I would like to annotate a 3D protein structure with its domains and mutated/altered aminoacids and produce a nice looking, high quality picture for publication purposes. Does anyone have any suggestions?
I haven't used it for a while, but I'd recommend VMD (https://www-s.ks.uiuc.edu/Research/vmd/). It allows you to produce very high quality images and works with POV-Ray. There is a bit of a learning curve, but it's well worth the effort.