First, let's answer the question in the subject: to download pdb_95.pir, go to http://salilab.org/modeller/supplemental.html

pdb_95.bin is generated from pdb_95.pir in the very first script in the basic modeling tutorial. I suggest you work through that tutorial.

On 8/11/12 7:33 AM, Nandha Kumar wrote: > 1.why use pdb _95.pir&bin?

pdb_95.pir contains sequences of structures in PDB. We search through it to look for possible templates that have known PDB structures.

> 2.another modelling protein using pdb_95 .pir&bin?

You can query the database using any protein - it's not specific to the tutorial sequence.

Ben Webb, Modeller Caretaker