On Fri, Jan 17, 2014 at 11:46 AM, Angel HerrŠez <angel.herraez@uah.es> wrote:
> Visible is a bit different. With proteins, any atom in a group that
> is shown with a cartoon (for instance) is "visible" even though it is
> not a ball or star itself.

So is e.g. a beta carbon in an amino acid displayed as cartoon only.

Is that also "displayed" ?

yes. DISPLAYED is specifically what you have indicated are not to be hidden.

$ load "c:/jmol-dev/bobtest/cyclohexane_movie.xyz"
35 models

$ select displayed
630 atoms selected
$ select visible
18 atoms selected

Definitely not the same thing. As I said, there is a bug:

load $C\C=C\CC
select _C
wireframe off
spacefill off
display !_H
select visible // 5† (but nothing is showing)

That's a bug that probably goes back to 2006.

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Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN

If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900