It also depends on the sequence homology of your target to your template. With low sequence homology, it's usually better to do the alignment by hand, since you can then manually align secondary structure elements.

On Mon, Jun 02, 2003 at 01:13:03PM -0400, Eric Feyfant wrote: > You should check the Align2D command > > Eric > > > ------------------------------------ > Eric Feyfant, Ph.D. > Computational Chemistry > Wyeth Research > 200 Cambridge Park Drive > Cambridge, MA 02140 > tel: +1 617 665 5656 > fax: +1 617 665 5682 > email: efeyfant@wyeth.com > > >>> Modeller Care modeller-care@salilab.org 06/02/03 12:18PM >>> > > Forwarded by the list owner > ----------------------------------------------------- > > > > Dear Sir, > > I have a few questions before starting modelling. I would like to know how > one can use modeller for aligning the sequences that have the structure > (treated as templates for modelling) and that do not have a solved structure > (our target). I couldn't get the answer for this question from the modeller > tutorial. > > Expecting the answer as soon as possible. > > Thanking You > > Nethaji > > > > >