datvc
Manual
The following sections briefly describe how to run DATVC from the command-line, the required input and runtime output
Introduction
DATVC estimates the molecular weight (MW) for proteins based on the Volume of Correlation method (Rambo & Tainer, 2013).
The Volume of Correlation of a particle, \(V_c\), is defined as:
\[V_c = \frac{I(0)}{\int_0^\infty s\cdot I(s) ds}\]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 \(V_c\), a MW estimate for proteins may be obtained as:
\[MW = \left(\frac{V_c^2 / R_g}{c}\right)^k\]The constants \(c=0.1231\) and \(k=1.0\) were empirically determined by the authors.
Running datvc
Usage:
$ datvc [OPTIONS] <SASDATA(s)>
OPTIONS known by DATVC are described in the next section, the required argument(s) FILE(S) in the section on input files.
Command-Line Arguments and Options
DATVC 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.
DATVC 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) |
| -v | --version | Print version information and exit. |
| -h | --help | Print usage information and exit. |
Mandatory arguments to long options are mandatory for short options as well.
Runtime output
DATVC output consists of result lines for each input file with the following values: smax (\(\AA^{-1}\)), Vc, MW (Da), file name.
datvc input files
DATVC 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.
$ datvc --rg=15.0 --i0=6.47 --first=2 lyzexp.dat
0.300184 148.568 11953.7 lyzexp.dat
Here the Molecular Weight is calculated to 11954 Da.
Molecular Weight from regularised SAS data (.out);
values for --rg, --i0 are taken from the .out file.
$ datvc ly01.out
0.300200 151.401 12075.8 ly01.out
Here the Molecular Weight is calculated to 12076 Da.