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EMBL Hamburg Biological
Small Angle Scattering
BioSAXS

FFMAKER manual

ffmaker

Written by P. V. Konarev, V.V.Volkov, D.I. Svergun
Post all your questions about FFMAKER to the ATSAS Forum.

© ATSAS Team, 1999-2015

Table of Contents

Manual

The program FFMAKER is designed to facilitate the creation of the form-factor file for OLIGOMER but can also be used for combining heterogenous data into one file that can be later used for different types of plotting/analyses (e.g. for plotting of time-resolved data sets and/or for singular value decomposition analysis).

Introduction

The input files for FFMAKER can be pdb models and/or the scattering data files (tha latter ones can be either from ASCII *.dat files where column 1 will be taken as S-axis, column 2 as intensities or from GNOM output files where desmeared curve - "Ireg" column will be taken for intensity)

In the case of a PDB file, the program runs CRYSOL and takes the scattering curve from *.int file. In the case of a DAT (TXT) file with the scattering curve, the program takes the second column of the file for the form-factor component. In the case of OUT file (GNOM output), the program takes the desmeared curve (Ireg column) for the form-factor component.

Running FFMAKER

FFMAKER (versions from atsas 2.6 or later releases) shall also calculate the contrasts for each of the components (in the case of input pdb files), that will be later used by OLIGOMER (versions from atsas 2.6 or later releases) in order to properly normalize the volume fractions of the components. This additional adjustment of the volume fractions due to the constrasts will have influence (up to 3-4% of correction for volume fractions) mainly for heterogenous systems (e.g. mixtures of protein-DNA or protein-RNA molecules), for homogenous systems (e.g. mixtures of proteins) there will be no difference whether to take or not to take into account the contrast information (it means the results from earlier or later versions of FFMAKER and OLIGOMER will be the same for the latter case).

FFMAKER and OLIGOMER supports the absolute and relative paths to the input file names (that can be important for Linux/OS users), by default the programs are looking for the input files from the current working directory.

To process multiple data sets in the batch mode, simply pass multiple file names on the command line. Most shells will automatically expand wildcard expressions such as *.dat into all matching file names.

Command-Line Arguments and Options

The following program options can be given as keys with parameters:

Short OptionDescription
-undat Angular units for *.dat files (1: A-1=default; 2: nm-1; 3: 2pi*s A-1; 4: 2pi*s nm-1)
-unout Angular units for *.out GNOM files (1: A-1=default; 2: nm-1; 3: 2pi*s A-1; 4: 2pi*s nm-1)
-smin minimum value of angular axis s
-smax maximum value of angular axis s
-lmmax Maximum order of harmonics (min = 1, max = 50, default 15) that will be used while calculating the theoretical scattering curve from the input pdb model.
-ns Number of points in the theoretical curve (max = 256) calculated from the input pdb model.
-out the name of the output file, default is ffmaker.log
-sgrid the name of the file containing the 'master'-grid of the angular axis that will be used for the form-factor calculations. This option is needed only if you have input data defined at different angular ranges.
-constrain <confile.txt> Constraints between the volume fractions of the components (or the number fractions of the components). See 'Running OLIGOMER with volume/fraction constraints'.
-nmr need the name of the pdb file with NMR structure. Form factores from the first 20 conformers of the NMR structure will be calculated.

Interactive Configuration

FFMAKER asks for the number of the components, and then for each component one should provide the input file (either pdb model or scattering data or GNOM file).

Prompt Possible value(s) Default value Description
File name for component *.pdb, *.dat or *.out filename --- The name of the file containing the pdb model or the scattering data or GNOM output file.
Number of components between 1 and 50 1 if more than 50 input files are used, then the form-factor file only for the first 50 input files will be calculated.
Output formfactor file filename *.dat by default: ff.dat

FFMAKER Input Files

The input files for FFMAKER can be pdb models and/or the scattering data files (tha latter ones can be either from ASCII *.dat files where column 1 will be taken as S-axis, column 2 as intensities or from GNOM output files where desmeared curve - "Ireg" column will be taken for intensity)

FFMAKER Output Files

FFMAKER creates a output file named ff.dat as default or as specified using the -out option. If the file already exists, the results can be appended to the file using '-append' option.

Examples

Example 1

The formfactors will be created from 1.dat and 2.dat files (using their column 2 as intensity values) with the angular axis in nm-1, column 1 will be read from dat files and multiplied by 0.1 factor

$> ffmaker 1.dat 2.dat -undat 2

Example 2

All experimental data files with "pdb" extension from the working directory will be taken and CRYSOL will run for these files with the parameters -smax=0.3, -ns=201 and -lmmax=20. The formfactors will be taken from the corresponding intensity values.

$> ffmaker *.pdb m1.dat -smax 0.3 -ns 201 -lmmax 20

  Last modified: January 12, 2015

© BioSAXS group 2015