[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 <hans...@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
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