The dihedral is computed based on position atoms for resid i
Arguments: |
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New in version 0.7.6.
The dihedral is computed based on position atoms for resid i
Arguments: |
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New in version 0.7.6.
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.
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.
Arguments:
- universe
Universe containing the trajectory
- segid1
segid of resid base pairing with bp2
- bp1
resid that base pairs with bp2
- segid2
segid same as that of segid of flipping resid
- bp2
resid below the base that flips
- segid3
segid of resid that flips
- i
resid of the base that flips
New in version 0.8.0.