Re: [modeller_usage] dna modelling

[Modeller Caretaker <modeller-care@ucsf.edu>]

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
--
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