ABOUT SCATTER

ScÅtter is a JAVA-based application for basic analysis of SAXS datasets. ScÅtter is developed by Robert Rambo at the Diamond Light Source (Didcot, UK). The program was previously developed at the SIBYLS beamline (12.3.1) of the Advanced Light Source, Berkeley, CA.

Current Version J - released 12 August 2021

Download via BioIsis

  • JAVA requirement:

    JAVA 12 (platform 12.0.2, OpenJDK 12) or greater for Windows, Mac OS X or LINUX

  • Starting ScÅtter:

    ScÅtter comes as a compressed zip file. Unzip the file into a directory, typically accomplished by double clicking the downloaded file. If the file was unzipped in a "Downloads" directory, simply drag the entire unzipped directory to a more permanent location.

    Open the directory and double-click "scatter.jar". The *.jar file can be moved to any suitable directory, just be sure to have the directory available to the system by setting appropriate path statements.

    Windows and LINUX users! Depending on security settings, ScÅtter may be started from command line using "java -jar scatter.jar"

    Apple OSX users: Scatter can be added to the dock. Just drag the jar file to the area next to the trash can. See link.

  • Intensity file:

    ScÅtter can read any 3 column text file (column 1: q, column 2: Intensity, column 3: error ) delimited by space or tabs. Header or footer information starting with # will be ignored. In addition, ScÅtter can read Bruker *.brml SAXS file formats. If you are experiencing problems, please contact Robert Rambo.

Future Updates

  • Independent component analysis for resolving individual scattering curves of components in a mixture.
  • Direct fitting of PDB models to scattering profiles.
  • Scatter 3 is deprecated and no longer supported.

Disclaimer

JAVA is a platform independent language that is entirely objected oriented. We tried to optimize the analysis around the object oriented platform. ScÅtter is released as an open source package on github.


Change Log

Release J - 12 August 2021

ATSAS fixes:

  • Fixed some issues with loading .out file from GNOM. Should work when running out file not created via Scatter.
  • BUG fix in averaging of SEC SAXS peak

Release IV.e - 29 September 2020

Scatter IV officially released! Scatter IV is now released. It represents a complete rebuild of Scatter using the JAVA openSDK 12. Scatter IV deprecates Scatter 3. New features include::

  • Dedicated SEC-SAS tab. Single data file representing the indexed collection of .dat files of the SEC run can be loaded via simple drag-n-drop.
  • Creation of .sec file after creating SEC-trace
  • Similarity plot to help guide merging of frames
  • SVD cumulative singular value plot for detecting small variations in signal
  • Auto PDF output of SEC-merging and Subtraction
  • FIND DMAX accessible as right mouse click in both Analysis and P( r ) tabs
  • Auto output of DENSS compatible file from refinement of P( r ) distribution

Release 2.1 c - June 30, 2014

Version 2.1c fixes a few bugs and has some added features by request:

  • Data is exported on Results tab
  • Filenames are no longer auto-generated (2FILE P(r) tab)
  • The previous specified working directory will be set on start-up
  • Limited access to ATSAS (DATGNOM AND DAMMIN/F) from ScÅtter GUI
  • User must specify directory of the ATSAS binaries in Settings tab
  • 2File (on P(r) tab) automatically calls DATGNOM on the data visible in plot
  • Output from DATGNOM is auto-loaded into DAMMIN/F tab for modeling.
  • Truncation of data in manual Guinier analysis carries over to the working dataset in Analysis tab
  • Crosshairs can be toggled off by right-click on graph (popup menu)

Release 2.0 beta - January 3, 2014

Version 2.0 is a major re-write of the entire program. Due to several bugs and user feedback, Scatter was refactored and improved with the following additional features:

  • Unlimited data files per collection
  • Output SVG and PDF formats
  • Colors and point size editor for individual datasets
  • Buffer subtraction
  • Multi-file chifree calculations
  • Regularized inverse transform using L1-norm
  • Complex formation detection algorithm
  • I(0)/Rg plots over all visible datasets

This is a beta release and we appreciate bug reporting from our users.

Release 1.7i - July 31, 2013

Fixed bug in windows 7, 8 and LINUX, program would not start due to error in determining home directory.

Release 1.7f - July 20, 2013

Fixed Windows 8 bug (directory determination would halt start of program).

Corrected scaling of mass when scale factor is not 1.0 when using Vc button.

Release 1.7e - July 19, 2013

Fixed repopulating of Results tab.

Release 1.7d - July 18, 2013

Fixed auto-zoom that was only affecting data with the max I(q) < 1.

Fixed bug in Guinier fitting. For datasets with I(q) < 1 in Guinier region, auto_Rg and manual Guinier would initially report -1 and 0 for I(0) and Rg until data was adjusted manually. Now, Scatter reports the proper parameters.


Release 1.7c - July 16, 2013

Fixed Chi_free calculation. FOXS rounds the q-value to one less significant figure. Scatter now actively rounds the number to find corresponding number in FOXS fit file. Rounded numbers are printed to console.