ARCIMBOLDO_LITE: single-workstation implementation and use

Abstract

ARCIMBOLDOsolves the phase problem at resolutions of around 2 Å or better through massive combination of small fragments and density modification. For complex structures, this imposes a need for a powerful grid where calculations can be distributed, but for structures with up to 200 amino acids in the asymmetric unit a single workstation may suffice. The use and performance of the single-workstation implementation,ARCIMBOLDO_LITE, on a pool of test structures with 40–120 amino acids and resolutions between 0.54 and 2.2 Å is described. Inbuilt polyalanine helices and iron cofactors are used as search fragments.ARCIMBOLDO_BORGEScan also run on a single workstation to solve structures in this test set using precomputed libraries of local folds. The results of this study have been incorporated into an automated, resolution- and hardware-dependent parameterization.ARCIMBOLDOhas been thoroughly rewritten and three binaries are now available:ARCIMBOLDO_LITE,ARCIMBOLDO_SHREDDERandARCIMBOLDO_BORGES. The programs and libraries can be downloaded from http://chango.ibmb.csic.es/ARCIMBOLDO_LITE.