rathankar rao wrote: > i need an important information on modelling. i have tried modelling > protein sequences but now that i would like to know whether dna could > also be modelled using modeller and if yes how can it be done. are > there any new files which i have to download or import it from the > package itself.
Modeller can model any residue which is in your template; there's nothing special about DNA in this regard. If you just want to treat it as a rigid body, use a BLK ('.') residue in your alignment. If you want to treat it as a 'real' residue, then you will first need to edit modlib/restyp.lib and add suitable 1-letter codes (rather than #) for the four bases, and then use these codes in your alignment to match the DNA residues in your template and model.
Ben Webb, Modeller Caretaker