WebMol is a Java-based PDB Viewer which can run as an applet in a web browser.

WHAT IF is a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, displaying the results of GROMACS calculations, analyse electron density maps, and much more.

WIEN2k allows the user to perform electronic structure calculations of solids using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave ((L)APW) + local orbitals (lo) method, one of the most accurate schemes for band structure calculations.

WODCA (World of Computer Assisted Synthesis Planning or Workbench for the Organization of Data for Chemical Applications) is a computer program for the interactive planning of organic syntheses, in particular, for the planning of organic syntheses in a retrosynthetic approach. Built-in catalogs of fine chemicals like those from Acros Organics or Fluka Chemical Company provide suitable starting materials for a synthesis target.

X-UTIL is a set of utility programs intended for (but not limited to) practising protein crystallographers.

XChemEdit is a package of programs which can draw and edit three-dimensional chemical structures; serve as a graphical interface to the GAUSSIAN, JAGUAR, MOPAC, and BOSS/MCPRO programs; display molecular orbitals, electron densities, and electrostatic potentials; animate normal mode vibrations; and compute solvent-accessible surface area, volume, and thermochemical properties.

Who in chemistry never experienced the following: You get your sample back from the analytical department and look shyly at the elemental analysis data - and they are way off. So what usually happens is that one tries to make the numbers fit by postulating solvent inclusion (like 1 mol of EtOH) and then get stressed out with a desktop calculator. That's where this tiny shiny utility comes into play.

XCrySDens (Crystalline Structures and Density) is a crystalline and molecular structure visualisation program, which can superimpose isosurfaces and contours onto crystalline structures and interactively rotate and manipulate them. XCrySDens also provides a (partial) graphical user interface for CRYSTAL, and a visualisation system for PWscf and WIEN2k.

XDrawChem is 2D molecule drawing program. Some notable features include the ability to retrieve structures from a network database given the name or CAS number; it can predict predict proton and C13 NMR shifts; and it can interface with OpenBabel to read and write multiple file formats.

XEASY is a program to display and assign 2D, 3D, and 4D NMR spectra.