Bad bond selection

[pett]

When using the tilde operator, bonds remain selected when they shouldn't. For example, "sel ~H" selects every bond in the structure, including those going to hydrogen atoms. This makes it look like the entire structure is selected unless you look closely. Chimera1 does not select the bonds to hydrogens in the same case.

I'm aware that fixing this is difficult, but nonetheless it should be fixed.

[Elaine Meng]

This may be the same as #1011 "atomspec should not include bonds with only end specified"

[Conrad Huang]

Merging with #1011.