Greetings Forum users I have recently installed modellerv9.2 on my system and am having real difficulty in getting started.I've tried to use the basic example tutorial, but I've a lot of questions: 1. How can i get PIR format for the input? I've only the sequence of my protein in fasta format. 2. From BLAST, i've a file.aln. Must I convert it in PIR format or in a file.ALI? How? 3, Then, how can i get a model of my protein's structure having one template (a pdb file)? 4. In the test.cod, for running my experiment, i've to insert all the template?
Many thanks in advance for your help, have a good day.
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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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Lella Sana -
Modeller Caretaker