Change bond colors

General Discussion
1

I really like using Avogadro (I have 1 and 2) and I am hoping that someone can help me change the bond color during rendering. Specifically, I want a single color on Ball and stick bonds (sticks-light gray) for an initial discussion of covalent bonding. Eventually, I was hoping to weight the color of the sticks based on electronegativity and/or dipole. I can do this in Blender but the lighting and camera are a challenge for me, I am not a grphic artist by any means. I am somewhat comfortable in Python but I really am having a hard time writingmy own code from the documentation for Avogadro2. This is for a (very boring) card game so I need only export a png. Any help/hints would be greatly appreciated.

2

Interesting. At the moment, there’s no way to do this, but it wouldn’t be terribly hard to add an option.

Let me clarify though - you want to customize the colors of the bonds but not the atoms themselves (e.g. when you color by electronegativity). Because right now, you can apply colors to the atoms and that will change the bond colors.

In short, you want the following bond color options:

  • uniform grey
  • electronegativity
  • (current default = based on atom colors)
3

@Siobhan Note there already is something related to your wish in Jmol, i.e. the optional display of dipoles between atoms of a molecule. The arrows are a bit thin, and their color – like the ones about the bonds – changes in one step from the one about one atom, to the other.

dipoles

4

Thanks for the speedy reply. Yes, I would like to color the bonds ONLY. Initially, just one color but down the road I would like to use the colors that are well captured in a space filling model on the “sticks” of the ball and stick model. In other words, I would like to render different percentages of the “stick” red or black in a carbon-oxygen bond in a way that is detectable by eye when rendered-red having a greater percentage of the “bond” than black. I understand chemists have the background knowledge and easily use the space filling model but I am targeting people learning about biology and I want to ease them into understanding polar bonds, polar molecules and polar bonds in nonpolar molecules. These different color options I think would help these learners “see it”.