Visualizing the atomic-scale structure from the output of a calculation is critical, both for understanding your system and disseminating the results. There are many available tools, but some useful suggestions are below.
When you make a PowerPoint with a given structure visualization, you should always provide an atom label color key!
Solid-State Systems
VESTA: Visualizing crystalline systems (e.g. CIF) and volumetric outputs from solid-state DFT calculations. It's free and fast but not the most beautiful.
pretty-lattice: Makes nice crystal structure images in the style of VESTA but prettier and with an atom legend.
One note: when you export a CIF, it doesn't open nicely in VESTA or ASE. But it does open in the CCDC's Mercury program that we have a license for, which can then export it to a more normal CIF other programs can open.
CrystalMaker: A commercial program for visualizing solid-state systems. Check out their YouTube channel for tutorials.
We have a license for v11 on the group Dropbox.
Molecular Systems
xyzrender: Python code to visualize molecular systems with depth-of-field rendering by default.
ChemCraft: Visualizing molecular systems (e.g. XYZ) and the outputs of molecular DFT calculations. The default style is ugly. Prettier templates are below, which you can add to /Chemcraft/schemes3.
There is a 150-day free trial, after which Andrew can purchase a license for you.
SAMSON: Publication-quality rendering, especially for molecular systems. There is a free academic license.
Professional Visualizations
If you are looking to make professional (cover art-quality) visualizations, the following tools are worth considering. Nobody in the group needs to do this, but if you are feeling artsy and ambitious by all means go ahead. Agentic AI tools are pretty good at using Blender.
Blender: A CGI library (not for routine visualizations). See CGFigures for a tutorial for scientists.
Oftentimes, when you download a crystal structure it may be missing hydrogen atoms, which are difficult to resolve crystallographically. You can automatically add hydrogen atoms to a structure using the CCDC suite's Mercury tool (💠Material/Property DBs ). For this easy task though, simply install the software program and follow these steps:
Import the CIF.
Edit > Auto Edit Structure and then press Apply. You will likely need to modify the results slightly.
Alternatively, for manual edits, do Edit > Edit Structure and then Add > Hydrogen Atoms.
If you wish to do this for many crystal structures, you are probably better off using the CSD Python API's add_hydrogensfunction.