Overview
The Compute I(q) and P(r) tab is used to calculate scattering intensity, I(q), and pair distribution functions, P(r), from sub-selected MMC structures. This step refines the computational models and aligns them with experimental data for improved analysis.
At this stage, SAXS-A-FOLD is ready to compute the P(r) and I(q) of all sub-selected structures. If this task was previously performed, the complete results will be shown upon accessing the tab. Otherwise, only the starting I(q) and P(r) plots will be displayed.
Fields in the Compute I(q) and P(r) Tab
Besides the standard Project Name and Description fields, the tab contains the following:
- I(q) Computation Method: Offers two options, that can also be run sequentially:
- PEPSI-SAXS
- CRYSOL 3.2.1-1
- Perform a Second P(r) NNLS Fit Using SDs: A switch enabling a second P(r) NNLS fit using the standard deviations (SDs) associated with the experimental P(r) data as weights. Default: not active.
Steps to Compute I(q) and P(r)
- Set I(q) Computation Method: Select the desired computation method (PEPSI-SAXS or CRYSOL 3.2.1-1), or both (ctrl click).
- Activate Second P(r) NNLS Fit (Optional): Enable the switch if a second P(r) NNLS fit is required.
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Start the Calculation: Press the Submit button to begin the P(r) and I(q) calculations. Progress is monitored in real time with:
- P(r) Original I(q) and P(r) graphs: Graphs are always displayed in the Starting model selection section
- P(r) Calculations: P(r) (if selected) updates are first displayed on the left side in the P(r) results section as calculations progress.
- I(q) Calculations: I(q) PEPSI-SAXS (if selected) updates appear as the calculations progress in the I(q) PEPSI-SAXS results section on the left side, once P(r) computations are complete.
- I(q) Calculations: I(q) CRYSOL 3.2.1 (if selected) updates appear as the calculations progress in the I(q) CRYSOL results section on the left side, once I(q) PEPSI-SAXS computations are complete .
Progress and Visualization
To avoid overloading the internet connection with interactive plots containing thousands of calculated curves, images are generated in blocks of 50 curves. A progress bar and associated messages below the updating images provide status updates.
Once calculations are complete, the NNLS fitting procedure runs automatically. Results are displayed graphically on the right side of the respecive advancement plots, and numerically, including:
- Goodness of NNLS fits.
- Contributing models (numbered based on their position in the MMC output).
- Percent contribution of each model to the NNLS fit.
- Individual P(r) and I(q) profiles for each contributing model.
Interactive Plots
The plots are interactive, allowing individual curves to be toggled on or off by clicking their symbol in the legend. This feature enables detailed exploration of specific models and their contributions to the NNLS fit.
All the calculated P(r) and I(q) can be downloaded in csv formatted files from the links provided at the bottom of each section. Two formats are available: "regular" csv where the data are saved in columns, and US-SOMO-compatible csv where the data are saved in lines.