The program OLIGOMER fits an experimental scattering curve from
a multicompoment mixture of proteins to find the volume fractions of
each component in the mixture.
The input data for oligomer is experimental SAXS or SANS scattering
curve from a mixture of several dictinct components and a set of
form-factors for each component of this mixture.
The experimental scattering intensity I(s) from a mixture of
K different particles (components) is written as:
I(s) = ∑(wi×Ii(s))
where wi and Ii(s) are
the volume fraction and the scattering intensity from the i-th component,
respectively.
Given the intensities from the components (form-factors), OLIGOMER
finds the volume fractions by solving a system of linear equations using the
algorithm of nonnegative or unconstrained least-squares to minimize the
discrepancy between the experimental and calculated scattering curves.
X-ray or neutron form-factors of proteins with known structure or of dummy
atoms models can be computed using the programs CRYSOL and
CRYSON respectively, which both are part of the
ATSAS package.
Prior to running the application a file containing the Scattering
intensity from the form-factors must be prepared in the format:
1st line: comment
from 2nd line: scattering vector (s), iForm1, iForm2 ...
here, s = 4 * π * sin (θ)/λ, [1/Angstroms]
Iform1, Iform2 etc are the scattering intensities of
the components. They should be normalized in such a way that
iForm(s=0) is equal (or proportional to) the square of
the molecular weight MW (or total scattering length).
OLIGOMER estimates molecular weights for calculation of volume
fractions and radii of gyration from experimental or model scattering
curves of components of the mixture. The latter values are used only
for determination of the average value of radius of giration for all
mixtures.
Therefore, one must enter the real values of molecular weight
for each component (for example, based on information about primary
sequence) in following cases:
scattering curves from components (i.e. sets of form-factors)
are standardized to Iexp(0) = 1
scattering curves from components calculated by
CRYDAM or CRYSOL
from dummy atom models built by programs DAMMIN
or GASBOR with beads not equal size
sets of form-factors are standardized to equally values of
Iexp(0)
If the iForm curves and not properly scaled, the fit not be affected
but the volume fractions will be incorrect.
If one just uses predicted CRYSOL curves from
different oligomers, no additional normalization of the form factors is required.
Please note: To quickly create form-factor file from pdb files and/or from scattering
data files (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) one can use program "FFMAKER" (runs on Windows) that automatically
creates form-factor file (one can use interactive or batch mode to run the program). To
see usage information type: "FFMAKER /help". There is no internal scaling in FFMAKER,
the curves will correspond to CRYSOL output files (if calculated from PDB models) or
to the input scattering curves (as they are).
the name of the output file, default is oligomer.log
/cst
adds constant as additional component. Default value is 10 times
greater than maximum I(0) value from the form-factor file.
This choice of constant will keep the volume fraction of the "constant"
component equal to 0 providing correction of the scattering curve
from parasitic constant background.
In batch mode one needs to provide only the option "/cst"
(without value for the constant).
The constant value can be changed only in interactive mode.
OLIGOMER reads experimental data and form-factors
(both should be in ASCII format).
After starting OLIGOMER you may specify:
Prompt
Possible value(s)
Default value
Description
Program option
0 or 1
0
option 0 - permits to run OLIGOMER for multiple data sets using one
form-factor file, option 1 - permits to use multiple form-factor
files for fitting one data file.
Input data, form-factor file name
filename
ff.dat
Input file should contain intensity values from at least one component.
It can be prepared by FFMAKER program from *.pdb, *.dat and *.out (GNOM)
files or manually by composing the following columns:
1st column - s-axis, 2nd column - intensity from component 1,
3rd column - intensity from component 2 etc.
Use constant as additional component
Y or N
N
if 'Yes' - additional constant component will be added,
that permits to improve the fit at higher angles, if required
Calculated MW and Rg
X1,X2
var
default values are estimated from form-factor intensity curves
Experimental data file name
filename
lys.dat
The name of the file containing the experimental SAXS profile from
multicomponent system
Angular units in the input file :
4*pi*sin(theta)/lambda [1/angstrom] (1)
4*pi*sin(theta)/lambda [1/nm ] (2)
2* sin(theta)/lambda [1/angstrom] (3)
2* sin(theta)/lambda [1/nm ] (4)
1-4
1
Formula for the scattering vector in the data file and its units.
Range for evaluation of scattering
X1,X2
var
default values are estimated from the full-range of experimental
data file
Use of non-negativity condition
Y or N
Y
if 'Yes' - the volume fractions values will be required to be positive
Output fit file
filename
*.fit
by default: experimental file name + .fit extenstion.
Plot the result
Y or N
Y
if 'Yes' - the fit curve and exp. curve will be plotted
Process another data set
Y or N
Y
if 'Yes' - the fitting procedure can be repeated for another data set.
The form factor files consists of the individual form factor of the components.
If they are derived by the program CRYSOL the
second column of the calculated form factors has to be used.
OLIGOMER creates a output file named oligomer.log as default or as specified using the /out option.
If the file already exists, the results are appended to the file.
*** O L I G O M E R ***
================================================================================
01-Sep-2009 17:26:17
Option 0: a set of form-factors and several sets of experimental data
Form-factor file test.dat
Real oligomer weights 20849 58193
Oligomer radii of gyration 22.57 34.37
Experimental data file Merge00.dat Range of Scattering angle: 0.02 0.27
Using non-negativity condition
Output file Merge00.fit
ChiSquare <MW> <Rg> Volume fractions +- errors
--------------------------------------------------------------------------------
Merge00.da 2.17 52869 33.82 0.143+-0.004 0.857+-0.002
================================================================================
If the brief /br option is used only the last line with the results is plotted.
If the batch mode is used, olig_summary.txt file is created, where
the information about the time (when the program was launched) and the
parameters of batch mode are stored.
OLIGOMER creates also *.fit file that contains 5 columns:
S-axis (1st column), experimental intensity Iexp(2nd column),
fit from OLIGOMER Ifit (3rd column), errors of intensity Ierr(4th column),
the difference curve (Iexp-Ifit) (5th column).
For processing all experimental data files with the names beginning with "m"
and with "dat" extension using the formfactor file ff2.dat. The fitting will be
applied from smin=0.5 for the experimental curves. The fits will be plotted and
output oligomer.log file will have the brief format.
