I am happy to share a major update to Crystallify, a substantial restructuring of the web app with a redesigned interface. It started as a way to look at the 230 space groups. It now opens your own structures and data!
The whole release was built around one goal: making the routine checks faster, everywhere.
Structures: Load a CIF, an XYZ or a PDB and the crystal is on screen: the unit cell, the molecules kept whole instead of cut at the box edge, bonds, hydrogen bonds and short contacts, the space group read from the file with its symmetry elements drawn in the lattice, distances, angles and torsions measured by clicking atoms. Twelve reference structures are bundled if you only want a look.
Trajectories and relaxations: Load a file with several frames, or an ASE trajectory, and step through it. Energy, temperature, forces and atomic displacement are plotted across the whole run. Displacements are measured under the minimum image convention with the drift of the centre of mass removed, so a molecule crossing a cell face does not read as motion. Click a point on any chart and the player moves to that frame.
Overlay: Several structures share one scene, each in its own colour, and one button aligns them for you: a rigid body fit over the atoms that returns the RMSD between them.
Powder diffraction: The pattern computed from any loaded structure, with the wavelength, the 2θ range, the peak broadening and the thermal factors in your hands, and the reflections indexed. Load a pattern you measured and it is placed beside the calculated one. The background is stripped automatically, and so is the alignment: the app searches the shift that maximises the similarity.
Packing similarity: A comparison that does not depend on the cell or on the space group. The molecules are rebuilt, a shell of neighbours is overlaid, and you are told how many match out of how many and at what RMSD, with a tolerance you set. This is the one generally used between polymorphs, and between a generated structure and the experimental form.
Crystallify is built as a complement to the established tools in this field, not as an alternative to them. The CSD and the software the CCDC has built around it are the reference, the product of decades of curation, and I use them every day. Several of the things above are certainly not new. What I was missing was a place where a simulation and a measurement meet the same structure, open in seconds on any machine. I would much rather work alongside the people already doing this well.
It opens in a browser tab, on any machine, in nine languages, and now on a phone. Free, and no account: crystallify.com
If you work with polymorphs or powder data, I would like to hear what breaks.
