ARCIMBOLDO_LITE: single-workstation implementation and use.
ARCIMBOLDO solves 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_BORGES can 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. ARCIMBOLDO has been thoroughly rewritten and three binaries are now available: ARCIMBOLDO_LITE, ARCIMBOLDO_SHREDDER and ARCIMBOLDO_BORGES. The programs and libraries can be downloaded from http://chango.ibmb.csic.es/ARCIMBOLDO_LITE.
Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain.
Massimo
M
Sammito
Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain.
Claudia
C
Millán
Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain.
Dawid
D
Frieske
Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain.
Eloy
E
Rodríguez-Freire
Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain.
Rafael J
RJ
Borges
Structural Biology, ICREA at IBMB-CSIC, Baldiri Reixach 13-15, 08028 Barcelona, Spain.
Isabel
I
Usón
D000595:Amino Acid Sequence; D003201:Computers; D003628:Database Management Systems; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software
D011506:Proteins
ARCIMBOLDO_BORGES; ab initio; phasing; small fragments