I want to make 3d molecular graphics similar to those found on Wikipedia. In the page for benzene, you can see the structure looks like this: enter image description here

However, if I go to the interactive image as shown in here:

enter image description here

I get an interactive image that looks like this: enter image description here

To me, the second image doesn't look nice, and I prefer the first one. However, I cant seem to find a way to get the image of first type for any molecule after converting from SMILES. I want to draw the structure of, say for example, Bismabenzene? How do I produce a graphical image for that if it's not available on Wikipedia?

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    $\begingroup$ PyMol comes to mind. There are a ton of freebies out there. In the day (and still) there's RasMol. $\endgroup$ May 15, 2017 at 3:36
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    $\begingroup$ Maybe eMolecules? Don't take my word for any of it, I'm old and not as informed as others on this site. $\endgroup$ May 15, 2017 at 4:13
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    $\begingroup$ @ToddMinehardt C'mon, to me you seem to be quite up to date! Anyway, just in case you need one: Here's a brotherly hug from a fellow chemist who has celebrated his 20th birthday more than once too ;-) $\endgroup$ May 15, 2017 at 4:23
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    $\begingroup$ The person who made the benzene image (and many other molecules) has instructions for how they do it on their user page, if that helps: en.wikipedia.org/wiki/User:Benjah-bmm27/MakingMolecules $\endgroup$
    – Carmeister
    May 15, 2017 at 5:31
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    $\begingroup$ @KlausWarzecha - :) $\endgroup$ May 15, 2017 at 20:09

3 Answers 3


You can generate the geometry for your molecule of choice by drawing it in Avogadro. More often than not, you want to refine the geometry through a force field calculation.

Avogadro supports multiple ways of visualization, which all can be configured according to your preferences. A ball-and-stick model, which you seem to prefer, is included.

If you want to generate an animation from the input file, QuteMol might be one option.

The interactive visualization on the wikipedia page of benzene is generated using JSmol, which is a JavaScript implementation of Jmol.

If you are only interested in online tools, MolView could be an option.

  • $\begingroup$ Anything that's online? I'm not up for downloading software for now $\endgroup$ May 15, 2017 at 4:24
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    $\begingroup$ Wow, MolView is a really cool toy. It's so much faster than Molcalc, unfortunately less accurate, but nevertheless a good starting structure generator. $\endgroup$ May 15, 2017 at 7:00
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    $\begingroup$ @Martin-マーチン Honestly, I wasn't aware of the tool until 2 hrs ago :D Online searches are a blessing ;-) $\endgroup$ May 15, 2017 at 7:04

Have a look at Molcalc. It's fully online and uses JSmol as a visualiser.

Alternatively you can browse the Pitt Quantum Repository for structures that have already been calculated.

  • $\begingroup$ I want it to look like the one on Wikipedia $\endgroup$ May 15, 2017 at 5:22
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    $\begingroup$ @Pritt If you want them to look like the ones on Wikipedia, I suggest you follow the link Carmeister has posted. You'll need to download and install programs though. $\endgroup$ May 15, 2017 at 7:02

That Benzene molecular model you found on Wikipedia is uploaded by Ben, (a chemistry PhD student at the University of Bristol). He uses Avogadro and/or CCDC Mercury. Both of them are free, cross-platform molecule editors which can be used to make 3-D Ball-and-stick models.

He previously used to have Accelrys Discovery Studio using which he made the original benzene molecule, but it is no longer supported. enter image description here

See this tutorial on his user page about making molecules. Hope this helps. Have fun making molecules!

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    $\begingroup$ You have pretty much repeated the comment above from Carmeister. Please expand on this answer, otherwise it will be deleted and changed to a comment. $\endgroup$ Oct 4, 2021 at 17:43

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