Hello everyone, I’m starting my thesis on chemistry education in high schools, focusing on the use of an epistemological approach and leveraging Avogadro to help students understand chemical bonds, particularly studying the difference between a dipeptide and an alanine dimer composed of hydrogen bonds.
I’d like to ask how I can change the color of a hydrogen bond (currently yellow) to a darker shade so that I can use the images with a white background. Also, for some molecules, when I use the Van der Waals representation with spheres and apply coloring based on partial charges, I get a uniform gray color instead of variations based on charge differences. Could this be a system bug?
Thank you for your help and for your time in supporting such a great software! Thanks again.
I’m not sure what version of Avogadro you’re using, but it sounds like 1.2? (Avogadro 1.99 currently uses a light blue color for hydrogen bonds.)
At the moment, there isn’t a feature to change the color of hydrogen bonds, although it’s a good idea. For what it’s worth, I tend to use either a black background or a turquoise / blue-green background because it helps to show hydrogen atoms better IMHO.
As far as the partial charges – it would really help to know what OS you’re using and ideally post an example file.
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