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Related Concept Videos

X-ray Crystallography02:18

X-ray Crystallography

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The size of the unit cell and the arrangement of atoms in a crystal may be determined from measurements of the diffraction of X-rays by the crystal, termed X-ray crystallography.
Diffraction
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The serial position effect is a cognitive phenomenon where individuals are more likely to recall the first and last items in a list compared to those in the middle. This effect is divided into the primacy effect and the recency effect. The primacy effect is observed when the initial items in a list are remembered better. This occurs because these items are rehearsed more frequently or receive more elaborative processing, allowing them to be encoded into long-term memory more effectively. For...
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Inertial Frames of Reference01:03

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Newton’s first law is usually considered to be a statement about reference frames. It provides a method for identifying a special type of reference frame: the inertial reference frame. In principle, we can make the net force on a body zero. If its velocity relative to a given frame is constant, then that frame is said to be inertial. So, by definition, an inertial reference frame is a reference frame where Newton's first law holds valid. Newton's first law applies to objects with...
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Non-inertial Frames of Reference01:27

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A reference frame accelerating or decelerating relative to an inertial frame is a non-inertial frame. To help understand this, consider what taking off in an airplane, turning a corner in a car, riding a merry-go-round, and the circular motion of a tropical cyclone all have in common. All these systems are accelerating, decelerating, or rotating relative to the Earth; hence, they all are non-inertial frames. All these systems exhibit inertial forces, which merely seem to arise from motion,...
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A problem-solving strategy is a plan of action used to find a solution. Different strategies have distinct action plans. Trial and error involves trying different solutions until one works. For instance, to fix a broken printer, you might check ink levels, ensure the paper tray isn't jammed, and verify the printer's connection to your laptop. This method can be time-consuming but is commonly used. Thomas Edison, for example, used trial and error to find a suitable filament for the light...
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In an NMR sample, precise measurement of the absolute absorption frequencies of nuclei is difficult. A standard internal reference compound is added, and the frequency difference between the reference signal and sample signals is measured.
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Fixed Target Serial Data Collection at Diamond Light Source
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SPIND: a reference-based auto-indexing algorithm for sparse serial crystallography data.

Chufeng Li1,2, Xuanxuan Li3,4, Richard Kirian1,2

  • 1Department of Physics, Arizona State University, Tempe, Arizona 85287, USA.

Iucrj
|February 5, 2019
PubMed
Summary
This summary is machine-generated.

SPIND, an auto-indexing algorithm, efficiently indexes sparse diffraction patterns using minimal Bragg peaks. This method enhances serial femtosecond crystallography data quality and reduces experimental resource needs.

Keywords:
Bragg peaksX-ray free-electron lasersXFELauto-indexing algorithmsdiffract-then-destroydynamical studieselectron diffractionserial crystallography

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Area of Science:

  • Crystallography
  • Materials Science
  • Biophysics

Background:

  • Sparse snapshot diffraction ('stills') analysis is crucial for structural determination.
  • Indexing algorithms often struggle with sparse data, requiring extensive experimental conditions.
  • Efficient indexing is key to reducing sample and beam time in crystallography.

Purpose of the Study:

  • Introduce SPIND (sparse-pattern indexing), a novel auto-indexing algorithm.
  • Demonstrate SPIND's effectiveness on challenging sparse inorganic crystal data.
  • Evaluate SPIND's impact on serial femtosecond crystallography (SFX) data quality and efficiency.

Main Methods:

  • Developed SPIND, an algorithm requiring only five Bragg peaks and unit-cell parameters.
  • Tested SPIND on simulated data of 5-amino-2,4,6-triiodoisophthalic acid monohydrate (I3C).
  • Integrated SPIND with CrystFEL for processing SFX data from membrane proteins (human δ-opioid receptor and NTQ chloride-pumping rhodopsin).

Main Results:

  • SPIND successfully indexed sparse inorganic crystal data, outperforming common algorithms.
  • Integration with CrystFEL improved indexing rates and data quality for SFX.
  • Demonstrated suitability for small unit-cell inorganic crystals and enhanced protein crystallography data.

Conclusions:

  • SPIND offers a robust solution for indexing sparse diffraction data, including challenging inorganic samples.
  • The algorithm significantly improves SFX data processing, reducing experimental costs.
  • SPIND is a valuable tool for advancing crystallographic studies with limited data.