• Manual
  • Introduction
  • Running datporod
    • Command-line arguments and options
    • Runtime output
  • datporod input files
• Examples
  • Porod Volume
  • Porod Exponent

Manual

The following sections briefly describe the method implemented in DATPOROD, how to run DATPOROD from the command-line on any of the supported platforms and the required input files.

Introduction

DATPOROD may be used to either calculate the Porod Exponent or the Porod Volume. To calculate the Molecular Weight from the Porod Volume, DATMW with the option --method=porod may be employed.

To calculate the Porod Exponent, DATPOROD uses the following relationship:

where \(A\) is a general scaling factor, \(C\) an optional constant to subtract and \(B\) corresponds to the Porod Exponent. For proteins a Porod exponent of approximately \(4.0\) is expected. Only experimental data points in the range [--first, --last] are used.

The excluded volume of a particle, \(V_p\), can be computed from a scattering curve using the Porod equation:

where \(Q = \int_0^\infty s^2 \cdot I(s) ds\) is the Porod Invariant. To calculate \(Q\), the scattering curve is completed in the range \(0 \le s \lt s(\text{first})\) by extrapolation using the Guinier approximation, using the \(R_g\) value provided by the user.

However, direct application of this formula to the experimental data can be confronted with difficulties related to high noise level at higher angles; therefore the smooth regularized curve produced by GNOM or DATGNOM is preferred. An appropriate constant \(K^4\) is subtracted from each data point to force the \(s^{-4}\) decay of the intensity.

Running datporod

Usage:

$ datporod [OPTIONS] <SASDATA(S)>

OPTIONS known by DATPOROD are described in the next section, the required argument(s) SASDATA(S) in the section on input files.

Command-Line Arguments and Options

DATPOROD requires the following command line arguments:

Absolute as well as relative paths to data files are accepted. Instead of a file name, one of the arguments may be given as ‘-‘ to read regularised SAS data (.out) from stdin.

DATPOROD recognizes the following command-line options:

By default, DATPOROD calculates the Porod Volume. To obtain the Porod exponent, use --exponent. To enable constant subtraction, add --constant.

Runtime Output

When calculating the Porod Volume, DATPOROD prints the maximum scattering angle used (\(s_{max}\)), the volume estimate (\(\AA^3\)) and the file name to standard output.

When calculating the Porod Exponent, DATPOROD prints the parameters A, dA, B, dB, C, and dC as well as a goodness-of-fit measure (red. \(\chi^2\)) and the file name to standard output. Here dA, dB and dC are the corresponding error estimates for A, B and C, respectively.

datporod input files

DATPOROD expects background-subtracted experimental SAS data (.dat) or regularised SAS data (.out) files.

If SASDATA is a regularised SAS data (.out) file, reciprocal space \(R_g\) and \(I(0)\) stated in the file are used, but may be overridden by the corresponding command-line options.

Multiple inputs may be provided at once, but note that any --rg and --i0 values specified are applied to all inputs the same.

Examples

Porod Volume

Porod Volume from experimental SAS data (.dat); values for --rg, --i0 and --first from AUTORG.

$ datporod --rg=15.0 --i0=6.47 --first=2 lyzexp.dat
   0.498363        15060.2      lyzexp.dat

Here the Porod Volume is calculated to 15060\(\AA^3\).

Porod Volume from regularised SAS data (.out); values for --rg, --i0 are taken from the .out file.

$ datporod ly01.out
   0.498363        18854.8      ly01.out

Here the Porod Volume is calculated to 18855\(\AA^3\).

Porod Exponent

Porod Exponent from experimental SAS data (.dat).

$ datporod --exponent --first=35 --last=110 lyzexp.dat
   0.328575E-03   0.454158E-04    4.22142       0.722494E-01    0.00000        0.00000           1.54      lyzexp.dat

Here, the Porod Exponent is calculated to 4.22 +/- 0.07, with a goodness-of-fit measure of a red. \(\chi^2\) of 1.54. No constant was subtracted, hence the constant is reported as 0.0.