The program DAMMIN implements a method to restore ab initio low resolution shape of randomly oriented particles in solution (e.g., biological macromolecules) from its small angle X-ray scattering. A search volume which encloses the particle (e.g., a sphere of sufficiently large radius R) is filled with N densely packed spheres of radius r, referred to as dummy atom. Given the fixed spatial positions, the shape of the dummy atom model is completely described by a vector X with N components which assigns each dummy atom either to the solute phase (i.e. protein in this case) or to the solvent phase. (In a general approach implemented in the program MONSA, the number of phases can be up to 4 in order to deal with protein complexes and protein-RNA complexes.) For an adequate description of a structure the number of dummy atoms usually reaches a few thousands. The task of shape reconstruction from the scattering data is thus transformed to the problem of finding a configuration X where a goal function f(X) is minimized. The goal function takes into account the discrepancy between the experimental data and the calculated scattering of the dummy atom model, as well as several aspects of the model quantified as penalties. In order to guarantee a compact and inter-connected model, the looseness penalty and the disconnectivity penalty are introduced. The peripheral penalty ensures that the model is close to the center of the search volume. The contribution of the penalties to the goal function is expected to be 10-50% for the final model. Simulated annealing (SA) is used to perform the global minimization of the target function. For details on the method, please refer to the publication cited above.
The latest binary release (version 5.3) on 13 August 2007 is available on major platforms including UNIX/Linux (32 and 64 bit), Mac OS X and all Windows operating systems.
Running DAMMIN
Command-Line Arguments and Options
The program DAMMIN53 can be started in the batch mode when arguments are given:
$> dammin53 GNOMFILE [OPTIONS]