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Re: molecular modelling
- To: "Dr. Ahsan Salim" <das AT paknet3.ptc.pk>
- Subject: Re: molecular modelling
- From: Andras Fiser <andras@viol>
- Date: Mon, 27 Jul 1998 11:19:51 -0400
- Cc: "'modeller_usage@listsrv.ucsf.edu'" <modeller_usage>, prochem AT digicom.net.pk
- Organization: The Rockefeller University
- Reply-to: andras@tuba
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 AT rockvax.rockefeller.edu
New York, NY 10021-6399, USA # http://salilab.org/~andras