Structural Molecular Biology

Illuminating Biological Structures at the Atomic and Molecular Levels

X-ray Spectroscopy & Imaging

SSRL has five hard X-ray Spectroscopy beam lines and three Microfocus Imaging beam lines dedicated or shared for biological, biomedical and bioenergy research funded by the NIH and DOE-BER. The SMB group supports and develops technical instrumentation and theoretical methods for state-of-the-art tender and hard X-ray spectroscopy and EXAFS studies on metalloproteins, cofactors and metals in biology. The SMB group has also contributed to the development of a wiggler end-station beam line and facilities for X-ray emission and Raman spectroscopy, HERFD and RIXS measurements on biological and biomimetic systems. A holistic imaging methodology combining spectroscopy and X-ray fluorescence has been developed on three beam lines encompassing μm-cm scale specimen over the tender & hard X-ray regime integrating hardware and software for seamless measurement across the stations.


X-ray Absorption Spectroscopy

Techniques

  • Low-temperature XAS
  • Single-crystal XAS
  • EXAFS

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Advanced Spectroscopy


Techniques

  • RIXS
  • XES
  • XRS

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X-ray Fluorescence Imaging

Techniques

  • XRF Mapping
  • Micro-XANES
  • Micro-EXAFS imaging

View details »


The SMB group maintains and operates standard and specialized in-hutch instrumentation for a variety of research programs. These include; cryostats for low-temperature measurements, detector systems serving dilute and concentrated samples and specialized instrumentation for tender-energy and single-crystal XAS measurements. Experimental details about beam lines and information about their specific capabilities are listed under each beam lines technical page.

X-ray Absorption Spectroscopy
Advanced Spectroscopy
X-ray Fluorescence Imaging

The data collection softwares used on the spectroscopy beam lines include XASCollect and XASSCAN. Beam line computers are also equipped with the data analysis softwares EXAFSPAK and SixPACK.

Data Collection

XAS Collect is the SSRL X-ray Absorption Spectroscopy data acquisition program. It is designed to allow quick and easy XAS experimental setup and data collection, and to make optimal use of available beam time. It has many facilities, including some on-line analysis capability, all of which are described in the on-line documentation and in the manual can be obtained by clicking the link below. Click here to see the XAS Collect Manual. In addition, the XASSCAN software in used on BL9-3 and used to interface with the 100-element Ge detector.

Data Analysis

EXAFSPAK and SIXPACK

The data analysis packages EXAFSPAK and SIXPACK are available free of charge. Both are currently installed on the XAS beamline computers. Windows and a variety of Unix versions are currently available. These, and the manual for EXAFSPAK, can be obtained here. The manual for SIXPACK can be obtained here.

Other Programs

FEFF: http://leonardo.phys.washington.edu/feff/
Demeter: https://bruceravel.github.io/demeter/
IFEFFIT: http://cars9.uchicago.edu/ifeffit/
GNXAS: http://gnxas.unicam.it/

Utilities

Some useful utilities to aid user measurements are provided below.

Eulerian to Kappa Geometry Calculator

Ion Chamber Photon Flux Calculator