Software

Alchemy

Alchemy was originally developed as a set of shell scripts to download a PDB file and the electron density data to analyze localized difference density around metals. This is a placeholder for a Python version that can identify incorrect metal modeliing, identifying when too light a metal is modeled, and distinguishing between too heavy a metal or partial occupancy. The script was used in the paper "Assessing Metal Ion Assignment Accuracy in Protein Data Bank Models via Elemental Spectroscopy" - Edward H. Snell, Geoffrey W. Grime, Samuel M. Webb, Catia Costa, M. Elizabeth Snell, John F. Hunt, Liang Tong, Gaetano T. Montelione, Rachel Zigweid, Bart L. Staker, Peter J. Myler, and Elspeth F. Garman - JCIM 2026.

The new Python based Alchemy is now available at https://github.com/snell-lab/alchemy. This is described fully in the Alchemy paper currently in review. Keep checking for updates.