If the template is also a dimer and you say it is a homodimer then it means that the sequence should also be the same. Your target is also a homodimer which means here too the chains have similar amino acid sequence. If one chain of the target is homologous in sequence with the respective chain of the template then the other chain of the target should also be similar to the respective chain of the template. Here you do not have to do any modification in the script file or elsewhere, just align the two chains of the target with the two chains of the template and the modeller will automatically produce the dimer model, as Dr Sanchez has pointed out in his mail. Make sure that the alignment file is of correct format and the chains are separated by / sign.

regards

asmat ---------- > From: R Senthil Kumar skumar@www.cdfd.org.in > To: Roberto Sanchez Roberto.Sanchez@physbio.mssm.edu > Cc: modeller_usage@salilab.org > Subject: Re: Regarding obtaining dimer form > Date: Friday, November 30, 2001 5:29 AM > > > > Dear friends, > > > Thank you very much for your replies.First i will tell my problem > clearly. > > > I am having a protein of 274 amino acids.When i searched for the template > for this protein it picked up the template which is of homodimer in > nature. i.e, it is having > > aaaaaaaaaaaaaa/aaaaaaaaaaaaaaaaa(two chains).My protein is also belong to > the same family of template.In this family homodimer is of active form. > > My protein matching with only to the first chain. > > If i go ahead with this alignment i will get my peotein in monomeric form. > > My question is > > > 1.Whether i can go ahead and get my protein in monomeric form and after > that i can do any trick to convert it into homodimer form-->how to do > this. > > > 2.else in the alignment itself can i do any trick so that i can get > homodimer model of my protein--->how to do this. or in the script file. > > If you tell me it will be of very helpful to me.Expecting reply from you.

> > from, > Senthil kumar.R >