Nucleic Acids: Difference between revisions
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== Base-Pair Parameters == | == Base-Pair Parameters == | ||
PMFLib offers two variants of the base-pair parameters: local and simple. They differ in the definition of the y-axis and the procedure to calculate six base-pair parameters | PMFLib offers two variants of the base-pair parameters: local and simple. They differ in the definition of the y-axis and the procedure to calculate six base-pair parameters, ''i.e.'', Shear, Stretch, Stagger, Buckle, Propeller, Opening. | ||
The simple version is provided by [[CV:NASBPP|NASBPP]]. It uses an explicitly defined y-axis and Buckle, Propeller, Opening parameters are calculated as dihedral angles. | |||
The local version is provided by [[CV:NASBPP|NASBPP]]. It uses a y-axis derived from the reference frames of two nucleobases and all parameters are calculated using the CEPH procedure. | |||
Both implementations are fully compatible with [https://x3dna.org/ 3DNA]. The collective variable [[CV:NASBO|NASBO]] implements simple Opening only and thus it should be a little bit computationally faster than [[CV:NASBPP|NASBPP]]. | |||
[[File:SF3.png|center|600px]] | [[File:SF3.png|center|600px]] | ||
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== Base-Pair Step Parameters == | == Base-Pair Step Parameters == | ||
PMFLib offers two variants of the base-pair step parameters: local and simple. They differ in the definition of the y-axes, ''i.e.'', Shift, Slide, Rise, Tilt, Roll, Twist. | |||
The simple version is provided by [[CV:NASSTP|NASSTP]]. It uses explicitly defined y-axes of two base pairs and all parameters are calculated using the CEPH procedure. | |||
The local version is provided by [[CV:NALSTP|NALSTP]]. It uses y-axes derived from the reference frames of four nucleobases and all parameters are calculated using the CEPH procedure. | |||
[[File:SF3.png|center|600px]] | |||
Reference coordinates for nucleobase rings are provided in the following table: | Reference coordinates for nucleobase rings are provided in the following table: | ||