The END_RAPID.com script takes standard structure factors, a coordinate file, and a phenix refine input file to create an absolutely-scaled Electron Number Density (END) map and a corresponding noise Refinement Against Perturbed Input Density (RAPID) map.

END/RAPID is distributed open source and requires less than 1 MB of disk space. Two implementations are available: the original shell script (END_RAPID.com) requires CCP4 and Phenix; the Python port (END_RAPID.py) requires only Phenix (no CCP4 needed). Both are freely available to academics.

Compatibility: validated with CCP4 9.0 and Phenix 2.1 (June 2026). Both scripts automatically handle eff files from all Phenix versions, including the ddr { } block introduced in Phenix 2.x. No manual editing of the eff file is required.

Source on GitHub

Download tarball

Manual

When citing END/RAPID, please refer to: Lang PT, Holton JM, Fraser JS, Alber T. “Protein structural ensembles are revealed by redefining X-ray electron density noise.” PNAS USA. 111:237–247 (2014).