IOTA: integration optimization, triage and analysis tool for the processing of XFEL diffraction images.
Serial femtosecond crystallography (SFX) uses an X-ray free-electron laser to extract diffraction data from crystals not amenable to conventional X-ray light sources owing to their small size or radiation sensitivity. However, a limitation of SFX is the high variability of the diffraction images that are obtained. As a result, it is often difficult to determine optimal indexing and integration parameters for the individual diffraction images. Presented here is a software package, calledIOTA, which uses a grid-search technique to determine optimal spot-finding parameters that can in turn affect the success of indexing and the quality of integration on an image-by-image basis. Integration results can be filtered usinga prioriinformation about the Bravais lattice and unit-cell dimensions and analyzed for unit-cell isomorphism, facilitating an improvement in subsequent data-processing steps.
Department of Molecular and Cellular Physiology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA; Department of Neurology and Neurological Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA; Department of Photon Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
Artem Y
AY
Lyubimov
Department of Molecular and Cellular Physiology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA; Department of Neurology and Neurological Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA; Department of Photon Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
Monarin
M
Uervirojnangkoorn
Department of Molecular and Cellular Physiology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA; Department of Neurology and Neurological Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA; Department of Photon Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
Oliver B
OB
Zeldin
Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Aaron S
AS
Brewster
Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA; Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Thomas D
TD
Murray
Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Nicholas K
NK
Sauter
Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
James M
JM
Berger
Department of Molecular and Cellular Physiology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA; Department of Photon Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA.
William I
WI
Weis
Department of Molecular and Cellular Physiology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA; Department of Neurology and Neurological Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA; Department of Photon Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
Axel T
AT
Brunger
X-ray free-electron lasers; XFELs; computer programs; diffraction data processing; indexing and integration; serial femtosecond crystallography