Thanks, Thomas....

On Mon, Jun 3, 2013 at 9:36 AM, Thomas Holder <> 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.



On Jun 3, 2013, at 8:34 AM, Robert Hanson <> 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, 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

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