I realize that this may be difficult or impossible to implement, but I'll write it here at least for the record.
I'm working on base pairing in RNA molecules, both canonical and noncanonical pairs. Example: 5S rRNA from E.coli, which is chain A in 2WWQ.pdb There are several reported GU pairs. One is between residues 9 and 111. When I look at it in Jmol and give calculate hbonds two Hbonds are created, between [U]111:A.N3 #7670 -30.643002 -82.178 -45.936 [G]9:A.N1 #5486 -28.97 -83.12399 -42.726 [U]111:A.O2 #7669 -28.472 -82.802 -45.579 [G]9:A.N2 #5488 -26.938 -84.215996 -42.416 both of them sprout at a funny angle relative to the rings and over 3.7 angstroms length. Visual inspection suggests another 2 bonds as more reasonable, both are ca. 3 angstroms [G]9:A.O6 #5485 -30.924 -81.826 -42.938 [U]111:A.N3 #7670 -30.643002 -82.178 -45.936 [U]111:A.O2 #7669 -28.472 -82.802 -45.579 [G]9:A.N1 #5486 -28.97 -83.12399 -42.726 So it seems to me that Jmol is generating suboptimal Hbonds, based maybe on atom names rather that distance and aligning. I remember discussion on this list about admissible angles and distances when calculated Hbonds were implemented, but that was centered on proteins. Are nucleic acids out of those rules? I am attaching the state script.
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Date: 9 Mar 2011, 21:30
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