Given a molecular geometry in the .xyz file format, how can I use Avogadro on the command line to render an image of it?

The website states that there is some command line API available, but I can't seem to find any documentation/information about it. Alternatively, are there any other molecular visualization tools that provide a convenient command line interface for image rendering of .xyz files?

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    $\begingroup$ Pymol does a pretty good job and you can do everything using the command line. There's also a lot of documentation on it. $\endgroup$
    – DSVA
    Feb 6, 2017 at 15:56
  • $\begingroup$ @DSVA Thanks for pointing that out ; ) I think I will go into that direction for now. Do you know if pymol can also directly render to png without starting the UI? $\endgroup$ Feb 6, 2017 at 16:08
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    $\begingroup$ Yes, you can start it in command line mode (pymolwiki.org/index.php/Command_Line_Options) or use API and the command you are looking for is "png" pymolwiki.org/index.php/Png $\endgroup$
    – DSVA
    Feb 6, 2017 at 16:12
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    $\begingroup$ That's awesome. I really needed that functionality for a presentation on thursday. I somehow have a lot of geometries to analyze, so I needed some kind of access to rendering geometries from python. I think that really is what I was searching for : ) You made my day, thanks! $\endgroup$ Feb 6, 2017 at 16:17

2 Answers 2


There is no way to currently do this using Avogadro, although Python bindings have been "in the works" for a while. The problem is, with volunteer developers, there's not always enough free time to tackle all features.

You can create pseudo-3D images using Open Babel. I developed this for the Pitt Quantum Repository to give SVG and PNG images in the search interface. It's not perfect, but I like the effect.

obabel beta-carotene.xyz -O beta-carotene-2d.svg -xS -xd -xb none

enter image description here

The -xS indicates this 3D "ball and stick" style, -xd prevents the molecule name from being included, and -xb none gives transparent background to the SVG (useful for presentations).

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    $\begingroup$ This current rendering is available in the development version of Open Babel - a slightly different version is available in 2.4.x. The new "tweaks" add some scaling to atom sizes and opacity to give a depth effect, which works well in most molecules. Suggestions are welcome. $\endgroup$ Mar 23, 2017 at 18:24
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    $\begingroup$ I really think that convenient solutions for batch job visualizations of molecules (e.g. md trajectories) are lacking. The only solution I found so far is pymol, which however I quite dislike due to their licensing choice (e.g. real 3d rendering lacking in free version and so on). So this is quite interesting... $\endgroup$ Mar 23, 2017 at 18:41
  • $\begingroup$ Agreed on the need for convenient solutions for batch visualization. I was hopeful that we'd have Python bindings for Avogadro2 by now, but the student tackling that last year in Google Summer of Code disappeared (likely doing some other research). $\endgroup$ Mar 23, 2017 at 18:46
  • $\begingroup$ @deusexmachina You may be able to script VMD to do this -- Geoff, thoughts? It's Tcl/Tk driven, right? $\endgroup$
    – hBy2Py
    Mar 27, 2017 at 15:59
  • $\begingroup$ @hBy2Py - that's likely true, although I can't find any documentation on running VMD as a command-line tool. $\endgroup$ Mar 27, 2017 at 19:54

If what you want is a simple 2D structure, OpenBabel can do it for you. Say you have a structure named beta-carotene.xyz:


The following command issues a 2D depiction of the above:

$ obabel beta-carotene.xyz -O beta-carotene-2d.png -xp 600 -x0 molfile


  • 1
    $\begingroup$ Its about 3D structures. $\endgroup$ Mar 4, 2017 at 17:25

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