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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.

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    $\begingroup$ I think the sphere radius in the ball-and-stick representation is typically unrelated to the physical radii - instead it's made sufficiently small compared to the "stick length" that the figure is visually clear. Compare with space-filling models. $\endgroup$
    – Anyon
    Nov 17 '20 at 21:00
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    $\begingroup$ @Anyon there are software that uses information about radii to define the radius in the ball-stick representation. They look good (must of the time). $\endgroup$
    – Camps
    Nov 18 '20 at 11:41
  • $\begingroup$ Making/preparing figures is one of the big task in order to have a well presented work. I just think that it is like an art, and then, very hard to "standardized". $\endgroup$
    – Camps
    Nov 18 '20 at 11:43
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    $\begingroup$ @Camps, I agree with you. But wouldn't it be great to have a set of guidelines to prepare good figures for molecular structures? The main motivation behind this question is my frustration of having to fine-tune the configurations of every figure and the feeling of starting from scratch with every new project. I use PyMOL so I can reuse scripts and that is nice but not good enough sometimes. Maybe there is no other way and I'll have to think more like an "artist". Thanks! $\endgroup$ Nov 20 '20 at 14:19
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In terms of the colours, the main elements in organic chemistry are usually represented via the following colours:

  • H - white
  • C - black
  • N - blue
  • O - red
  • S - yellow
  • Cl - green

In terms of sphere radius, it makes sense to use a value that is specific to the atom, for example the van-der-Waals radius (e.g. 25% of the van-der-Walls radius). If you use that, then the H-atoms appear smaller than the other atoms.

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    $\begingroup$ +1. That's actually a great answer. These conventions are almost "second nature" now, so I hadn't thought of writing this when the question was first asked! $\endgroup$ Nov 24 '20 at 21:28

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