Hydrogen bonds
Support for display and calculation of Hydrogen bonds in proteins and nucleic acids
Note: this feature only applies to 
pdb format files of macromolecules (proteins and nucleic acids) -- or equivalent formats than supply all the needed atom and residue identification, like possibly mmcif.
Display and rendering of hydrogen bonds
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Calculation of hydrogen bonds
In Jmol up to 11.8 there were just two ways to calculate hydrogen bonds: the RasMol way and a Jmol way. In both these cases these weren't really hydrogen bonds, they were what we can call pseudo-hydrogen bonds that do not involve actual H atoms.
- When the value for
hbondsAngleMinimumwas 0, Jmol used the RasMol calculation and ignored both the angle and distance checking. - When
hbondsAngleMinimumwas set to something else, Jmol used its own calculation and did the angle and distance checking.
Jmol 12.0 introduces "true" hydrogen-bond calculation, and that changes the picture. The change is that if you have a pdb file with no H atoms and you do nothing special, Jmol will do just what it did before -- Rasmol hydrogen bonds. But if you want Jmol's calculation of pseudoHydrogen bonds, rather than obtusely setting the hbondsAngleMinimum value to something other than 0 degrees, you simply use
set hbondsRasmol false
Then hbondsAngleMinimum defaults to 90 and hbondsDistanceMaximum defaults to 3.25 for pseudo-hydrogen bonds and 2.5 for standard hydrogen bonds.
The choice of standard or pseudo simply revolves around whether hydrogen atoms are in the selected atom set or not.
