I’d like to use new scorefunction from article by O’Meara et al., 2015, from JCTC. Acording to supplementary info the published ElecHBv2 is the Talaris2013. There is missing line ‘yhh_planarity 0.5’ in my installation (in comparison with published article). Should I add this line or is it set there by default? what does this line mean.
The yhh_planarity is not on by default in Talaris2013. The reason is that at the time that Talaris2013 was being finalized, the data were equivocal about whether it was worth it. Current thinking is that it does help the geometry of tyrosine groups, but doesn’t necessarily help with more general metrics. (yhh_planarity is a score term related to the planarity of the hydroxyl hydrogen in tyrosine residues) It doesn’t hurt things, so it won’t harm anything to add it, however it isn’t yet “standard”, so adding it would no longer be (exactly) the Talaris2013 weights set. For comparison sake, you may want to leave it out.
Personally, I’d just leave things as-is unless you’re having issues with tyrosine hydroxyl geometries.