GASBOR

GASBOR is program for ab initio reconstruction of protein structure by a chain-like ensemble of dummy residues. It has been published along with the paper ߵDetermination of domain structure of proteins from X-ray solution scatteringߴ of D.I. Svergun, M.V. Petoukhov & M.H.J. Koch.

Works on following platforms: Windows (WinNT, Win95, Win98, Win2K, Win XP, Vista), Linux.

Algorithm description

The use of GASBOR is similar to that of DAMMIN or DAMMIF. Most of parameters have the same meaning. The most important difference is that the protein structure is represented not by dummy spheres on lattice (called dummy atoms in DAMMIN/DAMMIF, but not corresponding to real atoms), but rather by an ensemble of dummy residues (corresponding to average residue densities) placed anywhere in continuous space with a preferred number of close distance neighbours for each atom. The centers of these residues aim to approximate positions of the C-α atoms in the protein structure. The number of residues should be equal to that in the protein.

Note, however, that these residues are anonymous, in the sense that their ordinal numbers in the model has nothing to do with the numbering primary sequence of the protein!

Accordingly, the program does not subtract any Porod constant from the experimental data. In DAMMIN, it was recommended to discard high angle portions of the scattering patterns; in GASBOR, on the contrary, one should use them. The program is able to fit the data up to the resolution of 5 ångströms, i.e. momentum transfer s=4*π*sin(θ)/λ = 1.2 [1/Ångström].

Running GASBOR

UNIX/LINUX users: It may be necessary to first increase stack size limit, before running the program:

bash$ ulimit -s unlimited

otherwise program crashes with Segmentation fault, because default stack limits are too small for OpenMP programs.

Command-Line Arguments and Options

Major parameters can be specified from the command line (see below) to run the program in batch mode.
Usage:

  gasbor <gnom.out> <Num_DRs> [/lo <log file name>] [/sy <symmetry>] [/id <"project description">]

where gasbor should be replaced by the full program name (e.g. gasbor22p.l86), gnom.out and Num_DRs are GNOM output file name and the number of dummy residues in asymmetric part (compulsory parameters) and /lo, /sy, /id are additional keys for log file name (by default, name of GNOM file with the extension .log), symmetry (P1 by default) and project description (by default, content of the command line.) If project description consists of more than one word, it should be quoted.