Thursday, August 17, 2017

cheminformatics - How do I make 3d molecular graphics similar to those shown on Wikipedia?


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?




Answer



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.


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