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@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 >
On 04/02/2010 11:00 AM, Daniel Fernandez wrote: > 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.
The input template files are just PDB files, which you can download from the PDB website. The alignment files are just text files, which you can easily create in any text editor (vi, emacs, Notepad, etc.). It is true that the Modeller tutorial assumes you know how to use a text editor. ;)
Ben Webb, Modeller Caretaker
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Daniel Fernandez -
Modeller Caretaker