Hi Thomas,

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.

Sincerely,
--
Maurício M Rigo

2012/9/14 Thomas Holder <speleo3@users.sourceforge.net>
Hi Maurício,

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.

http://salilab.org/modeller/

Hope that helps.

Cheers,
  Thomas

Maurício Menegatti Rigo wrote, On 09/14/12 19:44:
    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.
    CVGLTUW)

    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
    my file1.txt

    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
    Tel: +55 51 3308 9938 <tel:%2B55%2051%203308%209938>

--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen



--
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
Tel: +55 51 3308 9938