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 <spel...@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
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