OK, things are coming along in terms of describing the "display state"
of Jmol. My goal has been to incorporate a "visibility flag set" into
the atom and bond data structures. Pretty much that is done now,
although there are a couple of twists that I'm still not satisfied
with. Before I do much more, I'd like some input from the Jmol community.
The issue at hand has less to do with what is actually visible than
what ATOMS are identified as being visible. I'd like to know what YOU
would expect from commands such as:
select visible
center visible
getProperty("atomInfo","visible")
Specifically:
Q: In a protein or nucleic acid model, where one might display trace,
backbone, cartoon, ribbons, rockets, etc., independently of the atoms
or bonds themselves, what would YOU say should constitute "visible"
when only one of these renderings is in front of you?
For example, for a protein:
Q: If only the "backbone", which connects alpha-carbons is visible,
then should only those alpha carbons be identified as "visible"?
Q: If only a "trace" is visible, which does not go exactly through any
particular atoms, then should any atoms be identified as "visible"?
Q: What if we defined "visible" as "the atom is visible as a ball,
stick, star, halo, or dots, or the residue containing that atom is
visible in some Rasmol form"? Would that be logical? natural? too strange?
Q: Are there situations where the atom is not "visible" but you can
nonetheless click on it or hover over it and see it identified? For
example, the trace-like "rope" of phosphorus atoms along the cartoon
of a DNA helix is NEAR the phosphorus atoms, but they are not actually
displayed. So perhaps they should be clickable but not visible? Or
should they be identified as "visible"?
In general:
Q: If only the label for the atom is visible, is the atom "visible"?
If we can agree on what "visible" means in this context, that would be
great. I've set this up so it's now trivial to create a definition for
"visible" anyway we want. But I need to know what people want, and I'd
just as soon introduce this once, not keep modifying it.
Thanks,
Bob Hanson
--
Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:[EMAIL PROTECTED]
http://www.stolaf.edu/people/hansonr
"Imagination is more important than knowledge." - Albert Einstein
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