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I have several .xyz files (each composed of several molecules) and I'd like to find an automated way to visualize and save them. I'd appreciate any guidance.

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    $\begingroup$ What do you mean by "visualize", e.g. what is the desired output format? Also, what kind of information needs to be visualized? $\endgroup$ – andselisk May 21 '20 at 16:34
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    $\begingroup$ Thanks for the reply. By visualization I mean I need something which reads my set of xyz files and saves their "images" automatically. I mean I don't want to save the figures one by one. About the posts you have referred me to, I feel they are not fully relevant cause I have the 3D coordinates (se don't need to generate them at this stage) and don't want to save the figures (extracted e.g from ASE) one by one. Ideally, I need some sort of TCL script for vmd where it can read xyz files sequentially and saves the images automatically. $\endgroup$ – Rose May 21 '20 at 18:01
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I recommend using software called ChemCraft. The software isn't free; however, they offer a 150 day trial period. I typically use this program to open formatted checkpoint files from Gaussian calculations to view orbitals. It has plenty of other functions, including the ability to open multiple .xyz files and save multiple images.

The default colors are a bit yucky, but I recommend using one of the following from the Display menu: CPK, GaussView, or Spartan. Those will color atoms with the typical scheme: Nitrogen (blue), Oxygen (red), etc.

I hope this helps!

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    $\begingroup$ There are also programs such as jmol, avogadro, and pymol (which can be obtained for free if you compile it yourself). There just isn't really any good reason to pay for a software if you all you want to do is use it for visualization. $\endgroup$ – jheindel Sep 19 '20 at 4:25

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