I have just checked in some nice functionality for "connect" in 11.1.
This is an old problem that was probably resolved, but I still
ran into it on a recent project and decided there could
be a simple solution.
Problem: You use "connect" to make new bonds, but then after that
you want to target just those bonds and give them certain characteristics
of radius and color/translucency.
(Sounds familiar, right?)
Solution: Two new capabilities of connect:
connect ... [color/translucency]
connect ... radius x.x
connect (_C) (_N) translucent red
# make all (existing) the carbon-nitrogen connections translucent red
connect 1.0 2.0 (_C) (_N) translucent red create
# make new carbon-nitrogen connections translucent red
connect (ligand) (protein) radius 0.1 yellow
# make all (existing) ligand-protein connections yellow, with radius 0.1
The command can be as simple as:
Using connect in this simple way is much like
set bondmode AND
color bonds ...
but it's more powerful, because the bonds don't have to be there
we can select bonds based on length as well as atoms.
And, in addition, with "connect" one can select two different sets of
one for one end of each bond and one for the other:
connect (_C) (_N) radius 0.2
This is simply not possible using wireframe, where only a single set of