Is there a tool that would help in creating rather intricate line drawings (not pre-rendered balls-and-sticks/wireframe/sticks/ORTEP diagrams) for a skeletal formula in 3D space?
To illustrate the question a bit further, here are two examples:
Organic molecules — An all-benzene catenane and a trefoil knot [1]:
Inorganic molecules — proton transfer in polyoxoniobate $\ce{[H_xNb10O28]^{(6-x)-}}$ [2, p. 111]:
I also saw a much larger line-art structure of an entire peptide drawn the similar way, but unfortunately I cannot find the reference at the moment.
Line-drawn structures like these are usually presented alongside with the determined crystal structures, so I naturally assume that there is a tool that would allow to convert a CIF file to an illustration like the ones shown above. However, I wasn't able to find anything relevant by screening the IUCr software list, and this already concerns me for several years.
Do people really use molecular editors like ChemDraw for this, or there is a more optimal way? Also, if ChemDraw is the tool for the job, are there any general recommendations as to how to efficiently draw structures like this in 3D space without loosing one's mind on estimating z-buffer for proper bonds' greyscaling/thickness/type based on the distance from the viewer as well as overlapping atoms and bonds?
I would really appreciate if someone who published similar work would share some tips regarding their workflow.
References
- Segawa, Y.; Kuwayama, M.; Hijikata, Y.; Fushimi, M.; Nishihara, T.; Pirillo, J.; Shirasaki, J.; Kubota, N.; Itami, K. Topological Molecular Nanocarbons: All-Benzene Catenane and Trefoil Knot. Science 2019, 365 (6450), 272–276. DOI: 10.1126/science.aav5021.
- Polyoxometalate Chemistry, 1st ed.; van Eldik, R., Cronin, L., Eds.; Advances in Inorganic Chemistry; AP, Academic Press, an imprint of Elsevier: Cambridge, MA San Diego, CA Oxford, 2017; Vol. 69.