Thanks a lot. But I am wondering what the output is. I need PDB files to do the virtual screening.

PDB files of course. Pymol will build you the PDB file.

And i could not load the fasta files into PyMol, how can i do this? thank you.

By using the script I can generate secondary structures by typing "build_seq SLGQ, ss=helix" for example but i could not upload fasta files to Pymol. i need to this for thousands of different tetramers

Use biopython to parse the fasta files, pass the seq info to pymol and then output the pdb file. It's not a one program solution, but it's very good and very simple.

Hello again, I have managed to do the line by line parsing of sequences and I am wondering how I can do the save as pdb step. manually it is just save .pdb, first_residue but i could not do inside my script. how can i reach the .pdb objects formed after running the build_seq command?

I would refer to the PymolWiki for this kind of questions. For a simple introduction to the Pymol API check this post I made a while ago. It should get you on the right path.

http://www.pymolwiki.org/index.php/Save#PYMOL_API

http://doeidoei.wordpress.com/2009/02/11/pymol-api-simple-example/

The following script works for me to convert multiple sequence FASTA to PDB files, I hope it works for someone else. The file.fasta contains all the fasta sequences. This script is saved with .pym extension. The build_seq.py and seq_convert.py files can be saved in the PyMol directory.

import build_seq
from Bio import SeqIO
document = "_document"
for seq_record in SeqIO.parse("file.fasta", "fasta"):
    build_seq.build_seq(seq_record.seq)
    cmd.select(document,"all")
    cmd.save seq_record.id+".pdb", document, -1, 'pdb')
    cmd.delete("all")

Pymol allows for python scripting. Therefore, as I said before, it is very easy to feed sequences in a for loop to pymol and have it output the corresponding structures. The first answer I gave you had all the links necessary to write the script you want.

Ok now I am becoming familiar with Phyton. I hope I can write the necessary script soon. Thank you.

On topic, Molsoft ICM can do that along with energy minimization with its scripting engine, but that's commercial, and I think you've already figured it out with Pymol

I want to have the structures and thus PDB files for each of the tetramers. Pymol is capable to do this job actually. Thanks

Hello Onat Im new in python. I have about 17000 peptide sequences that I need their PDB structures separately, the same as you. All of my sequences are in a file named seq.fasta. Could you please explain more how to do this by PyMOL? Tnx