Hi,
You should go through the tutorial ;-)
You'll need to perform a homology search using the PIR database which is prepared for you already -- see the Data sets section for pir_95. You'll need to format your pdb into modeller's alignment format -- see the format section.
After this homology search, sift through the top hits and then build an alignment from those and your target. You can align with however many templates you see fit.
Modeller has an automodel method which you can use that actually builds models between your template(s) and your target.
Checkout: http://salilab.org/modeller/tutorial/basic.html
Cheers, Paul
On Fri, Apr 2, 2010 at 9:33 AM, Daniel Fernandez dfernan@gmail.com wrote:
> Hi, > > I am trying to use modeller to fill in missing side chain or backbone atoms > in the 1ahoa protein. Do you have any suggestion on how to do that using > modeller, i.e., which one I should use as a template and as a target protein > for that problem. I am relatively new to the software and protein modelling > literature. Any help would be strongly appreciated. > > Best, > > Daniel > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > >