Hi, I wondered it if it would be possible to add a feature where you change the transparency of selected atoms. A number of DFT projects which we undertake use bulky catalysts which, while it is important to have them present in figures, making them transparent would help draw attention to the more important parts of the structure. If this would be possible for consideration it would be greatly appreciated. Furthermore, if it is already possible, I would be grateful for any pointers in the right direction. Thanks.
Avogadro 1.2 can tune the transparency of selected atoms rendered with the Van Der Waals display type.
The manual indicates how you can select, say iron atoms for display with the VdW type and then you can tune the transparency: Coloring Part of a Molecule - Avogadro
If this isn’t what you’re going for, do you think you could upload an image and annotate?
Hi, Thank you so much for your response.
I think this is slightly off what I’m looking for. So for example in the image below I have the catalyst selected and the active intermediate above it is what we want to see most of. In papers, we have to publish these with the catalyst still visible as it is important but not as important as the active intermediate. Therefore, to make it easier to take good quality pictures of the intermediate, but with the catalyst still visible, it would be helpful if I could select atoms like in the image and then increase it’s transparency.
Thanks again for the support.