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
Andrew's Recommendations: For solid-state materials, use VESTA for casual viewing. For more involved editing (e.g. adding adsorbates) and making production-quality figures, use SAMSON or CrystalMaker.
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.
SAMSON with the Crystal Creator extension: Interactive GUI that is great for modifying materials. There is a free academic license.
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. I opened a ticket with SAMSON to make it less annoying.
CrystalMaker: Publication-quality figures for solid-state systems. Check out their YouTube channel for tutorials.
We have a license for v11 on the group Dropbox.
Molecular Systems
Andrew's Recommendations: For molecular systems, use ChemCraft for casual visualizing/editing. For production-quality figures, use SAMSON.
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 figures, 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:
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.