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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?

Pritt says Reinstate Monica
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    PyMol comes to mind. There are a ton of freebies out there. In the day (and still) there's RasMol. – Todd Minehardt May 15 '17 at 03:36
  • @ToddMinehardt Any thats online? I'm not really up for downloading software for now. – Pritt says Reinstate Monica May 15 '17 at 03:39
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    Maybe eMolecules? Don't take my word for any of it, I'm old and not as informed as others on this site. – Todd Minehardt May 15 '17 at 04:13
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    @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 ;-) – Klaus-Dieter Warzecha May 15 '17 at 04:23
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    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: https://en.wikipedia.org/wiki/User:Benjah-bmm27/MakingMolecules – Carmeister May 15 '17 at 05:31
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    @KlausWarzecha - :) – Todd Minehardt May 15 '17 at 20:09
  • A little odd representation like the second one may happen if the structure originally was drawn and saved as *.mol file with explicit hydrogen atoms. If not switched off, Jmol will then compute the bonds automatically which however may be disabled (edit ->preferences -> bond). Yet in favour of Jmol, the same index card has two rulers defining bond tolerance and minimal bond distance, which offers quite some advantage (compared to CCDC Mercury, for example) in the display of crystal structures with positionally disordered chains. – Buttonwood May 15 '17 at 21:17
  • If you are by chance running a Linux based OS, there is a good chance your distro has Jmol in it's repos. It's large (~150M), but I had it downloaded, installed and running in about a minute. I like it. It takes common names, chemical names, SMILES, InChI and CAS, and of course create your own. And it is totally free (product and license) and guaranteed no adds or crapware included. This is the only *mol 3D type of product I've tried (I'm old too), so I can't say if it's better or worse than others. – airhuff May 15 '17 at 21:39
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    @PrittBalagopal It looks like it's just a demographic survey on the linked Discovery Studio Visualizer download page, rather than a limitation on who can download. I'd recommend something like Industy:Other JobFunction:Research JobRole:Student CompanyName: -- or whatever you feel is "closest" to your actual situation. Try for the best match, but don't worry too much if it's not exact. – R.M. May 20 '17 at 21:51
  • @R.M. Oh, that's nice, I'll try it. – Pritt says Reinstate Monica May 20 '17 at 23:48

3 Answers3

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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.

Klaus-Dieter Warzecha
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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.

Martin - マーチン
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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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    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. – Todd Minehardt Oct 04 '21 at 17:43