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Re: molecular modelling



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:
New York, NY 10021-6399, USA # http://salilab.org/~andras