[Jmol-users] calculating noncanonical base pairs in RNA

[A. H. <ang...@ua...>]

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.