Small Angle Scattering Links

Small-Angle X-ray Scattering (SAXS) and

Small-Angle Neutron Scattering (SANS)

Assembled by Blaine Mooers 28 Feb 2013. Please report dead links, corrections, and suggested additions to blaine-mooers at ouhsc.edu.


Indices

          Miscellaneous Links

          SANS beam lines

          SAXS beam lines

          SAXS Databases

          SAXS Examples: What you can do with SAXS

          SAXS fee for service

          SAXS Instrument Vendors

          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:


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


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SAXS beam lines


United States Synchrotrons


          Advanced Light Source, Berkeley, ALS 12.3.1. SAXS SIBYLS

          ALS SYSBIL 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

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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SAXS Examples: what kinds of experiments can you do with SAXS? (work in progress)

Determine Protein-Protein Interaction Potentials in Solution

          Kim et al. 2008

         

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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)

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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:

              SITUS — SAXS tutorial

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SAXS and Molecular Graphics – VMD:

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SAXS Software (alphabetical order):


         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.

         AXES: Analysis of X-ray Scattering in Explicit Solvent


         Bilbomd

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

         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


         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


         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

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

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

         SITUSpackage 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

         Colorado 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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SAXSReviews:

         


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.


          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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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

         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.


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


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2012

         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. "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.

          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

         Perry, J.J. and Tainer, J.A. (2013) Developing advanced X-ray scattering methods combined with crystallography and computation. Methods (in press)


          Petoukhov, M.V. and Svergun, D.I. (2013) Applications of small-angle X-ray scattering to biomacromolecular solutions. The International Journal of Biochemistry & Cell Biology 45, 429-437.


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SAXS Seminars, local

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

          Ed Snell, (Hauptman-Woodward Institute), May 29, 2013, OUHSC-OKC


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:

         coming soon

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SANS Workshops in USA:

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

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SAXS Workshops in USA:

         ALS, Advanced Light Source, Berkeley;

              Annual SIBYLS bioSAXS course; ~9-10 October.

         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.

         APS, beyond Rg, Advanced Photon Source, Argonne National Laboratory;

             Small-Angle Scattering Short Course 2013/2014: Beyond Rg; October 26 – 31, 2013.

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

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

         CHESS, Cornell:

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

         SSRL, Stanford Synchrotron Radiation Lightsource, Menlo Park;

              more time spent on advanced methods, three full days; March 18 - 20, 2013; $100 registration fee.

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