I've noticed that Jmol draws space-filling models with what look like rather larger van der Waal's radii than you would expect. If you look at:
http://macxray.chem.upenn.edu/tutorial/basepair.html
and change all the atoms to 100% VDW, the H's are really totally buried in the atoms to which they are hydrogen bonded. If I use the same PDB file in rasmol, I get a more reasonable looking display. The VDW radii displayed in the "Atom Properties" item on the "edit" menu in the Jmol application up to version 9 are reasonable, but the display looks "wrong". BTW, that menu item is "gone" from Jmol 10? (it would be nice to be able to adjust Atom Properties).
Pat
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