Thanks, Thomas....
On Mon, Jun 3, 2013 at 9:36 AM, Thomas Holder <thomas.hol...@schrodinger.com
> wrote:
> Hi Robert,
>
> you got the levels right.
>
> The cmd.get method actually doesn't support querying atom level settings,
> even though you can set them with cmd.set.
>
I see. That's helpful.
>
> Atom settings are not state specific, unless you have a discrete object.
>
I see, because then every atom in a multi-model file has is own record, and
thus its own unique ID. Sure. For now, Jmol is loading all PSE files as
though discrete=1. The Jmol equivalent of discrete=0 would be (in Jmol) *load
TRAJECTORY xxx.pse*, but I don't have that right now able to load some
models as trajectories and some not, as would generally be needed in PSE
file loading. So that will have to wait.
>
> Scenes do not store settings, so using spectrum_states overrides scene
> colors.
>
But a scene does store settings in the sense that there are, at least for
colors, for example, _!c_scene_xxx_sticks "settings". How does that fit in,
then? I'll look into that.
> Hope that helps.
>
definitely!
>
> Cheers,
> Thomas
>
> On Jun 3, 2013, at 8:34 AM, Robert Hanson <hans...@stolaf.edu> wrote:
> > I'm trying to understand settings. I see that there are at least these
> levels of settings:
> >
> > - global
> > - object
> > - state
> > - unique atom/bond
> >
> > Are there more?
> >
> > I'm unclear on when one overrides another. It looks to me that the
> general "getSetting" methods have the option of up to three levels of
> settings, but there are four here.
> >
> > Thus, for example:
> >
> > If I have unique settings for a bond and then apply the sort of script
> that Sid recently was interested in, that might change stick_color, would
> that unique bond setting be overridden?
> >
> > If a state's color is set using Spectrum_states.py, does that override
> already-set scene colors? Or is it incorporated into defined scenes then?
>
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger Contractor
>
>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
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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