ARCIMBOLDO

Crystallographic ab initio protein solution below atomic resolution. Ab initio macromolecular phasing has been traditionally limited to small proteins at atomic resolution (1.2 Å or better unless heavy atoms are present). ARCIMBOLDO constitutes a general method for 2 Å data, based on the combination of location of model fragments like small α-helices with PHASER and density modification with SHELXE. It is within CCP4 since January 2016.

Modes, all taking the same input (reflection data as .mtz and .hkl, plus a .bor configuration file):

• ARCIMBOLDO_LITE: simple, user-friendly implementation for straightforward cases; runs on all cores of a single machine, without requiring a grid, supercomputer or database.
• ARCIMBOLDO_BORGES: retrieves local polypeptide folds from the PDB (e.g. two helices or three strands in a particular disposition) and phases structures at 2 Å enforcing tertiary structure.
• ARCIMBOLDO_SHREDDER: structure solution using fragments derived from distant homologs or poor homology models, improved against the experimental data with PHASER’s rotation function and SHELXE; spherical and sequential modes.
• ARCIMBOLDO_LOW: phases challenging structures at low resolution and introduces verification, to assess the solution and the capacity of the data to establish it (e.g. coiled coils).