thank you for your response. Actually, the modeling part comes later in the process. First, I need to perform this step in pymol. In fact, it would facilitate the modeling process.
Maurício M Rigo
what you describe here is called homology modeling. Although PyMOL has some modeling capabilities, I'd strongly recommend to use a real homology modeling tool such as MODELLER to do this.
Hope that helps.
Maurício Menegatti Rigo wrote, On 09/14/12 19:44:
Tel: +55 51 3308 9938 <tel:%2B55%2051%203308%209938>Dear Pymol users,
I'm a begginer with command lines in Pymol. I'm trying to
complete the following task through a pymol script:
1) Write a file named "file1.txt" with an aminoacid sequence (e.g.
2) Open a .pdb molecule (file2.pdb) with the same number of
residues, but with a different sequence (e.g. ALTWSIK)
3) Write a code where the pymol will pick each residue of the
file2.pdb (I believe that this could be made by the mutagenesis
wizard command) and mutate for the respective aminoacid written in
4) Save the new filein .pdb format (file3.pdb)
I'll be very greatful for any help!
Thanks in advance,
-- M.Sc. Maurício Menegatti Rigo
Núcleo de Bioinformática do Laboratório de Imunogenética
Departamento de Genética
Instituto de Biociências
Universidade Federal do Rio Grande do Sul - Campus do Vale
Av. Bento Gonçalves, 9500 - Bairro Agronomia - Prédio 43323 M
CEP:91501-970 Caixa Postal 15053
Porto Alegre, RS, Brasil
MPI for Developmental Biology