I am a quantum chemistry beginer, and this picture color scheme is classic. I wonder how to make such pictures by myself.
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1$\begingroup$ "… this molecular structure picture": you have two pictures, which one you are interested in? The first one is pretty straightforward and can be obtained with Avogadro/Jmol/Mercury/MolView/Olex2/… The second one looks like an ORTEP diagram for atomic displacement parameters refined isotropically. Either way, you have to attribute all third-party illustrations. $\endgroup$– andselisk ♦Commented Mar 25, 2021 at 5:41
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$\begingroup$ Here's a web-based molecular 3d diagram maker: wwwtyro.github.io/speck $\endgroup$– Ben JCommented Sep 22, 2023 at 17:57
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1 Answer
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The first type of image is very easy to make. I would suggest Avogadro with POV-ray. Avogadro can be used to draw the structures (or open a file containing the information, like .mol2, .sdf etc.) and then high-quality images can be generated using POV-ray.
To do this, install Avogadro, then draw a structure, and then File> Export > POV-ray. A new subwindow will open, where you can specify the location of the POV-ray executable.
In my case, the executable is pvengine64.exe, it might be different in different platforms, or in different versions.
You can also change the resolution here. Finally, click "Render", and a new windows with POV-ray should open, and it should display the image, after a few seconds.
This is the image of the molecule that you showed in your question. The background looks like that because the "Alpha transparency" option is turned on in the Avogadro subwindow, which makes POV-ray render only the molecule, and there is no background.
As for the second picture, it looks like something that would be used in crystallography to represent probability ellipsoids of atoms. I don't know much about this, so I can't help you there.
answered Mar 25, 2021 at 12:47
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$\begingroup$ OK. btw, i found there's a bit difference between Avogadro and Avogadro 2 version. $\endgroup$ Commented Mar 26, 2021 at 8:53
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$\begingroup$ @kamisamaintherain Yes, Avogadro 2 is still under development afaik. Does it work with POV-ray? I have never used it. $\endgroup$ Commented Mar 26, 2021 at 8:54
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$\begingroup$ After File> Export, a Windows file window popped out directly. $\endgroup$ Commented Mar 26, 2021 at 9:01
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$\begingroup$ @kamisamaintherain Ah, maybe it saves the .pov file directly? If it saves the file, then you can right click and press "render with pov-ray" (on Windows at least) $\endgroup$ Commented Mar 26, 2021 at 13:38
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1$\begingroup$ I downloaded the first version, and it works fine. once again, thanks for your patience!!! $\endgroup$ Commented Mar 27, 2021 at 3:03