Dr. Ahsan Salim wrote: > I am trying to model a tetramer. The number of residues in the target protein are 141 each in 2 subunits and 146 each in the other two. The target is single, also a tetramer with the same number of amino acids in the four subunits. > Following is the format of the alignment file: > C; alignment in the PIR format > > >P1;----- > structureX:-----:1:A:146:D:name:source:: > ------------------------------------------------------------------------- > ---------------------------------------------/ > ------------------------------------------------------------------------- > ---------------------------------------------/ > ------------------------------------------------------------------------- > ---------------------------------------------/ > ------------------------------------------------------------------------- > ---------------------------------------------* > > >P1;----- > sequence:-----:1:A:146:D:name:source:: > ------------------------------------------------------------------------- > ---------------------------------------------/ > ------------------------------------------------------------------------- > ---------------------------------------------/ > ------------------------------------------------------------------------- > ---------------------------------------------/ > ------------------------------------------------------------------------- > ---------------------------------------------* > > Please make sure that the above format is correct. Moreover the total number of residues amounts to above 1000 which is more than the specified limit. Please suggest the solution. > Thanks

The above format is correct if we consider it as a theoretical approach.

If the total number of residues in the alignment exceeds 1000 you should use Modeller version ENORMOUS which can accomodate 2000 resiudes. Find executables on our website: guitar.rockfeleller.edu/pub/modeller/* .

Andras Fiser