CrystFEL: a software suite for snapshot serial crystallography

Abstract

Author(s) of this paper may load this reprint on their own web site or institutional repository provided that this cover page is retained. Republication of this article or its storage in electronic databases other than as specified above is not permitted without prior permission in writing from the IUCr.For further information see http://journals.iucr.org/services/authorrights.html Journal of Applied Crystallography covers a wide range of crystallographic topics from the viewpoints of both techniques and theory. The journal presents papers on the application of crystallographic techniques and on the related apparatus and computer software. For many years, the Journal of Applied Crystallography has been the main vehicle for the publication of small-angle scattering papers and powder diffraction techniques. The journal is the primary place where crystallographic computer program information is published.Crystallography Journals Online is available from journals.iucr.org J. Appl. Cryst. (2012 In order to address the specific needs of the emerging technique of 'serial femtosecond crystallography', in which structural information is obtained from small crystals illuminated by an X-ray free-electron laser, a new software suite has been created. The constituent programs deal with viewing, indexing, integrating, merging and evaluating the quality of the data, and also simulating patterns. The specific challenges addressed chiefly concern the indexing and integration of large numbers of diffraction patterns in an automated manner, and so the software is designed to be fast and to make use of multi-core hardware. Other constituent programs deal with the merging and scaling of large numbers of intensities from randomly oriented snapshot diffraction patterns. The suite uses a generalized representation of a detector to ease the use of more complicated geometries than those familiar in conventional crystallography. The suite is written in C with supporting Perl and shell scripts, and is available as source code under version 3 or later of the GNU General Public License.

Structure of the full-length glucagon class B G-protein-coupled receptor

“…Of these frames, ~6.5% contained potential crystal hits as identified using Cheetah 27 (more than 15 Bragg peaks of minimum 2 pixels in size and a signal to noise ratio better than 7 after local background subtraction). Of the 91,626 potential crystal hits, 57,573 diffraction patterns could be auto-indexed by CrystFEL 28 (indexing rate of 63%) using a combination of MOSFLM 29 , asdf 28 and DirAx 30 . Reflections from different crystals in random orientations were merged using a Monte Carlo integration of each reflection by CrystFEL 28 .…”

“…Of the 91,626 potential crystal hits, 57,573 diffraction patterns could be auto-indexed by CrystFEL 28 (indexing rate of 63%) using a combination of MOSFLM 29 , asdf 28 and DirAx 30 . Reflections from different crystals in random orientations were merged using a Monte Carlo integration of each reflection by CrystFEL 28 . The data used for the structure refinement were truncated at 3.0 Å based on the criteria of data correlation coefficient (CC*) cutoff of 0.5.…”

Accurate determination of segmented X-ray detector geometry

“…Detector frames containing diffraction patterns from individual crystals are first scanned for observable Bragg peaks ("detected peaks") [21], and patterns indexed using the freely available software package CrystFEL [11]. The process of crystal indexing determines the orientation and unit cell parameters of each crystal, enabling the best fit of the locations of Bragg peaks from a particular lattice ("predicted peaks").…”

“…The detector geometry is progressively refined by comparing the location of measured Bragg peaks to the location of peaks predicted once the crystal reciprocal lattice vectors have been determined using autoindexing [11,12]. This method can be applied using either a dedicated calibration sample or, in the case of an SFX experiment, from the serial crystallography data itself.…”

“…One needs a prescription describing where each pixel of each module is located in real space. Such prescription we call detector geometry, and can be saved in one of many representations including a separate text file (for example the geometry file format used for CrystFEL [10,11]) or lookup table for the coordinates of each pixel (such as the format used for Cheetah [10]). …”