DIMFOM

DIMFOM is a program for rigid body refinement of a homo- or heterodimeric structure composed of two subunits A and B. Given the partial amplitudes and envelope function of the two subunits in reference orientations evaluated by CRYSOL (stored in *.alm and *.flm files), the program finds best fit to the experimental scattering curve by rolling the A subunit on the surface of B at the offset delta (3 Angstrom by default). The surfaces of subunits are represented as envelope functions. Either asymmetric heterodimeric or symmetric homodimeric models can be built. The parameters of several best solutions are saved in the log file and can be retrieved by the program.

"Petoukhov, M.V. & Svergun, D.I. (2005) Global rigid body modelling of macromolecular complexes against small-angle scattering data. Biophys. J. 89 (2005) 1237-1250"

Running DIMFOM

What you need to run DIMFOM, are, first, the data file containing SAXS from the dimer (usually with extension *.dat), and, second, the   PDB  models of the two monomers.

 

You should run   CRYSOL  on the two   PDB  files in the "curve prediction" mode (i.e. without fitting any data). This will provide the amplitude files (extension *.alm) and envelope files (extension *.flm). DIMFOM must be run in the directory containing the relevant *.dat, *.alm and *.flm files.

Command-Line Arguments and Options

DIMFOM can be run from the command line as:

EXEFILENAME fn1 fn2 fn3 fn4 [Mode]  

where  

EXEFILENAME is the name of DIMFOM executable for the given operating system (e.g. dimfom04.exe for Windows)  
fn1  is the log file name,
fn2  is the experimental data file name,
fn3 and fn4  are the files containing partial amplitudes of fixed ( fn3) and movable ( fn4) subunits

The parameter   [Mode] defines the angular grid of the search:  
Mode = F is Fast mode (rough grid, fast search)  
Mode = S is Slow mode (fine grid, slow search)  
If   [Mode]  is not present, a "normal" mode is used (medium grid, medium search times)  

By defalult, DIMFOM saves the best solution (solution number 0). To retrieve a solution number   K, run  
EXEFILENAME fn1 K  
where   fn1  is the existing log file name,   K  is the ordial number of solution to be restored.

Interactive Configuration

If DIMFOM is started without command line parameters, the program runs in the dialogue mode, such that the user can change the parameters.  
The questions are self-explanatory and in all cases, default answers would run the program as in the batch mode.

Homodimer Case and P2 symmetry

If the names of the two   *.alm files are different, DIMFOM builds a model of the heterodimer without symmetry.  
If the two names are identical, DIMFOM assumes that the homodimer has a P2 symmetry and builds only symmetric models.

 

Hint:  If you wish to run a homodimer without P2 symmetry, copy the   *.alm and   *.flm files under another name, e.g. a00.alm => aa00.alm and a00.flm => aa00.flm  
However, DO NOT rename the   *.pdb file -- the reference to the file is inside the   *.alm file!

转载于:https://www.cnblogs.com/greencolor/archive/2010/10/07/1845305.html