Ngo Duc Tri wrote: > I'm newbie in Modeller so I practice the Tutorial (Basic Example 1). > It's ok but when I model my protein, I don't know how we can obtain > the file pdb_95.pir which contains sequences that are 95% identity to > my protein? Which program or which command will I need to do? Can > anyone help me? Thank you very much.
The file pdb_95.pir is in the basic-example.zip file, which is available to download at the top of the 'basic example' tutorial web page. But it does not contain sequences that are 95% identical to your protein. It contains sequences for all structures in the PDB, filtered to remove redundancies (no sequence in that file is more than 95% identical to any other sequence in the file). This is all described in the instructions for step 1 of the basic tutorial.
Ben Webb, Modeller Caretaker