CHROMIXS

Purpose and scope

CHROMIXS is an interactive viewer and driver for SEC–SAXS data reduction. It loads a series of SAXS frames acquired during a size-exclusion chromatography run, displays their elution trace, and allows definition of buffer and sample frame ranges. From these selections, background-subtracted scattering curves and basic structural parameters are produced.

CHROMIXS does not perform model fitting or refinement. All quantitative analysis beyond background subtraction is delegated to established ATSAS command-line programs.

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Backend contract

  • Primary task: generate background-subtracted SAXS curves from SEC frames
  • Input: multiple experimental SAXS data files (typically .dat) representing consecutive SEC frames
  • Output: subtracted SAXS curves compatible with PRIMUS and downstream ATSAS tools
  • External programs used: AUTORG, DATGNOM, DATMW
  • Data safety: input files are never modified

This manual documents how CHROMIXS maps user selections to these backend operations. Algorithmic details are documented in the respective program manuals.

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Starting CHROMIXS

$ chromixs [DATA]

DATA may be:

  • a CHROMIXS project file → restores a previous session
  • a list of SAXS data files → builds a new SEC trace
  • omitted → starts with an empty workspace

When launched via the ATSAS Launcher, the same behavior applies.

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Conceptual user interface model

CHROMIXS consists of three persistent conceptual areas: 1. Trace plot Integrated scattering intensity as a function of frame index (or time). 2. Frame selections Logical definitions of buffer and sample frame ranges. 3. Data and processed views Visualization of raw and background-subtracted SAXS curves derived from the selections.

All interaction modifies one of these three entities. The GUI layout itself is incidental.

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Trace plot

After loading data, CHROMIXS computes an integrated intensity value for each frame:

\[I_{trace} = \frac{1}{n} \sum_{s_{min}}^{s_{max}} I(s)\]

with corresponding error estimates

\[\sigma(I_{trace}) = \sqrt{\frac{1}{n} \sum_{s_{min}}^{s_{max}} \sigma(I(s))^2}\]

The angular integration range s_{min}…s_{max} is configurable in the application settings.

The trace plot serves as the only location where frame selections are defined and modified.

Optional overlays:

  • point-wise error estimates
  • frame-wise radius of gyration
  • frame-wise molecular weight

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Frame selections

A frame selection is the central working unit in CHROMIXS. It consists of:

  • a set of sample frames
  • a set of buffer frames
  • the resulting processed (subtracted) data

Multiple frame selections may coexist and overlap. This allows comparison of different buffer definitions or analysis of multi-peak elution profiles.

Only the currently active selection can be modified. Inactive selections are hidden from the trace plot and locked against changes.

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Processing and derived quantities

Processing a frame selection performs the following steps: 1. Average buffer frames 2. Subtract averaged buffer from each sample frame 3. Estimate structural parameters:

  • Radius of gyration (AUTORG)
  • Maximum particle dimension (DATGNOM)
  • Molecular weight (DATMW)

The resulting curves and parameters are stored as ordinary ATSAS data files and can be opened directly in PRIMUS.

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Projects

A CHROMIXS project captures:

  • paths to all loaded data files
  • frame selections
  • plot configuration

Project files do not contain copies of the experimental data unless explicitly packaged.

Packaging projects

Projects can be packaged into a ZIP archive containing:

  • the project file
  • all referenced data files

This is intended for archival and data exchange.

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Plot interaction

All plots in CHROMIXS share a common interaction model:

  • zoom and pan
  • axis configuration
  • export as raster or vector graphics

Plot behavior is identical across views and documented centrally in Plotting in ATSAS.

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Typical workflow (minimal) 1. Load a directory of SEC frames 2. Inspect the elution trace 3. Define buffer and sample frame ranges 4. Process the selection 5. Open the subtracted curve in PRIMUS

This is sufficient for a complete SEC–SAXS background subtraction cycle.

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Limitations

CHROMIXS intentionally does not:

  • modify experimental data
  • perform fitting or modelling
  • replace PRIMUS or GNOM

It is a preparatory and inspection tool in the ATSAS analysis pipeline.