datporod
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 calculate the Porod Volume of a particle.
To calculate the Molecular Weight from the Porod Volume, DATMW with
the option --method=porod may be employed.
The excluded volume of a particle, \(V_p\), can be computed from a scattering curve using the Porod equation:
\[V_p = 2 \pi^2 I(0) / Q\]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:
| Argument | Description |
|---|---|
| SASDATA | One or more experimental SAS data (.dat) or regularised SAS data (.out) files. |
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:
| Short option | Long option | Description |
|---|---|---|
| --first <N> | Index of the first point to be used (default: 1) | |
| --last <N> | Index of the last point to be used (default: last data point) | |
| --rg <VALUE> | Experimental Radius of Gyration in the units of the data. This option is mandatory for experimental SAS data (.dat). | |
| --i0 <VALUE> | Experimental forward scattering in the units of the data. This option is mandatory for experimental SAS data (.dat). | |
| -u | --unit=<u|1|2|3|4> | Define angular units of the experimental SAS data (.dat) or regularised SAS data (.out) |
| -v | --version | Print version information and exit. |
| -h | --help | Print a summary of arguments, options, and exit. |
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.
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.
The options --i0, --rg, --first and --unit are applied identically to
all simultaneous input files.
Examples
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\(\AA^3\).