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Does anyone know how I can render chemical structures of small organic molecules to look like the below images? enter image description here enter image description here

I have been looking around, and I cannot seem to find an answer. The closest lead I had was this link saying you can "copy" your ChemDraw then "paste" into Chem3D. I looked through Chem3D's manual and found no such rendering style as the pictures linked above.

I know Chimera can do Simple Line Drawing but it seems to render small molecules only within the plane. I have seen plenty of examples of proteins, but I am trying to find something for small organic molecules.

I have also found references to the style named after the artist David Goodsell. I have seen this style referred as a non-photorealistic rendering referenced in this sci-hub link, page 11, figure 9. Again, I have seen this shell/toon shading for large biomolecules, but not for small molecules.

Any help would be appreciated. I linked to a few sources above hoping it might help someone else trying to find similar rendering styles.

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  • $\begingroup$ Have you tried ORTEP? These pics look like the output of one of the ortep options but you need to have the molecular structure of the compound which you might be able to find on conquest (CCCD) if it is known. Then take the cif file and load it to ORTEP. Personaly i (and most people) prefer Olex2 though. Alternatively, i think you could generate a coordinate file from a computational software (e.g. Gaussian) and get a similar picture with computed bond lenghts. $\endgroup$ – AMM Feb 25 '18 at 9:04
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    $\begingroup$ If you actually have the 3D coordinates for the atoms then you can use PyMOL for even prettier - but highly customisable - pictures, e.g. here (see here for parametrisation). $\endgroup$ – lemon Feb 25 '18 at 16:30
  • $\begingroup$ @AMM I see, these structures do look standard among the crystallography community. I will consider trying Olex2. I am concerned if this style is a "standard," when presented in a presentation or publication the structure will infer as s crystal structure and not a result of an optimized electronic structure theory calculation. $\endgroup$ – user3587374 Feb 25 '18 at 19:03
  • $\begingroup$ @lemon I do have all the 3D coordinates so I will have to try PyMOL. I have never used the software, and the learning curve seemed intimidating. None the less, I will give it a try. $\endgroup$ – user3587374 Feb 25 '18 at 19:06
  • $\begingroup$ If the compound is known and the structure exists then most computational people will use it to optimize their geometry. If not they start from something similar and add the missing atoms. In either case the the software used for optimization (e.g. gaussian) can generate nice pictures. It is not very clear to me why you need the pics to look like above which looks quite old (hence why i sugessted ortep). $\endgroup$ – AMM Feb 25 '18 at 19:43

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