I think the current way is to use the pk1 and pk2 selections.

Assuming you're not using the distance wizard, Ctrl-right-click selects
something as pk1 and gets rid of the other pkX selections.
Double-right-click selects something as the next pkX selection.  So ..
Ctrl-right click to select the first atom.  Then double-right-click to
select the second atom.  Then type "dist" to show the distance.

If you're using the distance wizard, you can use any combination of
ctrl-right-clicks and double-right-clicks.

(I have never used MacPyMOL, but I think this is the same across all


> The ref manual says to measure distances you can ctrl-shift left, and
> then right click to select the positions to measure. I can ctrl-shift
> left click to select the first atom, but ctrl-shift right click doesnt
> do anything. My workaround is to ctrl-shift left click twice, which
> displays the path to the atom in the command history window. I can then
> copy paste them in behind a dist command.
> Can anyone else confirm this behaviour?
> Thanks,
> --Michael
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