XRDL is reciprocal space viewer written in Java. It is also released as part of JSV. It allows real-time rotation of the reciprocal lattice points. This software is 'Charityware'.

XVibs is a utility for animating molecular vibrations. Normal modes are read from a file automatically determined to be from Aces2, Gamess, PC Gamess, Gaussian 90/92/95/94/98, ADF, Dalton, Jaguar, MOPAC, or HyperChem. Separate animation files are written for each vibration.

Yet Another extended Huckel Molecular Orbital Package (YAeHMOP) is intended to be an easy to use, transparent, extended Huckel calculation and visualization package which can perform calculations on both molecular and extended materials in 1,2, or 3 dimensions.

Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. Yambo relies on the Kohn-Sham wavefunctions generated by the DFT codes abinit and Pwscf.

YASARA Dynamics contains YASARA View and adds support for molecular simulations. Beside the YASARA NOVA Force Field and the new highly accurate YAMBER force fields, you can use other well known MD force fields like AMBER, and run accurate all-atom MD simulations in aqueous solution with Particle Mesh Ewald longrange electrostatics at twice the speed you know from other programs. YASARA Dynamics is not a black box with input and output files, but shows the MD simulation in real-time on screen. You can fully interact with the scene, pull atoms or whole molecules around.

Explore macromolecular structures interactively with YASARA View, whose innotive 3D engine is up to 35 times faster than OpenGL. You can load multiple structures at the same time, create publication-quality ray-traced images including labels, and program your own macros and Python plugins.

Molecular visualisation and animation program, which can be used to create production quality images, and movies, using either the built in renderer or by exporting the scenes to POVRAY.

ZMM is a molecular modeling program for theoretical studies of systems of any complexity: small molecules, peptides, proteins, nucleic acids, and ligand-receptor complexes. ZMM searches optimal structures in the space of generalized coordinates: torsion angles, bond angles, bond lengths, positions of free molecules and ions, and orientation of free molecules.

Zodiac is an advanced molecular editor for molecular modelling and computer aided drug design, that offers tools such as energy minimisation, database management, molecular property prediction and front ends to various docking and QM programs. It is cross platform and released under the GPL.

ZORTEP is a mouse driven, menu based graphical ORTEP program. This allows the 'real-time' graphical rotation and manipulation of structures and/or thermal ellipsoids on the screen.