There a difference in behaviors of labelPointers as labels are offset
in different directions from the atoms they label.
For labels that are offset *below and to the right*, the upper left
corner is the anchor - this is perfect, because the pointer really
lines up well with the label.
When a label for an atom is offset *above and to the right* of the
atom, the pointer label is anchored to the upper left corner of the
label, and gives the label a disconnected appearance - the pointer
doesn't really line up with the label. If the anchor point were the
lower left corner, it would be a better match.
When a label is *above and to the left* of the atom, the anchor seems
to be at the top center of the label, and the pointer actually goes
through the label itself to reach that point. So using the bottom
center (see below) or better yet, bottom right corner, would solve this.
For labels that are offset *below and to the left*, the anchor
becomes the top center of the label, which is OK, but top right might
I am using Jmol 11.3.40, and have labelAlignment set to center or left.
Molecules in Motion
Interactive Molecular Structures