datmow
Manual
The following sections briefly describe how to run DATMOW from the command- line, the required input and runtime output
Introduction
DATMOW estimates the molecular weight (MW) for proteins based on the apparent volume method (Fischer et al., 2010). The method is based on the Porod Equation (cf. DATPOROD), however, the \(Q\) integral is not calculated to infinity, but intentionally truncated at \(s_max\):
\[Q' = \int_0^{s_{max}} s^2 \cdot I(s) ds\]where 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.
With \(Q'\), an apparent volume \(V'\) may be calculated, equivalent to the Porod Volume:
\[V' = 2 \pi^2 I(0) / Q'\]This apparent volume estimate \(V'\) may then be mapped to a molecular weight estimate using an empirical calibration as described in the reference.
Running datmow
Usage:
$ datmow [OPTIONS] <SASDATA(s)>
OPTIONS known by DATMOW are described in the next section, the required argument SASDATA file(s) in the section on input files.
Command-Line Arguments and Options
DATMOW requires the following command line arguments:
| Argument | Description |
|---|---|
| SASDATA(S) | 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.
DATMOW recognizes the following command-line options:
| Short option | Long option | Description |
|---|---|---|
| --i0=<VALUE> | Forward scattering intensity (I(0)) | |
| --rg=<VALUE> | Radius of gyration (Rg) | |
| --first=<N> | Index of the first data point to use. Default: 1. | |
| -u | --unit=<u|1|2|3|4> | Define angular units of the experimental SAS data (.dat) or regularised SAS data (.out) files. |
| -v | --version | Print a summary of arguments, options, and exit. |
| -h | --help | Print usage information and exit. |
Runtime output
DATMOW output consists of result lines for each input file with the following values: smax (\(\AA^{-1}\)), Q’, V’ (apparent volume), V (Volume, \(\AA^3\)), MW (Da), file name.
datmow input files
DATMOW 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
Molecular Weight estimate from experimental SAS data (.dat);
values for --rg, --i0 and --first from AUTORG.
$ datmow --rg=15.0 --i0=6.47 --first=2 lyzexp.dat
0.451733 0.953803E-03 20695.3 14002.3 11552.4 lyzexp.dat
Here the Molecular Weight is calculated to 11552 Da.
Molecular Weight from regularised SAS data (.out);
values for --rg, --i0 are taken from the .out file.
$ datmow ly01.out
0.451700 0.934577E-03 21121.0 14369.3 11855.2 ly01.out
Here the Molecular Weight is calculated to 11855 Da.