PyMOL Glow/Highlight Feature?

[ivan-the-bio-lover-42]

Hello!

It's my first post here and I apologize if this isn't meant to be in issues; it's my first time on GitHub. I've been using PyMOL for a while now and I absolutely love the visuals and animations/movies it can do. However, one thing I thought that I'd really like to see in native PyMOL is a feature to highlight a residue with a "glow" effect, as in, the selected object would act as its own light source akin to that of a lightsaber effect. It's a somewhat common effect I've seen in various biomedical animations. I'll provide some examples:

From a WEHI.tv animation, where the active site is highlighted: From various Boehringer Ingelheim animations on HIV-1

• Here, ball-and-stick representations and different sections of the cartoon ribbon are highlighted:
• Ball-and-stick models that are highlighted
• Hydrogen bonds that are highlighted. In PyMOL, highlighted measurement dashes could achieve a similar effect

In PyMOL, the light emitted from the glowing object would be the color the molecule originally was, so a green residue that is glowing inside a protein would give off a green glow. The intensity of the glow could perhaps be configured with commands such as 'set_glow, [number]'. It would be applied to any selectable objects such as molecules, atoms, as well as measurement dash objects. Perhaps it could be called 'highlight' or 'glow' and might be found in the label (L) or action (A) box. It'd be especially useful to have this as an included feature because it could really enhance the visuals of PyMOL. Aside from beautiful ray-traced images, I think the most important upside of such a feature is that these 'glow' or 'highlight' effects would be able to be incorporated directly into a PyMOL movie in a much more user-friendly manner as opposed to having to learn how to use third-party 3D software.

Thanks in advance! Ivan

[JarrettSJohnson]

Hi Ivan,

Thanks for the feature request. I'm a huge fan of this visual and would love to see it implemented in PyMOL. Although I have done some very preliminary work for it, pull requests are always welcome as well. My initial intuition was to also expose this as a highlight command where you'd supply a selection string. Alternatively, this may be able to also be done through atom settings.