Biomolecular Solution Scattering Links

Small Angle X-ray Scattering (SAXS), Small Angle Neutron Scattering (SANS), Wide Angle X-ray Scattering (WAXS), and Small Angle/Wide Angle X-ray Scattering Combined (SWAXS)

Blaine Mooers 15 August 2013. Please report dead links, corrections, and suggested additions to blaine-mooers at ouhsc.edu.

Link Indices (click on topic to navigate webpage)

Summary Points about Biological SAXS

Advantages of Access to a Local SAXS Instrument

Historical Milestones in SAXS

Conditions that justify modeling SAXS data with an ensemble

Miscellaneous Links

SANS beam lines

SAXS beam lines

SAXS Databases

SANS Examples

SAXS Examples by Experiment Type

SAXS Examples by Disease

SAXS Examples by Macromolecule Type

WAXS Examples

SAXS fee for service

SAXS Instruments

SAS Meetings

SAXS and Molecular Graphics–Chimera

SAXS and Molecular Graphics–PyMOL

SAXS and Molecular Graphics–SITUS

SAXS and Molecular Graphics–VMD

SAXS Software

SAXS Software Developer Groups

SAXS Reviews

SAXS Seminars, Local

SAXS TextBooks

SAXS Tutorials

SANS Workshops

SAXS Workshops


Summary Points about Biological SAXS

1. This a structure method that does not require crystals and works with proteins that might be difficult to crystallize (e.g., containing disordered domains).

2. SAXS enables the study of biological macromolecules in a variety of solution conditions ranging from near physiological to highly denaturing.

3. Ab initio structure reconstruction methods enable the making a 3-D molecular envelopes from 1-D scattering data.

4. The modeling of protein:protein and protein:nucleic acid complexes is a valuable application of SAXS. High resolution structures of individual components can be placed inside the SAXS molecular envelope by rigid body fitting.

5. SANS facilitates the study of complexes with one or more deuterated components.

6. Mobile surface loops and domains that move too much to be seen in crystal structures can be visualized by SAXS.

7. Ensembles of partly or fully unfolded proteins or RNAs can be studied by SAXS.

8. The size range for biological SAXS to 5 KDa to 50 MDa.

9. The samples must be aggregate-free (check with dynamic light scattering or multi-angle light scattering). The samples should also be free of interparticle effects.

10. To test for interparticle interactions, scattering data are typically collected at three or four concentrations ranging from 1 to 10 mg/ml. The sample volume per measurement is 30 microliters. Data are collected from a matching buffer sample that should be obtained by dialysis. The interparticle interactions can be weakened by increasing the buffer concentration.

11. Avoid inorganic buffers like phosphate and cacodylate. Use MOPS, MES, or TRIS which scavenge free radicals generated by X-ray damage. 1-5 mM DTT, TCEP, and 2-mercaptoethanol also protect proteins from excessive radiation damage. So does glycerol but you must have a matching concentration in your buffer sample.

12. Take care with detergents. Some detergents scatter X-rays very strongly.

13. Methods of working membrane proteins using SAXS are summarized on pages 313-317 of the following review: Lipfert, J. and Doniach, S. (2007) Small-angle X-ray scattering from RNA, proteins, and protein complexes. Annu. Rev. Biophys. Biomol. Struct. 36, 307-27.

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Advantages of Access to a Local Instrument

1. Many samples are stable only for a one week or two after purification. Scheduled time at a beam line has to be arranged a minimum of two weeks in advance for a rapid access program and several months for regular programs.

2. Many samples are to hard transport without freezing. Many samples lack freezing protocols.

3. Many samples need the solution conditions optimized to eliminate aggregation or interparticle effects. There is not much time during a trip to a beam line to optimize solution conditions.

4. Interparticle effects are hard to detect by other methods.


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Historical Milestones in SAXS from Rambo and Tainer (2013)

Year Event Reference
1915 Debye equation nnn
1939 Guinier approximation equation
1949 Scattering equation Debye and Bueche
1951-1957 Porod, Debye, Kratky
1964 SAS model tRNA Timashef 1961 ; Witz, 2003
1970 Contrast variations, Multipole expansion Stuhrmann
1970s Synchrotron SAXSn
1977 Indirect Fourier Transformation Glatter
1980 Information Theory Applied to SAXS Moore 2000
1987 30S SAS model
1992 GNOM, the application of the Tikhovnov regularization to the inverse problem Svergun
1995 CRYSOL Svergun et al.
1998-2000 ab initio methods:
  • DaliGA
  • DAMMIN
  • SAXS3D
  • GASBOR
2007 Ensemble methods:
  • EOM
  • MES
  • BSS-SAXS
  • EROS
after 2013 Residue-level Structure Determination with SAXS Data

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Conditions that justify modeling SAXS data with an ensemble proposed by Rambo and Tainer (2013)

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Miscellaneous Links

SAS Portal , THE home for Small Angle Scattering

SAXS Links Software for small angle scattering, maintained by Diamond Light Source, UK

Dmitri Svergun (EMBL), a leader of the biological SAXS field

Biological small-angle scattering wikipedia

SAXS wikipedia

List of synchrotron radiation facilities

EMBL, Practical Course: Solution Scattering from Biological Macromolecules

Biosync

Biosaxs links

SAXier, a forum about SAXS

SAXS data analysis

SAXS data processing

Dyksterhuis, introduction to SAXS

Kreichbaum

concentric shell model, calculate scattering from cylinder

UTMB SAXS and SANS Group, access restricted to Gulf Coast Consortia, have many links

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SANS beam lines

United States

ORNL, Oak Ridge National Lab,

LENS, Low Energy Neutron Source, Indiana U.

NIST, Center for Neutron Research

Lujan Neutron Scattering Center at LANSCE, Los Alamos National Laboratory, Low-Q Diffractometer, 0.003 to 0.5 Å-1

EPSCOR Neutron Scattering Network


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SAXS beam lines


United States Synchrotrons


          Advanced Light Source, Berkeley, ALS 12.3.1. SAXS SIBYLS (described in a 2013 paper)

                ALS SIBYLS proposal deadlines: 15th of the month for a two-month run cycle beginning one-and-half months after the preceding submission deadline

                (e.g., apply before Dec. 15th and get time between Feb.1 and Mar. 30th).

               ALS proposal link

          Advanced Photon Source, Argonne National Lab, Chicago. biocat ID-18

          APS, small-angle x-ray scattering

          CHESS, MacCHESS BioSAXS

          NSLS SAXS X9 line

          NSLS X21

          SSRL BIOSAXS BL 4-2

proposal deadlines, SAXS under UV/X-ray

Foreign Synchrotrons

Australian Synchrotron SAXS 15ID

BioSAXS scattering cells

ESRF BM29

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SAXS Databases:

BIOISIS, Integrated Structures in Solution Databank; the "Protein Data Bank" of SAXS; can download saxs data and use as tutorials

Citing BIOISIS: Rambo, R. (2009). BIOISIS, http://www.bioisis.net/.

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SANS Examples


SAXS Examples

SAXS Examples by Experiment Type

Ab initio shape determination

anomalous scattering

Complexes

Domain Motion

Determine Protein-Protein Interaction Potentials in Solution

Kim et al. 2008

Phasing Diffraction Data with Envelope from SAXS

Hao 2006

Homology Model Selection

NMR and SAXS

Mobile surface loops

time-resolved SAXS

Unfolding studies

Determine Protein-Protein Interaction Potentials in Solution

Kim et al. 2008

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SAXS Examples by Disease

Cancer

Diabetes

Heart

Infectious Disease--Bacteria

Infectious Disease--Eucaryote

Infectious Disease--Viral

Prion Diseases

Vision


SAXS Examples by Macromolecule Type

Complexes of proteins

complexes of proteins and DNA

complexes of proteins and RNA

Complexes of Protein and Peptides

Complexes of Protein and small molecular ligands

DNA

disordered proteins

glycoproteins

glycans

integral membrane proteins

metalloproteins

RNA

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WAXS Examples

combining WAXS and crystallography to locate heavy atoms

Hong and Hao 2009

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SAXS fee for service

BioSAXS.com

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SAXS Instruments

Anton Par

Bruker

Hecus MicroCALIX, bought by Bruker

Rigaku wiki

Rigaku bioSAXS1000

BioSAXS-1000

 Dec 2012: 5 BioSAXS systems sold and 3 of those are installed:

    UTMB (installed), IGBMC (France - installed), Brown Univ (installed),

    McMaster Univ (Canada - installation by Feb), Masaryk Univ (Czech Rep - installation by Feb)

  Peer reviewed papers with data collected with the BioSAXS-1000:

     Polizzi et al. (2013) Biochemistry 52, 3888 – 3898.

Xenocs SAXS and WAXS systems

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SAXS Meetings

SAS2012, International Small-Angle Scattering Conference , 18-23 November 2012, Sidney, Australia; held once every three years

SAS2015, International Small-Angle Scattering Conference , 12-18 September 2015, Berlin, Germany

SAS2018, International Small-Angle Scattering Conference, sponsored by APS ,October 2018, Traverse City, Michigan

Link to SAXS meetings

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SAXS and Molecular Graphics – Chimera:

Calculate SAXS curves from pdb file (uses FoxS): /Tools/Higher-Order Structure/Small-Angle X-ray Profile

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SAXS and Molecular Graphics – PyMOL:

SAXS envelopes:

   set solvent_radius, 5

   set mesh_solvent, 1

   If importing a PDB structure, use the [A] drag coordinates command to move the model

   (Use the SHIFT-mouse to move or rotate the model)


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SAXS and Molecular Graphics – SITUS:

unfinished

    SITUS — SAXS tutorial

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SAXS and Molecular Graphics – VMD:

unfinished

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SAXS Software (alphabetical order):


Allosmod-FoXS v, uses sampling algorithms to generate structures that are then put into FoXS to calculate scattering profile

AquaSAXS– , calculate SAXS from pdb file.

ATSAS on-line

ATSAS– download version 2.4 Data Analysis Software for Mac 10.6; 2.5 for Mac 10.7; windows and linux versions too.

   To get started with the ATSAS software on the Mac, type "primus" in a X11 or terminal window. It is usually installed /usr/bin. You may have to start it by typing "/usr/bin/primus"

AXES –: Analysis of X-ray Scattering in Explicit Solvent


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Bilbomd– a webapp that enables conformational sampling by molecular dynamics simulation with the SAXS data as a restraint

BioXTAS RAW – SAXS software; must "source .profile" prior to invoking with python RAW.py to fire up Enthought python

BioCAT's X-ray Tools– on-line Q range calculator.

CRYSOL– Svergun Group at EMBL-Hamburg, method of theoretical scattering profile calculation using multipole expansion

Dalai_GA –uses genetic algorithm to fit SAXS data with bead models

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Fast-SAXS-pro–, Yang Lab at Case Western, upload a PDB file and compute its theoretical SAXS profile. The PDB file can be of protein, DNA, RNA, or their complex. Coordinates can be at an atomic or a coarse-grained (e.g., Ca atoms of a protein)

FastSAXS–, predecessor of FAST-SAXS-pro, Ad Bax Group

FoXS–: a web server for rapid computation and fitting of SAXS profiles using the Debye Formula. Andre Sali group at UCSF, built into IMP, the Integrative Modeling Platform

FoXSDock–: Macromolecular Docking with SAXS Profile


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HyPred– server at U of Chicago: reads in a pdb and emails the user with predicted hydration shell densities and crystallographic water sites

HyPred– related software

hydropro– predicts Rg and other hydrodynamic parameters from 3D models


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IMP, Integrative Modeling Platform–, binary and source available

Irena– package for analysis of small-angle scattering data

SANS & USANS– Analysis with IGOR Pro

Igor 6.2–, required for Irena


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MES– Minimal Ensemble Search

MES tutorial

Nika–, 2-D to 1-D data reduction prior to analysis by Irena above, need Igor Pro


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RMsd_calc– (calculate RMSD for subset of atoms with current operator)

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SASfit– for fitting small-angle scattering curves

SASSIE– suite of program for generating molecular structures.

SASTBX –

SAXS 2011– , Colorado State University Software Package

SAXS software at ESRF, linux and windows binaries and source code

saxs3d; xlattice; pdb2xyz_saxs

SAXSgui– A Graphical User Interface for Visualizing, Transforming and Reducing SAXS Images (as well as Limited Fitting)

SaxsMDView, SAXSANA, TraceBeads, SaxsAnalysis, SVD and reconstruction, UnfoldingFit, CalibCCD at Tokyo University

SAXSview–, process 2-D data and 1-D data, source forge download

SAXS MoW– run from website, requires GNOM output with data in (angstrom)-1, calculates MW and oligimerization.

SAXSTER– uses SAXS profile to select homology model template.

ScÅtter– software for the analysis of biological SAXS datasets, computes the new statistics described in the 2013 Nature paper by Rambo and Tainer

SCULPTOR– interactive multi-resolution docking and visualization program for low-resolution density maps and atomic structures.

SITUS– package for the modeling of atomic resolution structures into low-resolution density maps e.g. from electron microscopy, tomography, or small angle X-ray scattering.

Singlebody– calculates p(r) and I(q) functions of models defined by sets of IF conditions using a Monte-Carlo approach. Cross section and thickness functions of cylinders and lamellae can be calculated as well. The program is freeware. Executable for Windows.

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WAXS profile calculator from , on-line, U of Chicago.

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Collections of SAXS Software

Links to sites involved in predicting SAXS profiles.

CCP13 SAXS software

Manfred Kriechbaum collection of java scripts for calculating SAXS profiles from geometric shapes

SAXS Software Wiki

SAXS software at ESRF

ESRF software

Sastbx: The Small Angle Scattering ToolBox

Sastbx Online Services

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SAXS Software Developer Groups

ado State, Data Analysis for Small Angle X-ray Scattering

EMBL-Hamburg, Biological Small Angle Scattering Group

ESRF, Grenoble, France; SAXS Platform for Structural Biology

UTMB SAXS and SANS Group, access restricted to Gulf Coast Consortia, have many links

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SAXS Related Software: Molecular Motion Simulation

ProDy--Python package for protein structural dynamics analysis.

DDPT--A Comprehensive Toolbox for the Analysis of Protein Motion


SAXS Reviews

2001

Doniach, S. (2001) Changes in biomolecular conformation seen by small angle X-ray scattering. Chem Rev 101, 1763-1778.


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2003

Koch et al. (2003) Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution. Q Rev Biophys 36, 147-227. (Comment: a very rigorous review.)

Vachette et al. (2003) Looking behind the beamstop: X-ray solution scattering studies of structure and conformational changes of biological macromolecules. Methods Enzymol 374, 584-615.

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2006

Das, R. and Doniach, S. (2006). Structural studies of proteins and nucleic acids in solution using small angle x-ray scattering (SAXS)," in Soft Matter: Scattering, Imaging and Manipulation, eds. Pecora, R. and Borsali, R., Kluwer Press.

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2007

Lipfert, J. and Doniach, S. (2007) Small-angle X-ray scattering from RNA, proteins, and protein complexes. Annu. Rev. Biophys. Biomol. Struct. 36, 307-27.

Putnam et al. (2007) X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution. Q Rev Biophys 40, 191-285. (Deep and complete review).

Stuhrmann, H. B. (2007) Small-angle scattering and its interplay with crystallography, contrast variation in SAXS and SANS. Acta Crystallographica. Section A, Foundations of Crystallography 64, 181-91.

Svergun, DI (2007) Small-angle scattering studies of macromolecular solutions. J. Appl. Crystallogr. 40, s10–s17.

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2009

Doniach, S. and Lipfert, J. (2009) Use of small angle X-ray scattering (SAXS) to characterize conformational states of functional RNAs. Methods Enzymol 469, 237-251.

Hura et al. (2009) Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS). Nat Methods 6, 606-612.

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2010

Rambo, R.P. and Tainer, J.A. (2010) Bridging the solution divide: comprehensive structural analyses of dynamic RNA, DNA, and protein assemblies by small-angle X-ray scattering. Curr Opin Struct Biol 20, 128-37. (Short Overview)

Yang, S., Parisien, M., Major, F. and Roux, B. (2010) RNA structure determination using SAXS data. J. Phys. Chem. B, 114, 10039-48.

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2011

Kathuria SV, Guo L, Graceffa R, Barrea R, Nobrega RP, Matthews CR, Irving TC, Bilsel O. (2011) Minireview: Structural insights into early folding events using continuous-flow time-resolved small-angle X-ray scattering. Biopolymers 95, 550-558.

Rambo, R.P. and Tainer, J.A. (2011) Characterizing flexible and intrinsically unstructured biological macromolecules by SAS using the Porod-Debye law. Biopolymers 95, 559-571.


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2012

Bernado, P. and Svergun, D.I. (2012) Structural analysis of intrinsically disordered proteins by small-angle X-ray scattering. Mol. Biosyst. 8, 151-67.

Czjzek, M., Fierobe, H.P., and Receveur-Brechot, V. (2012) Small-angle X-ray scattering and crystallography: a winning combination for exploring the multimodular organization of cellulolytic macromolecular complexes. Methods Enzymol 510, 183-210.

Doniach, S. and Lipfert, J. (2012) "Small and Wide Angle X-ray Scattering from Biological Macromolecules and their Complexes in Solution." In: Edward H. Egelman, editor: Comprehensive Biophysics, Vol 1, Biophysical Techniques for Structural Characterization of Macromolecules, H. Jane Dyson. Oxford: Academic Press, 2012. pp. 376-397.

Hammel, M. (2012). Validation of macromolecular flexibility in solution by small-angle X-ray scattering (SAXS). Eur Biophys J 41, 789-99.

Petoukhov, M. V., Franke, D., Shkumatov, A. V., Tria, G., Kikhney, A. G., Gajda, M., Gorba, C., Mertens, H. D. T., Konarev, P. V., Svergun, D. I. (2012). New developments in the ATSAS program package for small-angle scattering data analysis. J Appl Crystallogr, 45(2), 342-350.

Schneidman-Duhovny et al. (2012) Integrative structural modeling with small angle X-ray scattering profiles. BMC Structural Biology 12:17.

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2013

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SAXS Seminars, Local

John Tanner (U of Missouri) May 20, 2013, OU-Norman

Ed Snell, (Hauptman-Woodward Institute), June 19, 2013, 4 PM, BRC 109 OUHSC-OKC


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SAXS TextBooks

Lipfert and Donaich (coming September 3, 2013 ) Small-Angle X-Ray Scattering: Applications to Structural Molecular Biology.

Feigin, L.A. and Svergun, D.I. (1987). Structure Analysis by Small-Angle X-Ray and Neutron Scattering. New York: Plenum Press. p. 40. ISBN 0-306-42629-3. Download here

Glatter, Otto and Kratky, Otto (eds.): Small Angle X-ray Scattering. London: Academic Press (1982). Out of print but can download by clicking on authors's names.

Guinier, A. and Fournet, G. : Small-angle scattering of x-rays. New York: John Wiley & Sons (1955)

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SAXS Tutorials:

From sample prep to data deposition in 8 steps at BioISIS

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SAXS Working Groups:

Small Angles Net:

canSAS

smallangle.org, portal to SAS related information including lists of software

SANS Workshops in USA:

3rd Graduate Course on Neutron Scattering Applications in Structural Biology June 4 - June 8, 2013, application deadline April 22

people from EPSCOR state can get travel fellowships

4th Workshop on Neutron Scattering Applications in Structural Biology, Oak Ridge, Tennessee; June 24 - June 28, 2013; April 22 deadline


SAXS Workshops in USA, upcoming:

4th annual SIBYLS bioSAXS workshop ; Advance Light Source (ALS) at Lawrence Berkeley National Laboratory , Berkeley, CA. Registration: To attend the workshop you need register for the 2013 Advanced Light Source User Meeting. ALS user meeting will be held at Berkeley Lab October 7-9. Workshop will begin October 8th and continue through October 9th. When you registering, you must indicate ``Small Angle X-Ray Scattering Studies In Structural Biology'' as your workshop. Enrollment is limited to 30 participants. Inquires: Jane Tanamachi jtanamachi@lbl.gov.

APS, beyond Rg, SAXS Short-course Advanced Photon Source, Argonne National Laboratory, October 26 – 31, 2013. No registration fee. Registration closed at end of June.

SAXS Workshops in USA, recent past:

Biological SAS workshop at American Crystallography Association Meeting, July 20-24

This was a dual track workshop: Beginner's Track for those getting started with SAXS and Advanced Methods Track for experienced users ready to master advanced methods.

Organized by Richard Gillian, Cornell High Energy Synchrotron Source, and Edward Snell, Hauptman-Woodward Medical Research Inst.

Fee: Student or Postdoc - $100 / Academic, non-student - $150 / Corporate, non-student - $250

APS: Irena and Nika, Argonne National Lab, Chicago; SAXS Software Packages Irena and Nika Spring 2013 Course;

Thurs.- Fri., May 9-10, 2013 ; free ; limit of 20.

BNL-NSLS, Brookhaven National Lab-National Synchrotron Light Source; X9 SAXS Workbench;

April 18-21, 2013; free; deadline April 1

CHESS, Cornell:

two full days; March 21-23, 2013; $250 registration fee.

SSRL, Stanford Synchrotron Radiation Lightsource, Menlo Park;

three full days; March 18 - 20, 2013; $100 registration fee.

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