databsmw

• Manual
  • Introduction
  • Running databsmw
    • Command-line arguments and options
    • Runtime output
  • databsmw input files
• Examples

Manual

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

Introduction

If the collected data has been scaled to an absolute scale (refer to DATABSOLUTE), the molecular weight (MW) can be calculated using the forward scattering, contrast, and partial specific volume of the sample, as outlined in Jeffries et al., 2016. Calculating the MW from an absolute scale eliminates the need for a protein standard (see [DATMW(datmw.html)]), avoiding assumptions about the partial specific volume and contrast of the sample compared to the standard. For the most accurate results, it’s advisable to determine the partial specific volume and contrast for each individual sample. However, if contrast and partial specific volume of the sample are not known, empirically averaged values may be used (Mylonas & Svergun, 2007).

Running databsmw

Usage:

$ databsmw [OPTIONS] <SASDATA(s)>

OPTIONS known by DATABSMW are described in next section, the SASDATA argument in the section on input files.

Command-Line Arguments and Options

DATABSMW requires the following command line arguments:

Argument	Description
SASDATA	One or more experimental data 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 data from stdin.

DATABSMW recognizes following command-line options:

Short option	Long option	Description
	--psv <VALUE>	Partial Specific Volume in units of \(\text{cm}^3/\text{g}\); default: 0.7425
	--contrast <VALUE>	Contrast in units of \(10^{10} \text{cm}^{-2}\); default: 2.8086
	--i0 <VALUE>	The \(I(0)\) of the sample on absolute scale.
-v	--version	Print version information and exit.
-h	--help	Print a summary of arguments, options, and exit.

Runtime Output

The molecular weight from absolute scaling and the input file name are printed to stdout.

databsmw input files

DATABSMW expects background-subtracted experimental SAS data (.dat). These experimental intensities must be on an absolute scale, e.g. as calculated by DATABSOLUTE.

Examples

$ databsmw bsa_absolute_003.dat --i0 0.005677 --psv 0.732 --contrast 2.56
  72   bsa_absolute_003.dat