[responding to Folmer Fredslund, private message]

Thanks, Folmer. What I was missing was the difference between

  color colorName, selection

and

  set xxx_color, colorName

and

  set xxx_color, colorName, selection

Each of which does something totally different internally in PyMOL. I see now that scenes only reproduce the first of these. That is, they only set the "inherited" color of atoms that we see specifically when the representation color (dot_color, ribbon_color, sphere_color, etc, set by the second and third of these commands) is set to -1.

That's what was throwing me off.

For my purposes, it just means that I have to be careful to use only the COLOR command if I want scenes to reproduce changes in color.

Might be nice to explain that on the wiki. (Or, of course, maybe  I missed it there....)

Bob




On Thu, Jun 6, 2013 at 9:47 AM, Robert Hanson <hansonr@stolaf.edu> wrote:
I guess I still don't understand exactly what a scene is:

    "scene" saves and restores scenes.  A scene consists of the camera
    view, all object activity information, all atom-wise visibilities,
    all atom-wise colors, all representations, the global frame index,
    and may contain a text message to display on playback.

I get all of that except colors. How does that work in terms of "atom-wise colors" ?
When does the scene change colors? That is, what commands would I issue that would set colors that would be recalled by a scene change?



--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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




--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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