Structure Visualization

Overview

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 a atom label color key!

Visualization of 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 CrystalMaker.
  •  VESTA : Visualizing crystalline systems (e.g. CIF) and volumetric outputs from solid-state DFT calculations
  •  CrystalMaker : Publication-quality figures for solid-state systems. Check out their  YouTube channel  for tutorials
  •  Virtual NanoLab : Publication-quality figures for solid-state systems and can visualize the outputs of periodic DFT calculations. Can also visualize VASP output data.
  •  Blender : A CGI library. See  CGFigures  for a tutorial for scientists.
  •  Beautiful Atoms : Interface between ASE and Blender
  •  Molecular Nodes : Read .pdb and .mmcif files in Blender

Visualization of 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.

cpkcoloring1.bin
16KB, Uploaded 10 months ago

cpkcoloring2.bin
16KB, Uploaded 10 months ago
  •  SAMSON : Publication-quality figures, primarily for molecular systems
  •  IQMol : Visualizing Q-Chem output data
  •  IBOView : Prettiest orbital viewer