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EMBL Hamburg Biological
Small Angle Scattering
BioSAXS
 

CHROMIXS manual

CHROMIXS

Written by A. Panjkovich.
Post all your questions about CHROMIXS to the ATSAS Forum.

© ATSAS Team, 2016-2017

Table of Contents

Manual

The following sections describe how to use CHROMIXS to analyse SEC-SAXS data.

Introduction

The CHROMIXS program will load and plot a set of SAXS frames (usually thousands) as produced by a SEC-SAXS (size-exclusion-chromatography online SAXS) run. Frames are represented in respect to elution time, allowing the user to select buffer/sample regions and to generate a SAXS curve.

Running CHROMIXS

Usage:

$ chromixs [OPTIONS]

CHROMIXS can be run from the command-line without arguments, but it recognizes the following options. Mandatory arguments to long options are mandatory for short options too.

Short OptionLong OptionDescription
-d --datadir=<PATH> Data directory to load.
-o --outdir=<PATH> Output directory for subtracted data.
-f --file=<FILE> Project file to open.
-a --automatic=<PATH> Unsupervised processing of a data directory, GUI is not activated. In Mac, please use the "chromixs.bin" command.
-p --prefix=<PREFIX> PREFIX to prepend to output filenames, default is chromixs.
-n --namefilter=<RE> Escaped expression to filter frame filenames, default is \*.dat.
-v --version Print version information and exit.
-h --help Print a summary of options and exit.

Graphical interface

Once CHROMIXS is running and data has been loaded, the CHROMIXS window shows a plot of frame nr. vs. average intensity, a set of menus on the top and a set of tools on the right.

If molecular weight (MW), radius of gyration (Rg) or other additional data (e.g. UV) are being displayed (with a scale on the y-axis on the right side of the plot), the range of the right y-axis scale can be controlled with the mouse-wheel. Use Shift+mouse-wheel to control zooming on the right axis scale.

Screenshot of CHROMIXS

Tools

The buttons on the right of the CHROMIXS window trigger the most common operations:

NameDescription
Load Data Directory Select a directory to load SEC-SAXS data frames from.
Zoom Use the mouse to zoom in and out of the data plot.
Sample Automatic Selection The program will search for a sample region.
Buffer Automatic Selection The program will search for an optimal buffer region.
Sample Manual Selection Use the mouse to select sample frames from the plot.
Buffer Manual Selection Use the mouse to select buffer frames from the plot.
Selection Eraser Draws an area to clear buffer and/or sample selections.
Process Selection Obtain a subtracted SAXS curve from the selected frames.
Quit Exit CHROMIXS.

Menus

The tools described above are also available through CHROMIXS's menus. Additional actions, available only through the program menu (or their respective shortcuts), are described here:

NameDescription
File - Open chromixs project file Navigates the filesystem to open a chromixs project file.
File - Save chromixs project file Saves the current plot, including selections, to a chromixs project file.
File - Export plot in SVG format Exports the current plot in Scalable Vector Graphics (SVG) format for figure preparation.
File - Export elution profile Exports the frame nr. vs. average intensity data as a comma separated file (.csv).
File - Open selected frames in Primus Opens the currently selected frames (buffer or sample) in Primus for custom processing (e.g. scaling, averaging, statistical comparison with CORMAP, etc).
File - Configure (or 'Preferences' in Mac) This menu opens a configuration window, where CHROMIXS's inner parameters can be modified.
File - Close Project Closes current project and reinitializes the program.
Tools - Reset Selection Clears all selections regarding buffer and sample frames.
Analysis - Estimate Rg Values Estimates and plots radius of gyration (Rg) values for the selected sample region.
Analysis - Estimate MW Values Estimates and plots molecular weight (MW) values for the selected sample region.
Analysis - Load External Data Loads an external data set from the filesystem (e.g. UV data). Data is expected indexed by frame number (two-columns, one frame per row: frame nr. vs value).

Loading SEC-SAXS data from a frames directory

This option is available through the graphic interface once CHROMIXS is running (the Load Data Directory button at the top-right opens a dialog that can navigate to the frames directory) or as a command-line argument: --datadir=<PATH>.

Upon loading a data directory, CHROMIXS expects a collection of experimental data files (e.g. ./data/frames/*.dat) in ascii format containing 3 columns: (1) experimental scattering vector, (2) experimental intensity and (3) experimental errors. Data files should correspond to SAXS frames obtained during elution of the SEC column. No other *.dat should be present in the directory (e.g. averages, frames from previous runs, etc.). This format matches what is currently in use at EMBL P12 SAXS beamline (i.e. data/frames directory).

Ordering of the frames is important, the EMBL P12 filename format uses padded zeros (*0001.dat, *0002.dat) which alphabetically match the elution order and is what CHROMIXS uses as default. The frame nr. currently plotted corresponds to the order in which the frames were read in. In the case of SOLEIL/Nexus frames, where the order is written in the filename between hash symbols (e.g. XXX#9#.dat, XXX#10#.dat XXX#11#.dat), CHROMIXS will detect this nomenclature and sort the files appropriately. Again, the frame number displayed on the plot corresponds to the absolut order in which frames were read in, and does not necessarily match the number given in the filenames. If you use yet another format, please rename your frames so the elution order matches the alphabetical order.

Selection and processing of data frames

Standard operation after loading data is to select a range of sample frames with the corresponding tool. After selecting sample frames, a buffer region can be selected manually or predicted using the 'Buffer Automatic Selection' function. Once sample and buffer regions are chosen, the user can click on 'Process Selection' and CHROMIXS will subtract one buffer frame to each sample frame, scale the subtracted frames and average them. The output frame will be written to file in the working directory and displayed with the Primus program. Please see the PRIMUS manual for more details.

The output filename prefix can be set through the command-line option of the same name or through the configuration window.

Project file

The File menu allows the user to save a chromixs project file, which contains the data plot and selected regions. This file can be opened later to continue with the analysis. Currently, frame data are not saved within the chromixs project file, only their location in the computer's filesystem.


  Last modified: May 24, 2017

© BioSAXS group 2017