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
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 -- , Andras Fiser, PhD # phone: (212) 327 7206 The Rockefeller University # fax: (212) 327 7540 Box 270, 1230 York Avenue # e-mail:fisera@rockvax.rockefeller.edu New York, NY 10021-6399, USA # http://salilab.org/~andras
participants (2)
-
Andras Fiser -
Dr. Ahsan Salim