IOTA: integration optimization, triage and analysis tool for the processing of XFEL diffraction images

Artem Y Lyubimov; Monarin Uervirojnangkoorn; Oliver B Zeldin; Aaron S Brewster; Thomas D Murray; Nicholas K Sauter; James M Berger; William I Weis; Axel T Brunger

doi:10.1107/S1600576716006683

IOTA: integration optimization, triage and analysis tool for the processing of XFEL diffraction images

J Appl Crystallogr. 2016 May 11;49(Pt 3):1057-1064. doi: 10.1107/S1600576716006683. eCollection 2016 Jun 1.

Authors

Artem Y Lyubimov¹, Monarin Uervirojnangkoorn¹, Oliver B Zeldin¹, Aaron S Brewster², Thomas D Murray³, Nicholas K Sauter², James M Berger⁴, William I Weis⁵, Axel T Brunger¹

Affiliations

¹ 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.
² Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
³ 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.
⁴ Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
⁵ 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.

Abstract

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, called IOTA, 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 using a priori information about the Bravais lattice and unit-cell dimensions and analyzed for unit-cell isomorphism, facilitating an improvement in subsequent data-processing steps.

Keywords: X-ray free-electron lasers; XFELs; computer programs; diffraction data processing; indexing and integration; serial femtosecond crystallography.

Grants and funding

R01 GM102520/GM/NIGMS NIH HHS/United States