Re: [modeller_usage] I'm a beginner

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

Lella Sana wrote:
> 1. How can i get PIR format for the input? I've only the sequence of my 
> protein in fasta format.

Usually, it's easiest to do it by hand with a text editor. This is 
pretty straightforward, since you just have to add a '*' to the end of 
the sequence and add a PIR header.

> 2. From BLAST, i've a file.aln. Must I convert it in PIR format or in a 
> file.ALI? How?

You have to put it in PIR format for modeling. Again, it's easiest to do 
this by hand starting from the BLAST sequence output. You can call the 
file whatever you like.

> 3, Then, how can i get a model of my protein's structure having one 
> template (a pdb file)?

There are plenty of examples for that in the manual and tutorial. What 
problem are you having specifically?

> 4. In the test.cod, for running my experiment, i've to insert all the 
> template?

No. My guess is that you're looking at the template search example. If 
you already have a template from BLAST, you don't need to search for it 
with Modeller.

	Ben Webb, Modeller Caretaker
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