Criteria and Penalty weighting:

These parameters affect how strictly stacked bases or base pairs are identified.
If your current model is of low quality, more relaxed parameters may be desired.

Stacking parameters

max_d_c2plane_stack   Maximum allowed distance between center of base A and plane of stacking base B

min_d_c2plane_stack   Minimum allowed distance between center of base A and plane of stacking base B

max_d_c2c_stack   Maximum allowed distance between center of base A and center of stacking base B

max_ang_n_n_stack   Maximum allowed angle between normal vectors of base plane A and plane of stacking base B

max_ang_c2c_n   Maximum allowed angle between center2center vector of bases AB and normal of stacking base A

Base pair parameters

overall_cutoff   No basepairing if total penalty score above this value

hbond_distance   Penalty weight on hydrogen bonding distance deviations

atom_to_plane   Penalty weight on vertical distance differences between bonding atoms and plane of paired base

angle_baseplanes   Penalty weight on angle between baseplane normal vectors of paired bases

score_angle_abcd   Penalty weight on flipping orientation

hbond_angles_proper   Penalty weight on proper hbond angle baa2 and abb2 deviations, of bases A and B in bp.


Saenger parameter file:

 no input will use default parameters

