Preparing good figures is an important part of reporting molecular modeling results. There are many programs that can be used to visualize and generate images from all sorts of programs and approaches. However, each of them uses different colors for the elements and use arbitrary sphere sizes in ball-and-stick representations.
I know that a lot of these choices are a matter of taste, but are there any more or less accepted conventions for the color of each element in figures? Or for the choice of sphere radius in a ball-and-stick representation ( there are many possible choices: van der Waals radii, ionic radii, covalent radii)?
It would be great if there is some more or less universal representation that looks good and prevents me from editing figures too much.