-GENFIT

The general purpose of the program GENFIT is to fit SAS curves by applying different kind of models.

Each SAS curve can be smeared for the instrumental resolution function (wavelength band, slits dimension...). The fitting can be performed by using three different kind of minimization methods: (i) simplex, (ii) quasi-Newton and (iii) simulated annealing.

GENFIT contains around 40 models that can be used by different levels of experienced users.

At a basic level, GENFIT can be used to estimate the size of objects in solution: for example the gyration radius, or the radius of homogeneous spheres or the dimensions of cylinders or of ellipsoids.

Further step above the estimation of object dimensions is the investigation of particular characteristics. It is possible to determine the presence of one or more shells, with different scattering density, around the object, like there is the option to fit hollow cylinders with coatings and slides, each one of different scattering density. Classical approaches as Debye’s and Porod’s law are included in GENFIT models, too.

At an intermediate knowledge level, GENFIT can be used to verify structural features of proteins or lipids in solution. If crystallographic coordinates are known, it is possible to fit SAS curves using a form factor generated by Monte Carlo method from a PDB entry. The form factor can be calculated both considering proteins as homogeneous object and as formed by dummy atoms. In each case, GENFIT can fit the presence of hydration shells around the protein in solution. Since quite often experiments are carried on solutions containing different proteins at equilibrium conditions, it is possible to fit simultaneously, for one experimental curve, the presence of more than one kind of protein, each one referring to a precise PDB entry. Moreover, the structure factor due to protein-protein interactions can be taken into account, according to different approaches (Random Phase Approssimation, Hayter and Penfold…). If in solution proteins are subject to an unfolding process, there are some models able to fit worm-like structure or Gaussian chains, too.

Multilamellar vesicles and bicelles can be fitted varying their structural parameters, too.

At a deeper level, GENFIT can be used to simultaneously fit different experimental curves, optimizing parameters shared by more the one curve. This is the global fit strategy, according to whom it is possible to test a model imposing some parameters common to a set a experiments, performed in different experimental conditions.  

GENFIT Manual        GENFIT Manual pdf

GenfitGui.rar

-GRAFIT (F.Spinozzi, M.G.Ortore, R.Sinibaldi, P.Mariani)
 

General analysis of GiSAS curves by applying different kind of models. Includes data reduction procedures and 2D global fitting alghoritm. The fitting can be performed by using three different kind of minimization methods: (i) simplex, (ii) quasi-Newton and (iii) simulated annealing.
 

-SASMOL (F. Spinozzi, P. Mariani, A.Carbini)

Simulation of SAXS and SANS curves from protein crystallographic data (PDB files) using spherical armonics and dummy hydration water molecules. Includes simulated contrast variation and selective deuteration procedures.

To obtain the programs and more information about their use, please contact Dr. Francesco Spinozzi: f.spinozzi@alisf1.univpm.it