[modeller_usage] Preparing input files

[Daniel Fernandez <dfernan AT gmail.com>]

Hi,

I think I will start with a more basic question.  I am new to modeller and bioinformatics in general. 

If I have a target protein, i.e., 1ahoa protein I want to model, how can I prepare the input files (i.e. alignment and template files) for that protein??? any suggestions? tutorials or read about this?  the modeller tutorial assumes one knows how to prepare the files to be read by modeller, and I actually don't know that part.  Any advise would be strongly appreciated.

On Fri, Apr 2, 2010 at 12:33 PM, Daniel Fernandez <dfernan AT 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

--
Daniel F.

Department of Statistics, Harvard University
1 Oxford Street, Cambridge, MA 02138