H bonds are very poorly calculated (org.jmol.viewer.Frame.calcHbonds()). See 1qg7.pdb for example.
If I uderstood the code correctly, than all the possible neighbours of O and N atoms (within some radius in space) are found and checked if they are not bonded yet. Perhaps angles of potential H-bonding partners should be checked as well or some other properties - the model used right now doesn't do, it's just that it nobody notices as it is very rarely needed.
In 1qg7 many H-bonds are formed within the neigbours in the same beta strand while some bonds in neighbouring beta strands forming a beta sheet are left out.
Mojca
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