Miguel wrote:
Be advised that this 'isVisible' flag was designed for internal use only.
More importantly, the concept of 'visible' is not as well-defined as one
might think.
If this makes it into 'production' code then we will need to make sure that
the concept is well-documented and well-understood.
Sure. I agree. It would go under the category of "atom expressions".
Please say more, Miguel. Perhaps what "visible" means. Currently, I
think, it means:
(1) the atom is in a displayed frame
and
(2) the atom has at least one of the following:
a. spacefill > 0
b. wireframe > 0
c. a halo highlight
Note that cartoons and such do NOT constitute visible, because they are
not atoms.
When you have:
select *
wireframe off;spacefill off; cartoon on
select visible
you get:
0 atoms selected
The only secondary structural visualization that constitutes visible is
"backbone", which is really
a wireframe connection between alpha carbons in a protein or (what?) in
a nucleic acid. So
select *
wireframe off;spacefill off; backbone on
select visible
gives you (for 1crn.pdb):
46 atoms selected
More to know?
Bob
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