[Question] Threshold used to define base stacking

[kntkb]

I would like to annotate base stacking for molecular simulation structures. I understand that the criteria for base stacking (and pairing) was calibrated against high resolution structures, and might not be optimal for simulated structures as described in the example notebook.

I looked into the earlier paper of barnaba published in 2014 describing the distribution of base stacking parameters in Figure 2 and Figure SD3 (supporting information). I can see that the ρij is in the range of 0 - 4 angstroms for base stacking and the distribution could be quite different among base pairs.

The current ρij threshold is set to 2.5 angstroms, but would it make sense to increase this threshold to say ~4 to handle molecular simulation structures and low-resolution structures?

[kntkb]

Closing issue because this was merged with #54