pymol-open-source icon indicating copy to clipboard operation
pymol-open-source copied to clipboard

Fix H-bonding issue in DistSet SelectorGetDistSet

Open norbert1000 opened this issue 1 year ago • 4 comments

When using the dist command with mode=2 for structures that have sensibly placed polar hydrogens, it becomes apparent that many hydrogen bonds with very good geometry are missed. The problem only affects atom pairs in which both atoms can have a donor and an acceptor function (i.e. waters, Ser, Thr, His and ligands).

Origin of this behavior is the DistSet SelectorGetDistSet function in layer3/Selector.cpp:

if(ai1->hb_donor && ai2->hb_acceptor) { //check for suitable geometry } else if(ai1->hb_acceptor && ai2->hb_donor) { //check for suitable geometry } else { //no hydrogen bond }

norbert1000 avatar Jun 11 '24 16:06 norbert1000