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I use VESTA mostly for crystal structure visualizations.

What other options are available?

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ASE

The Atomic Simulation Environment (ASE) has visualization capabilities. It is a python environment that allows direct interaction with a lot of atomistic simulation tools.

https://wiki.fysik.dtu.dk/ase/

Visual Molecular Dynamics (VMD) and XCrySDen are the two tools I personally work with the most time. They produce nice graphics and can visualize densities etc. VMD also has rendering capabilites by invoking e.g. PovRay.

https://www.ks.uiuc.edu/Research/vmd/

http://www.xcrysden.org/

The Visualization Toolkit (VTK) and its graphical interface ParaView are capable of rendering truly stunning images and animations but have a rather steep learning curve.

https://vtk.org/

https://www.paraview.org/

I am sure there are a lot more options than this though.

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pymatgen & ASE

I'm a big fan of simplicity and integration in my python-based and Julia-based workflow.

Therefore I typically directly use the visualisation features from pymatgen, such as pymatgen.vis.structure_vtk, and ASE, for example ase.visualize. Mostly I use them anyway to build up my problem. They have some features for analysing results as well, but those I have not used so far.

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OVITO

OVITO is a great tool for visualising supercells and simulation cells with a large number of atoms. There are plenty of modifications available that facilitate analysis, and it also has a Python interface for those who would like to work with scripts.

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AtomEye

My favorite for working with inorganic crystals. But I moved to biomolecules several years ago, so I don't know how it compares with newer programs.

AtomEye has no menu. It is driven by pressing keys on keyboard. Mouse can be used for rotation, selection, etc, but surprisingly many things can be done with keyboard only.

It could handle millions of atoms from large-scale MD simulations, although I mostly used it for smaller configurations. AtomEye assumes that the system is under periodic boundary conditions (PBC) in a parallelepiped box. It's possible to shift the system under PBC (shift+mouse drag) - any atom can be moved to the middle of the PBC box. This was a useful feature I haven't seen in other programs.

Built-in coloring options were also nice - one can switch with a key press to coloring by coordination number or by sheer strain.

I don't have data at hand to make a nice screenshot. Looking into disk backup I found these pictures of SiC that were made with AtomEye:

enter image description here

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Jmol

For visualisation there's also a standalone Java application Jmol, which has a GUI and a more powerful command-line "console". I particularly like it for quickly visualising vibrational modes. However, it lacks tools to construct a simulation cell, unlike some of the other options people have mentioned.

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OlexSys Olex2

For some applications there exists a elegant software called Olex2 which matches most of the crystallographic requirements of dealing with large systems like metal–organic frameworks.

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  • $\begingroup$ In addition to the PDF manual Olex2 ships with, I would also recommend to keep a copy of Ilia Guzei's Notes on OLEX (a PDF is currently available at UWM — select "OLEX2 manual" on the right panel) at hand both as a reference book and as a self-teaching assistant. $\endgroup$
    – andselisk
    Commented Jan 24, 2021 at 19:23
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Avogadro

Avogadro is generally considered to be a “molecular editor,” designed to construct and view molecules and materials in 3D. It's a cross-platform software. Even when its mainly used for constructing molecules, it's also useful for creating and visualizing unit cells and slabs.

These are some tutorials for constructing:

It can also generate input files for different DFT codes

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MERCURY

Mercury is a specialized software to treat/manipulate crystal structures. It is part of the Cambridge Structural Database (CSD).

From Mercury's site, it allows you to:

  • Generate packing diagrams, define and visualize Miller planes, and take slices through a crystal in any direction.
  • Build and explore networks of intermolecular contacts to gain an understanding of the strengths and weaknesses of structures and identify the key interactions that drive crystal packing.
  • Display space-group symmetry elements
  • Calculate and display voids (free space in crystal structures) based either on contact surface or solvent accessible surface
  • Perform molecule-based gas phase calculations via an interface to MOPAC
  • Calculate intermolecular potentials and display e.g. the strongest user-defined interactions in the crystal structure
  • View Bravais, Friedel, Donnay and Harker (BFDH) theoretical crystal morphologies.

The free version can be downloaded in this link (available for Windows, Linux and Mac) and the instructions to activate it are here.

Two examples of images produced with it (from it's site):

Fig. 1. Refcode ASETEZ - Iron-molybdenum inorganic ring (shown with orange and blue polyhedra, respectively)

Fig. 1. Refcode CUIMDZ01, a polymorph of a copper imidazolate framework (often called a 'ZIF' that shows the copper polyhedra and channel structure of the void space


(source: cam.ac.uk)

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iRASPA

fast & beautiful visualization of porous materials (but not only)

Features according to https://iraspa.org/iraspa/

  • structure creation and editing,
  • creating high-quality pictures and movies,
  • Ambient occlusion and high-dynamic range rendering,
  • collage of structures, (transparent) adsorption surfaces, text-annotation,
  • cell replicas and supercells, symmetry operations like space group and primitive cell detection,
  • screening of structures using user-defined predicates,
  • GPU-computation of void-fraction and surface areas in a matter of seconds.

iRASPA of MIL-101 (rendering 14k atoms)

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XCrySDen

  • Official website:http://www.xcrysden.org/XCrySDen.html

  • XCrySDen is a crystalline and molecular structure visualization program aiming at the display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. It runs on GNU/Linux. It also possesses some tools for analysis of properties in reciprocal space such as the interactive selection of k-paths in the Brillouin zone for the band-structure plots and visualization of Fermi surfaces.

  • It can visualise chemical structures for the following ab initio simulation software:

    • Quantum ESPRESSO
    • WIEN2k
    • CRYSTAL
    • GAUSSIAN
    • Orca
    • FHI98MD
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Crystal Impact Diamond

Crystal Impact Diamond, despite being a commercial product, offers a free demo-version. One can import a structure, adjust its appearance and use screen capturing software for saving the image/animation.

Import of the following files is supported: DIAMDOC, DSF, EDF, DS1, CFG, CIF, CRY, CSD, DAT, PDB, ENT, INS, RES, DAT, IDF, KPL, XYZ, EMO, MOL, MOL2, MDL, CSSR.

From Diamond Help Library shipped with version 4.6.4 (stand 2014-10-28):

Limitations of the Demonstration Version

Note: It depends on the license file, whether Diamond runs in full or in demonstration mode (with the limitations mentioned below).

This article informs you about limitations of Diamond running in demonstration mode as compared with Diamond running as full version. This information is not valid for the full version of Diamond.

The demonstration version is identical with the full version except of the restrictions mentioned below:

In case of trouble when using Diamond, please pay attention to the following hints:

No saving

Changes in structure documents cannot be saved in the original file formats of Diamond versions 3 and 4 (the Diamond Document format, "diamdoc") and the Diamond Structure File format ("DSF"), which has been used by version 2 and 1.x of Diamond.

That means, whenever you call one of the functions that save the current structure document either with the "old" file name (File/Save) or with a new file name (File/Save as...), this will fail. Instead, a message box will remember you of this restriction.

Additionally, the function "File/Save all" is not available for this reason.

If you close a structure document window - either by closing the window, by using the "Close all" command from the "Window" menu, or by closing the application window of Diamond -, this will be closed immediately, even if the structure document has been changed or is new. That means, the usual prompt ("Save modifications in...?" - Yes/No/Cancel) will not appear!

The "Auto Save" function - which you can find on the Desktop tab of the Options dialog (Tools/Options) will not work, too.

"Diamond Demonstration Version" banner

A banner with "Diamond Demonstration Version" will be written into saved bitmaps, Windows Metafiles, and printouts.

Crystal Impact Diamond - main window screenshot

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VESTA

You can try VESTA. It is good, lightweight and works on Windows and Linux platforms. It is good for viewing and production level image quality manipulation. https://jp-minerals.org/vesta/en/download.html

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    $\begingroup$ The question is about alternatives to VESTA, so strictly speaking this isn't an answer to OP's question. However, it may be useful to other readers - perhaps especially if it can be expanded further to showcase VESTA's capabilities. $\endgroup$
    – Anyon
    Commented Mar 9, 2021 at 15:48
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    $\begingroup$ @Anyon since the question title changed to just be freely available visualization software, rather than alternatives to VESTA, it is probably worthwhile to have a VESTA answer. I think the question being more general now will make the list more useful to future readers. $\endgroup$
    – Tyberius ♦
    Commented Apr 12, 2021 at 16:04
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    $\begingroup$ @Tyberius Maybe I'm missing something, but I don't think the title has changed substantially since version 1, and the body of the question still asks "I use VESTA... What other options are available?". As evidenced by my previous comment, I agree that having a VESTA answer is worthwhile. $\endgroup$
    – Anyon
    Commented Apr 12, 2021 at 16:29
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Beautiful Atoms

Beautiful Atoms is a Python package for editing and rendering atoms and molecules objects using Blender. A Python interface that allows for automating workflows.

Features:

  • Model: space-filling, ball-stick, polyhedral, cavity and so on.
  • Support file: cif, xyz, cube, pdb, json, VASP-out and so on.
  • Support structure from ASE and Pymatgen
  • Volumetric data (Isosurface and 2D slicing)
  • Animation
  • GUI
  • Flexible: Python script, run interactively or in background.
  • High quality rendering: 3D models
  • Free, Open Source: Easy to download and install.
  • Cross-platform: (Linux, Windows, macOS)

Here are some nice pictures:

https://beautiful-atoms.readthedocs.io/en/latest/gallery.html

Crystal structure

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  • $\begingroup$ it looks really mesmerizing. thanks for sharing $\endgroup$
    – Greg
    Commented Apr 27, 2023 at 2:05
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MoleView

  • Super lightweight
  • Developed based on standard plotting library (Matplotlib)
  • Very easy to install pip install moleview
  • All-in-one command moleview your_file.xyz
  • More info: https://github.com/moleview/moleview

enter image description here

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UnityMol

  • Conceived with biological systems in mind, but relevant for any molecular system
  • Modern interface: recent and still under active development
  • Supported formats: PDB, mmCIF, GRO, Mol2, XYZ and SDF files, OpenDX potential maps, XTC trajectory files
  • Important number of representation formats and coloring/rendering options
  • VR (Virtual Reality) support (interactive mode), and presented as a "video game-based computer graphic software"
  • Open-source with a free-to-use licence for academics
  • Available on Windows, MAC and Linux
  • Official website: http://www.baaden.ibpc.fr/umol/

Screenshot taken from the official website front page

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CrysX - 3D Viewer

https://www.bragitoff.com/crysx-3d-viewer/

(Disclaimer: I am the developer of this software.)

The crystal visualizer tool is available for Windows, MacOS, Linux and Android devices. The visualizer enables the users to open popular .cif, .xyz, .cub, .mol, etc.format files to visualise crystal as well as molecular structures and isosurfaces. The visualizer is built using a gaming engine (Unity3d) ensuring stellar, never-before seen graphics on any other molecule/crystal visualizer. This makes the app really useful for researchers to prepare illustrations and figures for their research papers, thesis and dissertation. The app lets the users visualize lattice planes, and draw vectors to indicate electric/magnetic fields.

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    $\begingroup$ Note when quoting from another site, you can include a > before that section to format it as a quote. Also, if you have any affiliation with the product, it's always good to mention this. $\endgroup$
    – Tyberius ♦
    Commented Dec 3, 2022 at 13:25
  • $\begingroup$ @Tyberius Thank you for the useful advice! I have made the suggested changes, $\endgroup$
    – user6041
    Commented Dec 4, 2022 at 16:15
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    $\begingroup$ @NewbieQuantumChemist could you please make the images a bit smaller? It takes a long time to scroll through this answer. $\endgroup$
    – Nike Dattani - No Free Time
    Commented Dec 4, 2022 at 16:18
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nglview and nvc

Recently I found it hard to make the pymatgen structure_vtk visualization method to work. I believe it might be deprecated in favour of crystal_toolkit.

Another simple, fully Python based (Jupyter notebook) option is nglview, which can visualize pymatgen structures as well.

Additionally, nvc is an nglview wrapper for specifically visualizing crystal structures.

It works for quick inline visualization of structures.

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PyMOL

  • Molecular visualization system built on top of a python backend that can be used for scripting
  • Powerful and flexible interface with GUI and command line options
  • Conceived with biological systems in mind, but relevant for any molecular system
  • Commercial product, but built on an open-source foundation and available for free for Educational-Use-Only
  • Available on Windows, MAC and Linux. Can be installed with conda
  • Official website: https://pymol.org/

Screenshot taken from the official website front page

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3Dmol

3Dmol is rather easy to use https://3dmol.csb.pitt.edu/

It is easy to use in web on Jupyter notebooks

https://william-dawson.github.io/using-py3dmol.html

https://first-principle-tools.ew.r.appspot.com

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  • $\begingroup$ Is it capable to draw crystal structures or only molecular-like data? $\endgroup$
    – Camps ♦
    Commented Oct 3, 2022 at 17:35
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    $\begingroup$ 3dmol can visualize the unit cell too. $\endgroup$
    – Peter Koval
    Commented Oct 3, 2022 at 21:16
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Multiwfn

Multiwfn is an extremely powerful program for realizing electronic wavefunction analysis, which is a key ingredient of quantum chemistry.

Multiwfn is free, open-source, high-efficient, very user-friendly and flexible, it supports almost all of the most important wavefunction analysis methods.

Multiwfn is maintained by Tian Lu at Beijing Kein Research Center for Natural Sciences (http://www.keinsci.com). Multiwfn is always in active development, the original paper is J. Comput. Chem., 33, 580-592 (2012).

Here is the resource link: http://sobereva.com/multiwfn/

Image taken from a video tutorial of Multiwfn

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